@article {pmid37272702,
year = {2023},
author = {Lu, J and Wang, H and Wang, C and Zhao, M and Hou, R and Shen, Q and Yang, S and Ji, L and Liu, Y and Wang, X and Liu, S and Shan, T and Zhang, W},
title = {Gut phageome of the giant panda (Ailuropoda melanoleuca) reveals greater diversity than relative species.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0016123},
doi = {10.1128/msystems.00161-23},
pmid = {37272702},
issn = {2379-5077},
abstract = {The gut flora is a treasure house of diverse bacteriophages maintaining a harmonious and coexistent relationship with their hosts. The giant panda (Ailuropoda melanoleuca), as a vulnerable endemic species in China, has existed for millions of years and is regarded as a flagship species for biodiversity conservation. And yet, limited studies have analyzed the phage communities in the gut of giant pandas. Using viral metagenomic analysis, the phageomes of giant pandas and other relative species were investigated. Our study explored and compared the composition of phage communities from different animal sources. Giant pandas possessed more diverse and abundant phage communities in the gut compared with other relevant animals. Phylogenetic analyses based on the phage terminase large subunit (TerL) showed that the Caudovirales phages in giant pandas also presented highly genetic diversity. Our study revealed the diversity of phage communities in giant pandas and other relative species, contributing to the health maintenance of giant pandas and laying the groundwork for molecular evolution research of bacteriophages in mammals.IMPORTANCEGut phageome plays an important role in shaping gut microbiomes by direct interactions with bacteria or indirect influences on the host immune system, potentially regulating host health and disease status. The giant panda (Ailuropoda melanoleuca) is a vulnerable and umbrella species for biodiversity conservation. Our work explored and compared the gut phageome of giant pandas and relative species, contributing to the health maintenance of giant pandas.},
}

@article {pmid37166164,
year = {2023},
author = {Sun, H and Lv, B and Zhu, H and Zeng, Z and El-Ashram, S and Li, J and Chao, Y and Wang, J and Wang, Z},
title = {Selenized glucose improves rat semen quality by improving the gut microbiota and serum metabolome.},
journal = {Food & function},
volume = {14},
number = {11},
pages = {5105-5119},
doi = {10.1039/d3fo00692a},
pmid = {37166164},
issn = {2042-650X},
mesh = {Male ; Rats ; Animals ; Semen Analysis ; Semen/metabolism ; *Gastrointestinal Microbiome ; *Selenium/metabolism ; Glucose/metabolism ; Rats, Sprague-Dawley ; Metabolome ; Testosterone ; },
abstract = {Selenium (Se), a well-known antioxidant, is important for male fertility and sperm quality. The gut microbiota is involved in vital activities and cross-talk between reproduction and the gut axis. It is still unclear whether the gut microbiota mediates the impact of selenium on semen quality, and what the underlying mechanisms may be. A selenized glucose (SeGlu) derivative is a novel organic Se compound. After 7 days of acclimation, the Sprague-Dawley (SD) male rats (230 g, 6 weeks) were divided into three drinking groups: deionized water group (CK), SeGlu 0.15 group (0.15 mg Se per L), and SeGlu 0.4 group (0.4 mg Se per L). All animals were euthanized 30 days post-treatment. Serum and intratesticular testosterone and semen parameters were measured. Metagenomic and non-targeted metabolomic approaches were used to study the effects of SeGlu on the gut microbiota and serum metabolites of rats. In both the SeGlu 0.15 Group and the SeGlu 0.4 Group, we found a significant increase in seminiferous epithelium thickness. While the SeGlu 0.4 Group had a tendency to increase with insignificant difference, the SeGlu 0.15 Group significantly improved the sperm viability, survival rate, and seminal plasma fructose. SeGlu had no effect on intratesticular testosterone levels, or abnormal sperm counts. Measured serum testosterone levels using ELISA and LC-MS, which showed a decreasing trend. ELISA did not reveal significant differences, but LC-MS indicated a significant decrease in SeGlu 0.4 group. Meanwhile, the SeGlu 0.15 Group reduced the abundance of harmful bacteria such as Rikenella, Barnesiella, Tenacibaculum, and Aeromonas while increasing the abundance of beneficial microbiota such as Intestinimonas, Christensenella, Coprococcus, and Butyrivibrio. Linear discriminant analysis Effect Size (LEfSe) identified the SeGlu 0.15 group's feature genera as Roseburia, Clostridium, Ruminococcus, and Eubacterium. Serum metabolites showed that the SeGlu 0.15 Group increased 5 beta-androstane-3,17-dione while decreasing estrone and 2-methoxyestradiol (2-MeOE2). In conclusion, the SeGlu 0.15 Group can significantly alter the levels of several sex hormones in serum, improve the quality of rats' sperm, and reduce harmful bacterial colonization. SeGlu 0.15 may be used as an effective dietary supplement.},
}

Male
Rats
Animals
Semen Analysis
Semen/metabolism
*Gastrointestinal Microbiome
*Selenium/metabolism
Glucose/metabolism
Rats, Sprague-Dawley
Metabolome
Testosterone

@article {pmid37271802,
year = {2023},
author = {Rolon, ML and Tan, X and Chung, T and Gonzalez-Escalona, N and Chen, Y and Macarisin, D and LaBorde, LF and Kovac, J},
title = {The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {128},
pmid = {37271802},
issn = {2049-2618},
mesh = {Food Microbiology ; Fruit ; Seasons ; Longitudinal Studies ; Cross-Sectional Studies ; *Listeria monocytogenes/genetics ; *Microbiota/genetics ; Food Contamination/analysis ; },
abstract = {BACKGROUND: Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3).

METHODS: A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples.

RESULTS: The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples.

CONCLUSIONS: This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.},
}

Food Microbiology
Fruit
Seasons
Longitudinal Studies
Cross-Sectional Studies
*Listeria monocytogenes/genetics
*Microbiota/genetics
Food Contamination/analysis

@article {pmid37210808,
year = {2023},
author = {Lamichhane, S and Härkönen, T and Vatanen, T and Hyötyläinen, T and Knip, M and Orešič, M},
title = {Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.},
journal = {Environment international},
volume = {176},
number = {},
pages = {107965},
doi = {10.1016/j.envint.2023.107965},
pmid = {37210808},
issn = {1873-6750},
support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Female ; Humans ; Infant ; Mothers ; *Microbiota ; Maternal Exposure ; Bacteria/genetics ; *Fluorocarbons/toxicity ; *Environmental Pollutants ; *Alkanesulfonic Acids ; },
abstract = {There is growing evidence suggesting that chemical exposure alters gut microbiota composition. However, not much is known about the impact of per- and polyfluoroalkyl substances (PFAS) on the gut microbial community. Here, in a mother-infant study, we set out to identify the gut bacterial species that associate with chemical exposure before (maternal) and after (maternal, infant) birth. Paired serum and stool samples were collected from mother-infant dyads (n = 30) in a longitudinal setting. PFAS were quantified in maternal serum to examine their associations with the microbial compositions (determined by shotgun metagenomic sequencing) in mothers and infants. High maternal exposure to PFAS was consistently associated with increased abundance of Methanobrevibacter smithii in maternal stool. Among individual PFAS compounds, PFOS and PFHpS showed the strongest association with M. smithii. However, maternal total PFAS exposure associated only weakly with the infant microbiome. Our findings suggest that PFAS exposure affects the composition of the adult gut microbiome.},
}

Adult
Female
Humans
Infant
Mothers
*Microbiota
Maternal Exposure
Bacteria/genetics
*Fluorocarbons/toxicity
*Environmental Pollutants
*Alkanesulfonic Acids

@article {pmid36823282,
year = {2023},
author = {Pérez-Cataluña, A and Randazzo, W and Martínez-Blanch, JF and Codoñer, FM and Sánchez, G},
title = {Sample and library preparation approaches for the analysis of the virome of irrigation water.},
journal = {Journal of the science of food and agriculture},
volume = {103},
number = {9},
pages = {4450-4457},
doi = {10.1002/jsfa.12522},
pmid = {36823282},
issn = {1097-0010},
mesh = {Humans ; Virome ; *Viruses/genetics ; *Bacteriophages/genetics ; Water ; Metagenomics/methods ; },
abstract = {BACKGROUND: The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters.

RESULTS: Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families.

CONCLUSION: Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

Humans
Virome
*Viruses/genetics
*Bacteriophages/genetics
Water
Metagenomics/methods

@article {pmid37267060,
year = {2023},
author = {Du, B and Xiao, X and Wang, H and Li, W and Xia, Z and Yang, P and Huang, SK and Yuan, R and Liu, J and Han, M and Zou, Y and Zhu, J and He, D and Lyu, J and Jin, X and Xu, X and Wang, J and Yang, H and Xiao, L and Liu, X and Kristiansen, K},
title = {Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model.},
journal = {Environmental health perspectives},
volume = {131},
number = {6},
pages = {67004},
pmid = {37267060},
issn = {1552-9924},
mesh = {Humans ; Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Ovalbumin/pharmacology ; Caco-2 Cells ; *Hypersensitivity ; Inflammation ; Bacteria ; },
abstract = {BACKGROUND: Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment-microbiota-immunity triangular relationship and to what extent BaP-induced remodeling of the gut microbiota contributes to intestinal allergic inflammation remain to be established.

OBJECTIVES: We investigated the impact of BaP on intestinal allergic inflammation and examined the relationship between this effect and gut microbiota dysbiosis. We explored the potential ability of intestinal bacteria to degrade BaP and alleviate cytotoxicity as a detoxification strategy to counteract the effects of BaP exposure.

METHODS: We combined microbiome shotgun metagenomics with animal histological and intestinal allergic inflammatory responses to assess the effects of BaP (50μg/mouse per day) in a 23-d toxicity test in antigen-induced allergic female mice. In addition, genome annotation, quantitative analysis of BaP, and in vitro cytotoxicity-tests using CaCo-2 cells were conducted to infer the role of intestinal bacteria in BaP detoxification.

RESULTS: BaP exposure impacted the taxonomic composition and the functional potential of the gut microbiota and aggravated antigen-induced intestinal allergic inflammatory responses. The level of inflammatory cytokines correlated with the abundance of specific bacterial taxa, including Lachnospiraceae bacterium 28-4 and Alistipes inops. We identified 614 bacteria harboring genes implicated in the degradation of BaP, and 4 of these bacterial strains were shown to significantly reduce the cytotoxicity of BaP to CaCo-2 cells in vitro.

DISCUSSION: Using allergic female mice as a model, we investigated the relationship between BaP, microbiota, and host immune reactions, highlighting the role of gut bacteria in BaP-aggravated allergic reactions. Our findings offer novel insight toward establishing the causal relationship between BaP exposure and the occurrence of allergic disorders. Identifying gut bacteria that degrade BaP may provide new strategies for ameliorating BaP cytotoxicity. https://doi.org/10.1289/EHP11874.},
}

Humans
Female
Animals
Mice
*Gastrointestinal Microbiome
Ovalbumin/pharmacology
Caco-2 Cells
*Hypersensitivity
Inflammation
Bacteria

@article {pmid37264481,
year = {2023},
author = {Liu, Y and Daniel, SG and Kim, HE and Koo, H and Korostoff, J and Teles, F and Bittinger, K and Hwang, G},
title = {Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {123},
pmid = {37264481},
issn = {2049-2618},
mesh = {Humans ; Child, Preschool ; *Dental Caries ; Cross-Sectional Studies ; Candida albicans/genetics ; *Microbiota ; Biofilms ; Streptococcus mutans/genetics ; Sugars/metabolism/pharmacology ; },
abstract = {BACKGROUND: Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by the synergistic polymicrobial interaction between the cariogenic bacterium, Streptococcus mutans, and an opportunistic fungal pathogen, Candida albicans. Although cross-sectional studies reveal their important roles in caries development, these exhibit limitations in determining the significance of these microbial interactions in the pathogenesis of the disease. Thus, it remains unclear the mechanism(s) through which the cross-kingdom interaction modulates the composition of the plaque microbiome. Here, we employed a novel ex vivo saliva-derived microcosm biofilm model to assess how exogenous pathogens could impact the structural and functional characteristics of the indigenous native oral microbiota.

RESULTS: Through shotgun whole metagenome sequencing, we observed that saliva-derived biofilm has decreased richness and diversity but increased sugar-related metabolism relative to the planktonic phase. Addition of S. mutans and/or C. albicans to the native microbiome drove significant changes in its bacterial composition. In addition, the effect of the exogenous pathogens on microbiome diversity and taxonomic abundances varied depending on the sugar type. While the addition of S. mutans induced a broader effect on Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog abundances with glucose/fructose, S. mutans-C. albicans combination under sucrose conditions triggered unique and specific changes in microbiota composition/diversity as well as specific effects on KEGG pathways. Finally, we observed the presence of human epithelial cells within the biofilms via confocal microscopy imaging.

CONCLUSIONS: Our data revealed that the presence of S. mutans and C. albicans, alone or in combination, as well as the addition of different sugars, induced unique alterations in both the composition and functional attributes of the biofilms. In particular, the combination of S. mutans and C. albicans seemed to drive the development (and perhaps the severity) of a dysbiotic/cariogenic oral microbiome. Our work provides a unique and pragmatic biofilm model for investigating the functional microbiome in health and disease as well as developing strategies to modulate the microbiome. Video Abstract.},
}

Humans
Child, Preschool
*Dental Caries
Cross-Sectional Studies
Candida albicans/genetics
*Microbiota
Biofilms
Streptococcus mutans/genetics
Sugars/metabolism/pharmacology

@article {pmid37264459,
year = {2023},
author = {Leung, MHY and Tong, X and Shen, Z and Du, S and Bastien, P and Appenzeller, BMR and Betts, RJ and Mezzache, S and Bourokba, N and Cavusoglu, N and Aguilar, L and Misra, N and Clavaud, C and Lee, PKH},
title = {Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {124},
pmid = {37264459},
issn = {2049-2618},
mesh = {*Polycyclic Aromatic Hydrocarbons ; Skin/chemistry ; *Air Pollutants/analysis ; Biodegradation, Environmental ; *Microbiota/genetics ; Environmental Monitoring ; },
abstract = {BACKGROUND: The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.

RESULTS: The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation.

CONCLUSIONS: This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin-microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions. Video Abstract.},
}

*Polycyclic Aromatic Hydrocarbons
Skin/chemistry
*Air Pollutants/analysis
Biodegradation, Environmental
*Microbiota/genetics
Environmental Monitoring

@article {pmid37264413,
year = {2023},
author = {Lu, DC and Wang, FQ and Amann, RI and Teeling, H and Du, ZJ},
title = {Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {126},
pmid = {37264413},
issn = {2049-2618},
mesh = {*Seaweed/microbiology ; *Ulva/genetics/microbiology ; *Laminaria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Rhodophyta/genetics ; *Microbiota/genetics ; },
abstract = {BACKGROUND: Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species.

RESULTS: We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera.

CONCLUSIONS: Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.},
}

*Seaweed/microbiology
*Ulva/genetics/microbiology
*Laminaria/genetics
RNA, Ribosomal, 16S/genetics
Bacteria
*Rhodophyta/genetics
*Microbiota/genetics

@article {pmid37263438,
year = {2023},
author = {Phulpoto, AH and Pirzada, T and Kanhar, NA},
title = {Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {164505},
doi = {10.1016/j.scitotenv.2023.164505},
pmid = {37263438},
issn = {1879-1026},
abstract = {Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at "exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions". The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as "PDB20, 91 %", "PDB14, 81 %", and "PDB16, 87 %" while for the blue B698, "PDB4, 86 %", "PDB20, 89 %", "PDB5, and PDB2, 80%". Moreover, in case of G492, maximum % removal was achieved with "PDB20, 93 %", "PDB5, 90 %", "PDB6, 90 %", "PDB16, 88 %", "PDB2, and PDB4, 89%". Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.},
}

@article {pmid37261715,
year = {2023},
author = {Andrianjakarivony, FH and Bettarel, Y and Desnues, C},
title = {Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {37261715},
issn = {1976-3794},
abstract = {The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.},
}

@article {pmid37261381,
year = {2023},
author = {Shao, Z and Shan, X and Jing, L and Wang, W and Li, W and Ren, Z and Zhang, BN and Huang, Y},
title = {Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes.},
journal = {Translational vision science & technology},
volume = {12},
number = {6},
pages = {1},
doi = {10.1167/tvst.12.6.1},
pmid = {37261381},
issn = {2164-2591},
mesh = {Humans ; Metagenome/genetics ; *Diabetes Mellitus, Type 2/complications/epidemiology/genetics ; *Microbiota/genetics ; Bacteria/genetics ; *Cataract/complications/genetics ; Conjunctiva ; },
abstract = {PURPOSE: Our objective was to investigate differences in the ocular surface bacterial composition in cataract patients with and without type 2 diabetes (T2D).

METHODS: Twenty-four diabetic patients with cataracts (group D) and 14 sex- and age-matched patients with age-related cataracts (group N) were recruited for this study. All samples underwent DNA extraction, fragmentation, purification, library construction, and metagenomic sequencing.

RESULTS: The overall conjunctival sac bacterial composition was similar between group D and group N, as determined by alpha diversity and beta diversity. Nevertheless, significant differences were observed in the relative abundance of specific bacteria. At the phylum level, group D had a significantly lower abundance of Chlamydiae, Tenericutes, Chloroflexi, Cyanobacteria, Cossaviricota, Chytridiomycota, Artverviricota, Zoopagomycota, Peploviricota, Deinococcus-Thermus, Preplasmiviricota, and Nucleocytoviricota. At the genus level, group D had a significantly lower abundance of Chlamydia, Mycoplasma, Salmonella, Chryseobacterium, Roseovarius, Desulfococcus, Kangiella, Anaerococcus, and Idiomarina but a significantly higher abundance of Parabacteroides, Phocaeicola, and Sphingomonas. Bacteria such as Aquificae, Parabacteroides, Flavobacterium, Austwickia, Aquifex, Tenacibaculum, and Chryseobacterium in group D and Tenericutes, Chlamydiae, Porphyromonas, Mycoplasma, Chlamydia, Kangiella, Idiomarina, Roseovarius, Aliiroseovarius, and Desulfococcus in group N could be used as conjunctival sac biomarkers, according to the linear discriminant analysis effect size. Gene Ontology functional annotation indicated that bacterial catalytic activity, metabolic processes, locomotion, virion, and reproduction were enriched in group D, while immune system processes were enriched in group N. In addition, the top 30 differentially expressed virulence factors (VFs) were all more enriched in group D.

CONCLUSIONS: The bacterial composition was similar between the two groups. Several bacterial strains that were reported beneficial in gut were decreased, and pathogenic bacteria were increased in T2D. Furthermore, group D had more active bacterial terms and increased VF expression, suggesting that the susceptibility of diabetic patients to infection is closely related to functional changes in the ocular surface flora. Our conjunctival microbiota atlas provides a reference for investigating ocular complications related to diabetes.

TRANSLATIONAL RELEVANCE: The altered composition and functional profile of the ocular microbial community in diabetic patients offer evidence for the need to prevent infection during cataract surgery.},
}

Humans
Metagenome/genetics
*Diabetes Mellitus, Type 2/complications/epidemiology/genetics
*Microbiota/genetics
Bacteria/genetics
*Cataract/complications/genetics
Conjunctiva

@article {pmid37260707,
year = {2023},
author = {Li, X and Yi, Y and Wu, T and Chen, N and Gu, X and Xiang, L and Jiang, Z and Li, J and Jin, H},
title = {Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1170748},
pmid = {37260707},
issn = {2235-2988},
mesh = {Humans ; *Carcinoma, Hepatocellular/diagnosis ; *Liver Neoplasms/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Metabolome ; Biomarkers ; Liver Cirrhosis/diagnosis ; Biomarkers, Tumor ; },
abstract = {Globally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.},
}

Humans
*Carcinoma, Hepatocellular/diagnosis
*Liver Neoplasms/diagnosis
*Gastrointestinal Microbiome
Quality of Life
Metabolome
Biomarkers
Liver Cirrhosis/diagnosis
Biomarkers, Tumor

@article {pmid37259063,
year = {2023},
author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L},
title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {295},
pmid = {37259063},
issn = {1471-2164},
mesh = {Humans ; Infant ; *Bacteriocins/genetics ; Metagenome ; *Gastrointestinal Microbiome/genetics ; },
abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.

RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (< 2 years) compared to adult-like metagenomes (2-107 years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.

CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.},
}

Humans
Infant
*Bacteriocins/genetics
Metagenome
*Gastrointestinal Microbiome/genetics

@article {pmid37224782,
year = {2023},
author = {Xu, M and Su, S and Jiang, S and Li, W and Zhang, Z and Zhang, J and Hu, X},
title = {Short-term arecoline exposure affected the systemic health state of mice, in which gut microbes played an important role.},
journal = {Ecotoxicology and environmental safety},
volume = {259},
number = {},
pages = {115055},
doi = {10.1016/j.ecoenv.2023.115055},
pmid = {37224782},
issn = {1090-2414},
mesh = {Animals ; Mice ; *Arecoline/pharmacology/toxicity ; Interleukin-6/metabolism ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Liver ; },
abstract = {Arecoline is a critical bioactive component in areca nuts with toxicity and pharmacological activities. However, its effects on body health remain unclear. Here, we investigated the effects of arecoline on physiologic and biochemical parameters in mouse serum, liver, brain, and intestine. The effect of arecoline on gut microbiota was investigated based on shotgun metagenomic sequencing. The results showed that arecoline promoted lipid metabolism in mice, manifested as significantly reduced serum TC and TG and liver TC levels and a reduction in abdominal fat accumulation. Arecoline intake significantly modulated the neurotransmitters 5-HT and NE levels in the brain. Notably, arecoline intervention significantly increased serum IL-6 and LPS levels, leading to inflammation in the body. High-dose arecoline significantly reduced liver GSH levels and increased MDA levels, which led to oxidative stress in the liver. Arecoline intake promoted the release of intestinal IL-6 and IL-1β, causing intestinal injury. In addition, we observed a significant response of gut microbiota to arecoline intake, reflecting significant changes in diversity and function of the gut microbes. Further mechanistic exploration suggested that arecoline intake can regulate gut microbes and ultimately affect the host's health. This study provided technical help for the pharmacochemical application and toxicity control of arecoline.},
}

Animals
Mice
*Arecoline/pharmacology/toxicity
Interleukin-6/metabolism
*Gastrointestinal Microbiome
Lipid Metabolism
Liver

@article {pmid37196747,
year = {2023},
author = {Zhang, Z and Yang, H and Wang, B and Chen, C and Zou, X and Cheng, T and Li, J},
title = {Aerobic co-composting of mature compost with cattle manure: Organic matter conversion and microbial community characterization.},
journal = {Bioresource technology},
volume = {382},
number = {},
pages = {129187},
doi = {10.1016/j.biortech.2023.129187},
pmid = {37196747},
issn = {1873-2976},
mesh = {Cattle ; Animals ; Soil ; Manure ; *Composting ; *Microbiota ; Carbohydrates ; },
abstract = {The production of organic fertilizer by aerobic composting of cattle manure is an important way of its resource utilization. This study evaluated the effects of adding mature compost on the decomposition and microbial communities in the aerobic composting of cattle manure. The addition of mature compost shortens the composting cycle and results in a final lignocellulosic degradation rate of 35%. Metagenomic analysis showed that this was due to the proliferation of thermophilic and organic matter-degrading functional microorganisms, which enhanced the activity of carbohydrate-active enzymes. With the addition of mature compost, the microbial community exhibited stronger metabolic functions, especially carbohydrate and amino acid metabolism, which are the driving forces of organic matter degradation. This study deepens the understanding of organic matter conversion and microbial community metabolic functions when mature compost is used for livestock manure composting and provides a promising technology for livestock manure composting.},
}

Cattle
Animals
Soil
Manure
*Composting
*Microbiota
Carbohydrates

@article {pmid37191684,
year = {2023},
author = {Lu, J and Sha, H and Chen, J and Yi, X and Xiong, J},
title = {Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution.},
journal = {Applied microbiology and biotechnology},
volume = {107},
number = {12},
pages = {4093-4107},
pmid = {37191684},
issn = {1432-0614},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota ; Environmental Pollution ; Nitrification ; Sulfates ; },
abstract = {Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.},
}

*Anti-Bacterial Agents/pharmacology
*Microbiota
Environmental Pollution
Nitrification
Sulfates

@article {pmid37188814,
year = {2023},
author = {Johansen, J and Atarashi, K and Arai, Y and Hirose, N and Sørensen, SJ and Vatanen, T and Knip, M and Honda, K and Xavier, RJ and Rasmussen, S and Plichta, DR},
title = {Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan.},
journal = {Nature microbiology},
volume = {8},
number = {6},
pages = {1064-1078},
pmid = {37188814},
issn = {2058-5276},
mesh = {Adult ; Aged, 80 and over ; Humans ; Longevity ; Virome ; Centenarians ; *Viruses/genetics ; *Microbiota ; *Bacteriophages/genetics ; },
abstract = {Distinct gut microbiome ecology may be implicated in the prevention of aging-related diseases as it influences systemic immune function and resistance to infections. Yet, the viral component of the microbiome throughout different stages in life remains unexplored. Here we present a characterization of the centenarian gut virome using previously published metagenomes from 195 individuals from Japan and Sardinia. Compared with gut viromes of younger adults (>18 yr) and older individuals (>60 yr), centenarians had a more diverse virome including previously undescribed viral genera, such as viruses associated with Clostridia. A population shift towards higher lytic activity was also observed. Finally, we investigated phage-encoded auxiliary functions that influence bacterial physiology, which revealed an enrichment of genes supporting key steps in sulfate metabolic pathways. Phage and bacterial members of the centenarian microbiome displayed an increased potential for converting methionine to homocysteine, sulfate to sulfide and taurine to sulfide. A greater metabolic output of microbial hydrogen sulfide in centenarians may in turn support mucosal integrity and resistance to pathobionts.},
}

Adult
Aged, 80 and over
Humans
Longevity
Virome
Centenarians
*Viruses/genetics
*Microbiota
*Bacteriophages/genetics

@article {pmid37169918,
year = {2023},
author = {Sanders, JG and Sprockett, DD and Li, Y and Mjungu, D and Lonsdorf, EV and Ndjango, JN and Georgiev, AV and Hart, JA and Sanz, CM and Morgan, DB and Peeters, M and Hahn, BH and Moeller, AH},
title = {Widespread extinctions of co-diversified primate gut bacterial symbionts from humans.},
journal = {Nature microbiology},
volume = {8},
number = {6},
pages = {1039-1050},
pmid = {37169918},
issn = {2058-5276},
support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; R01 AI050529/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Humans ; Phylogeny ; Pan troglodytes ; *Gastrointestinal Microbiome ; Primates ; *Hominidae/microbiology ; Bacteria/genetics ; },
abstract = {Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.},
}

Animals
Humans
Phylogeny
Pan troglodytes
*Gastrointestinal Microbiome
Primates
*Hominidae/microbiology
Bacteria/genetics

@article {pmid37141097,
year = {2023},
author = {Manghi, P and Blanco-Míguez, A and Manara, S and NabiNejad, A and Cumbo, F and Beghini, F and Armanini, F and Golzato, D and Huang, KD and Thomas, AM and Piccinno, G and Punčochář, M and Zolfo, M and Lesker, TR and Bredon, M and Planchais, J and Glodt, J and Valles-Colomer, M and Koren, O and Pasolli, E and Asnicar, F and Strowig, T and Sokol, H and Segata, N},
title = {MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.},
journal = {Cell reports},
volume = {42},
number = {5},
pages = {112464},
doi = {10.1016/j.celrep.2023.112464},
pmid = {37141097},
issn = {2211-1247},
support = {U01 CA230551/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Diet ; Metagenomics/methods ; },
abstract = {Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.},
}

Animals
Mice
*Microbiota/genetics
Metagenome
*Gastrointestinal Microbiome
Diet
Metagenomics/methods

@article {pmid37100126,
year = {2023},
author = {Du, X and Li, X and Cheng, K and Zhao, W and Cai, Z and Chen, G and Zhou, J},
title = {Virome reveals effect of Ulva prolifera green tide on the structural and functional profiles of virus communities in coastal environments.},
journal = {The Science of the total environment},
volume = {883},
number = {},
pages = {163609},
doi = {10.1016/j.scitotenv.2023.163609},
pmid = {37100126},
issn = {1879-1026},
mesh = {Ecosystem ; Virome ; *Ulva ; Bacteria ; Eutrophication ; *Viruses ; China ; },
abstract = {Viruses are widely distributed in marine environments, where they influence the transformation of matter and energy by modulating host metabolism. Driven by eutrophication, green tides are a rising concern in Chinese coastal areas, and are a serious ecological disaster that negatively affects coastal ecosystems and disrupts biogeochemical cycles. Although the composition of bacterial communities in green algae has been investigated, the diversity and roles of viruses in green algal blooms are largely unexplored. Therefore, the diversity, abundance, lifestyle, and metabolic potential of viruses in a natural bloom in Qingdao coastal area were investigated at three different stages (pre-bloom, during-bloom, and post-bloom) by metagenomics analysis. The dsDNA viruses, Siphoviridae, Myoviridae, Podoviridae, and Phycodnaviridae, were found to dominate the viral community. The viral dynamics exhibited distinct temporal patterns across different stages. The composition of the viral community varied during the bloom, especially in populations with low abundance. The lytic cycle was most predominant, and the abundance of lytic viruses increased slightly in the post-bloom stage. The diversity and richness of the viral communities varied distinctly during the green tide, and the post-bloom stage favored viral diversity and richness. The total organic carbon, dissolved oxygen, NO[3-], NO[2-], PO4[3-], chlorophyll-a contents, and temperature variably co-influenced the viral communities. The primary hosts included bacteria, algae, and other microplankton. Network analysis revealed the closer links between the viral communities as the bloom progressed. Functional prediction revealed that the viruses possibly influenced the biodegradation of microbial hydrocarbons and carbon by metabolic augmentation via auxiliary metabolic genes. The composition, structure, metabolic potential, and interaction taxonomy of the viromes differed significantly across the different stages of the green tide. The study demonstrated that the ecological event shaped the viral communities during algal bloom, and the viral communities played a significant role in phycospheric microecology.},
}

Ecosystem
Virome
*Ulva
Bacteria
Eutrophication
*Viruses
China

@article {pmid37093508,
year = {2023},
author = {Wijdeveld, M and van Olst, N and van der Vossen, EWJ and de Brauw, M and Acherman, YIZ and de Goffau, MC and Gerdes, VEA and Nieuwdorp, M},
title = {Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.},
journal = {Obesity surgery},
volume = {33},
number = {6},
pages = {1635-1645},
pmid = {37093508},
issn = {1708-0428},
mesh = {Humans ; *Gastric Bypass/adverse effects ; *Gastrointestinal Microbiome ; *Obesity, Morbid/surgery ; Quality of Life ; *Microbiota ; },
abstract = {PURPOSE: Roux-en-Y gastric bypasses (RYGB) are frequently accompanied by long-term gastrointestinal (GI) symptoms. Direct mechanistic insight into the causation of these symptoms is lacking, but changes in the intestinal microbiome have been proposed to play a role. With this study, we aimed to investigate whether a microbial predisposition exists before RYGB which is associated with GI symptoms during follow-up and to evaluate which microbial groups are involved.

MATERIALS AND METHODS: In total, 67 RYGB patients were included. Shotgun metagenomic sequencing was performed on fecal samples obtained just before and 1 year after surgery. To assess GI symptoms, patients filled out Gastrointestinal Quality of Life Index (GIQLI) questionnaires and were divided into groups based on their total GIQLI score and change in score (postsurgery versus baseline). Extremely randomized tree predictor models were used to identify the most distinctive microbial species associated with postoperative GI symptoms.

RESULTS: Beta diversity differed significantly between baseline and 1-year post-surgery samples, with the post-surgery microbiome resembling a more dysbiotic profile. The most predictive species regarding total GIQLI (AUC 0.77) or delta GIQLI score (AUC 0.83) were identified. Many of these species are known butyrate producers or species known to support them and/or species with anti-inflammatory properties, including Coprococcus eutactus, Faecalibacterium prausnitzii, and Ruminococcus callidus.

CONCLUSION: Beneficial commensal gut microbiota related to a high GI score were associated to adequate intestinal fermentative capacity, suggesting these species might have protective properties against postoperative GI malfunctioning.},
}

Humans
*Gastric Bypass/adverse effects
*Gastrointestinal Microbiome
*Obesity, Morbid/surgery
Quality of Life
*Microbiota

@article {pmid37088586,
year = {2023},
author = {Takaori, A and Hashimoto, D and Ikeura, T and Ito, T and Nakamaru, K and Masuda, M and Nakayama, S and Yamaki, S and Yamamoto, T and Fujimoto, K and Matsuo, Y and Akagawa, S and Ishida, M and Yamaguchi, K and Imoto, S and Hirota, K and Uematsu, S and Satoi, S and Sekimoto, M and Naganuma, M},
title = {Impact of neoadjuvant therapy on gut microbiome in patients with resectable/borderline resectable pancreatic ductal adenocarcinoma.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {23},
number = {4},
pages = {367-376},
doi = {10.1016/j.pan.2023.04.001},
pmid = {37088586},
issn = {1424-3911},
mesh = {Humans ; Neoadjuvant Therapy ; *Gastrointestinal Microbiome ; *Carcinoma, Pancreatic Ductal/drug therapy/surgery ; Deoxycytidine/therapeutic use ; RNA, Ribosomal, 16S ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Pancreatic Neoplasms/drug therapy/surgery ; Fluorouracil/therapeutic use ; Leucovorin/therapeutic use ; },
abstract = {BACKGROUND: /Objectives: Effects of chemotherapy on gut microbiota have been reported in various carcinomas. The current study aimed to evaluate the changes in the gut microbiota before and after neoadjuvant chemotherapy (NAC) in patients with resectable (R) and borderline resectable (BR) pancreatic ductal adenocarcinoma (PDAC) and understand their clinical implications.

METHODS: Twenty patients diagnosed with R/BR-PDAC were included in this study. Stool samples were collected at two points, before and after NAC, for microbiota analysis using 16S ribosomal RNA (16S rRNA) gene sequences.

RESULTS: Of the 20 patients, 18 (90%) were treated with gemcitabine plus S-1 as NAC, and the remaining patients received gemcitabine plus nab-paclitaxel and a fluorouracil, leucovorin, irinotecan, and oxaliplatin combination. No significant differences were observed in the α- and β-diversity before and after NAC. Bacterial diversity was not associated with Evans classification (histological grade of tumor destruction by NAC) or postoperative complications. The relative abundance of Actinobacteria phylum after NAC was significantly lower than that before NAC (P = 0.02). At the genus level, the relative abundance of Bifidobacterium before NAC in patients with Evans grade 2 disease was significantly higher than that in patients with Evans grade 1 disease (P = 0.03). Patients with Evans grade 2 lost significantly more Bifidobacterium than patients with Evans grade 1 (P = 0.01).

CONCLUSIONS: The diversity of gut microbiota was neither decreased by NAC for R/BR-PDAC nor associated with postoperative complications. Lower incidence of Bifidobacterium genus before NAC may be associated with a lower pathological response to NAC.},
}

Humans
Neoadjuvant Therapy
*Gastrointestinal Microbiome
*Carcinoma, Pancreatic Ductal/drug therapy/surgery
Deoxycytidine/therapeutic use
RNA, Ribosomal, 16S
Antineoplastic Combined Chemotherapy Protocols/therapeutic use
*Pancreatic Neoplasms/drug therapy/surgery
Fluorouracil/therapeutic use
Leucovorin/therapeutic use

@article {pmid36977970,
year = {2023},
author = {Amin, DH and Nageeb, WM and Elkelish, A and Makharita, RR},
title = {Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {54},
number = {2},
pages = {983-995},
pmid = {36977970},
issn = {1678-4405},
mesh = {*Metagenome ; Phylogeny ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Soil ; },
abstract = {Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity.Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.},
}

*Metagenome
Phylogeny
*Microbiota
Anti-Bacterial Agents/pharmacology
Soil

@article {pmid36963164,
year = {2023},
author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M},
title = {Decipher enzymes from human microbiota for drug discovery and development.},
journal = {Current opinion in structural biology},
volume = {80},
number = {},
pages = {102567},
doi = {10.1016/j.sbi.2023.102567},
pmid = {36963164},
issn = {1879-033X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Genomics ; Drug Discovery ; },
abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.},
}

Humans
*Gastrointestinal Microbiome
*Microbiota
Bacteria/genetics
Genomics
Drug Discovery

@article {pmid35995413,
year = {2023},
author = {Wang, G and Li, S and Yan, Q and Guo, R and Zhang, Y and Chen, F and Tian, X and Lv, Q and Jin, H and Ma, X and Ma, Y},
title = {Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome.},
journal = {Journal of advanced research},
volume = {48},
number = {},
pages = {75-86},
doi = {10.1016/j.jare.2022.08.011},
pmid = {35995413},
issn = {2090-1224},
mesh = {Humans ; Reproducibility of Results ; *Virome ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Viruses/genetics ; DNA, Viral/genetics ; },
abstract = {INTRODUCTION: Viruses in the human gut have been linked to health and disease. Deciphering the gut virome is dependent on metagenomic sequencing of the virus-like particles (VLPs) purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset.

OBJECTIVES: To develop an optimal method for viral amplification and metagenomic sequencing for maximizing the recovery of viral genomes.

METHODS: We performed parallel virus enrichment and DNA extraction to generate ∼ 30 viral DNA samples from each of 5 fresh fecal specimens and conducted the experiments including 1) optimizing the cycle number for high-fidelity enzyme-based PCR amplification, 2) evaluating the reproducibility of the optimally whole viral metagenomic experimental process, 3) evaluating the reliability of multiple displacement amplification (MDA), 4) testing the capability of long-read sequencing for improving viral metagenomic assembly, and 5) comparing the differences between viral metagenomic and bulk metagenomic approaches.

RESULTS: Our results revealed that the optimal cycle number for PCR amplification is 15. We verified the reliability of MDA and the effectiveness of long-read sequencing. Based on our optimized results, we generated 151 high-quality viruses using the dataset combined from short-read and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we uncovered significant differences in the efficiency and coverage of viral identification between viral metagenomic and bulk metagenomic approaches.

CONCLUSIONS: Our study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about the genome-level characterization of complex viral communities.},
}

Humans
Reproducibility of Results
*Virome
High-Throughput Nucleotide Sequencing/methods
Metagenome
*Viruses/genetics
DNA, Viral/genetics

@article {pmid37258870,
year = {2023},
author = {Yung, PYM and Tan, SM},
title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {303-315},
pmid = {37258870},
issn = {1940-6029},
mesh = {*High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.},
}

*High-Throughput Nucleotide Sequencing
In Situ Hybridization, Fluorescence/methods
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid37258866,
year = {2023},
author = {Arumugam, K and Bessarab, I and Haryono, MAS and Williams, RBH},
title = {Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {235-259},
pmid = {37258866},
issn = {1940-6029},
mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Base Sequence ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities. Here we outline bioinformatics workflows for the recovery and characterization of complete genomes from long-read metagenome data and some complementary procedures for comparison of cognate draft genomes and gene quality obtained from short-read sequencing and long-read sequencing.},
}

*Metagenome
Metagenomics/methods
*Microbiota/genetics
Sequence Analysis, DNA/methods
Base Sequence
High-Throughput Nucleotide Sequencing/methods

@article {pmid37258863,
year = {2023},
author = {Jadeja, NB and Kapley, A},
title = {Designing Knowledge-Based Bioremediation Strategies Using Metagenomics.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {195-208},
pmid = {37258863},
issn = {1940-6029},
mesh = {Biodegradation, Environmental ; *Metagenomics/methods ; Wastewater ; *Microbiota ; Metagenome ; },
abstract = {Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.},
}

Biodegradation, Environmental
*Metagenomics/methods
Wastewater
*Microbiota
Metagenome

@article {pmid37258862,
year = {2023},
author = {Arumugam, R and Ravichandran, P and Yeap, SK and Sharma, RSK and Zulkifly, SB and Yawah, D and Annavi, G},
title = {Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {175-194},
pmid = {37258862},
issn = {1940-6029},
mesh = {Animals ; *Endangered Species ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Animals, Wild ; High-Throughput Nucleotide Sequencing ; },
abstract = {The Tapirus indicus, also known as Malayan tapir, has been listed as a rapidly declining animal species in the past decades, along with being declared and categorized as an endangered species by the International Union for Conservation of Nature (IUCN) 2016. This tapir species is geographically distributed across several countries in Southeast Asia such as Peninsular Malaysia, Indonesia (Sumatra), South Thailand, and Myanmar. Amongst these countries, the Peninsula Malaysia forest is recorded to contain the highest number of Malayan tapir population. Unfortunately, in the past decades, the population of Malayan tapirs has declined swiftly due to serious deforestation, habitat fragmentation, and heavy vehicle accidents during road crossings at forest routes. Concerned by this predicament, the Department of Wildlife and National Parks (DWNP) Peninsular Malaysia collaborated with a few local universities to conduct various studies aimed at increasing the population number of tapirs in Malaysia. Several studies were conducted with the aim of enhancing the well-being of tapirs in captivity. Veterinarians face problems when it comes to selecting healthy and suitable tapirs for breeding programs at conservation centers. Conventional molecular methods using high-throughput sequencing provides a solution in determining the health condition of Malayan tapirs using the Next-Generation Sequencing (NGS) technology. Unaware by most, gut microbiome plays an important role in determining the health condition of an organism by various aspects: (1) digestion control; (2) benefiting the immune system; and (3) playing a role as a "second brain." Commensal gut bacterial communities (microbiomes) are predicted to influence organism health and disease. Imbalance of unhealthy and healthy microbes in the gut may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. In infancy, neonatal gut microbiomes are colonized with maternal and environmental flora, and mature toward a stable composition in two to three years. Interactions between the microorganism communities and the host allow for the establishment of microbiological roles. Identifying the core microbiome(s) are essential in the prediction of diseases and changes in environmental behavior of microorganisms. The dataset of 16S rRNA amplicon sequencing of Malayan tapir was deposited in the MG-RAST portal. Parameters such as quality control, taxonomic prediction (unknown and predicted), diversity (rarefaction), and diversity (alpha) were analyzed using sequencing approaches (Amplicon sequencing). Comparisons of parameters, according to the type of sequencing, showed significant differences, except for the prediction variable. In the Amplicon sequencing datasets, the parameters Rarefaction and Unknown had the highest correlation, while Alpha and Predicted had the lowest. Firmicutes, Bacteroidetes, Proteobacteria, Bacilli, and Bacteroidia were the most representative genera in Malayan tapir amplicon sequences, which indicated that most of the tapirs were healthy. However, continuous assessment to maintain the well-being of tapir for long term is still required. This chapter focuses on the introduction of 16S rRNA amplicon metagenomics in analyzing Malayan tapir gut microbiome dataset.},
}

Animals
*Endangered Species
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Animals, Wild
High-Throughput Nucleotide Sequencing

@article {pmid37258861,
year = {2023},
author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M},
title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {133-174},
pmid = {37258861},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; },
abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.},
}

*Metagenomics/methods
Metagenome
*Microbiota/genetics
Ecology
Computational Biology/methods
Data Analysis

@article {pmid37258860,
year = {2023},
author = {Gautam, A and Zeng, W and Huson, DH},
title = {DIAMOND + MEGAN Microbiome Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {107-131},
pmid = {37258860},
issn = {1940-6029},
mesh = {*Software ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; Databases, Factual ; Metagenome ; Algorithms ; },
abstract = {Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.},
}

*Software
*Microbiota/genetics
Sequence Analysis, DNA/methods
Metagenomics/methods
Databases, Factual
Metagenome
Algorithms

@article {pmid37258857,
year = {2023},
author = {Wang, D},
title = {Metagenomics Databases for Bacteria.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {55-67},
pmid = {37258857},
issn = {1940-6029},
mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).},
}

Phylogeny
*Metagenomics
Bacteria/genetics
Databases, Genetic
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid37258856,
year = {2023},
author = {Gihawi, A and Cardenas, R and Hurst, R and Brewer, DS},
title = {Quality Control in Metagenomics Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {21-54},
pmid = {37258856},
issn = {1940-6029},
mesh = {Reproducibility of Results ; *Metagenomics/methods ; Computational Biology/methods ; *Microbiota ; Research Design ; },
abstract = {Experiments involving metagenomics data are become increasingly commonplace. Processing such data requires a unique set of considerations. Quality control of metagenomics data is critical to extracting pertinent insights. In this chapter, we outline some considerations in terms of study design and other confounding factors that can often only be realized at the point of data analysis.In this chapter, we outline some basic principles of quality control in metagenomics, including overall reproducibility and some good practices to follow. The general quality control of sequencing data is then outlined, and we introduce ways to process this data by using bash scripts and developing pipelines in Snakemake (Python).A significant part of quality control in metagenomics is in analyzing the data to ensure you can spot relationships between variables and to identify when they might be confounded. This chapter provides a walkthrough of analyzing some microbiome data (in the R statistical language) and demonstrates a few days to identify overall differences and similarities in microbiome data. The chapter is concluded by discussing remarks about considering taxonomic results in the context of the study and interrogating sequence alignments using the command line.},
}

Reproducibility of Results
*Metagenomics/methods
Computational Biology/methods
*Microbiota
Research Design

@article {pmid37258855,
year = {2023},
author = {Benz, S and Mitra, S},
title = {From Genomics to Metagenomics in the Era of Recent Sequencing Technologies.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2649},
number = {},
pages = {1-20},
pmid = {37258855},
issn = {1940-6029},
mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Genomics ; *Microbiota/genetics ; Metagenome ; },
abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.},
}

Humans
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
Genomics
*Microbiota/genetics
Metagenome

@article {pmid37258543,
year = {2023},
author = {Liu, J and Sun, J and Yu, J and Chen, H and Zhang, D and Zhang, T and Ma, Y and Zou, C and Zhang, Z and Ma, L and Yu, X},
title = {Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {29},
pmid = {37258543},
issn = {2055-5008},
mesh = {Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Chenodeoxycholic Acid/pharmacology/therapeutic use ; Bile Acids and Salts ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD), the most common chronic liver disease, had no approved pharmacological agents yet. Obeticholic acid (OCA), a novel bile acid derivative, was demonstrated to ameliorate NAFLD-related manifestations. Regarding the role of gut-liver axis in liver disease development, this study aimed to explore the potential role of gut microbiota in the treatment of OCA in NAFLD mice induced by the high-fat diet (HFD). Antibiotic-induced microbiome depletion (AIMD) and fecal microbiota transplantation (FMT) confirmed the critical role of gut microbiota in OCA treatment for NAFLD by effectively alleviating histopathological lesions and restoring liver function impaired by HFD. Metagenomic analysis indicated that OCA intervention in HFD mice remarkably increased the abundance of Akkermansia muciniphila, Bifidobacterium spp., Bacteroides spp., Alistipes spp., Lactobacillus spp., Streptococcus thermophilus, and Parasutterella excrementihominis. Targeted metabolomics analysis indicated that OCA could modulate host bile acids pool by reducing levels of serum hydrophobic cholic acid (CA) and chenodeoxycholic acid (CDCA), and increasing levels of serum-conjugated bile acids, such as taurodeoxycholic acid (TDCA) and tauroursodesoxycholic acid (TUDCA) in the HFD-fed mice. Strong correlations were observed between differentially abundant microbes and the shifted bile acids. Furthermore, bacteria enriched by OCA intervention exhibited much greater potential in encoding 7alpha-hydroxysteroid dehydrogenase (7α-HSDs) producing secondary bile acids rather than bile salt hydrolases (BSHs) mainly responsible for primary bile acid deconjugation. In conclusion, this study demonstrated that OCA intervention altered gut microbiota composition with specially enriched gut microbes modulating host bile acids, thus effectively alleviating NAFLD in the mice.},
}

Mice
Animals
*Non-alcoholic Fatty Liver Disease/drug therapy/metabolism
*Gastrointestinal Microbiome
Chenodeoxycholic Acid/pharmacology/therapeutic use
Bile Acids and Salts

@article {pmid37254344,
year = {2023},
author = {Yao, L and Zhang, J and Lu, J and Chen, D and Song, S and Wang, H and Sun, M and Feng, T},
title = {Revealing the influence of microbiota on the flavor of kombucha during natural fermentation process by metagenomic and GC-MS analysis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {169},
number = {},
pages = {112909},
doi = {10.1016/j.foodres.2023.112909},
pmid = {37254344},
issn = {1873-7145},
mesh = {Fermentation ; Gas Chromatography-Mass Spectrometry ; *Microbiota/genetics ; Metagenome ; Saccharomyces cerevisiae ; Tea/chemistry ; },
abstract = {In this work, raw Pu-erh tea (RAPT) was employed for kombucha preparation, and the microbial composition and volatile flavor compounds of the fermented tea had been investigated during natural fermentation process. The head space-solid phase microextraction-gas chromatograph mass spectrometry (HS-SPME-GC-MS) was performed for volatiles analysis of unfermented tea and kombucha fermented for 3 days (KF-3) and 6 days (KF-6). Meanwhile, the microbial community of KF-3 and KF-6 were evaluated by metagenomic analysis. A total of 72 volatile compounds were identified and obvious changes in volatiles were observed during the fermentation process based on the results of GC-MS and principal component analysis (PCA). Metagenomic sequencing analysis demonstrated that bacterium Komagataeibacter saccharivorans and unclassified-g-komagataeibacter and yeast Saccharomyces cerevisiae and Brettanomyces bruxellensis were the most common microbes contained in the sampled kombucha communities. Furthermore, the relevance among microbial community and volatile compounds was evaluated through correlation heatmap analysis. The results suggested that the main flavor volatiles of kombucha (i.e., acids, esters and terpenes) were closely related to species of genus Komagataeibacter, Gluconacetobacter, Saccharomyces, Brettanomyces, Acetobacter, Novacetimonas and Pichia microorganisms. The obtained results would help to better understand microbial communities and volatile compounds of kombucha, which could provide useful information for enhancing the flavor quality of kombucha products.},
}

Fermentation
Gas Chromatography-Mass Spectrometry
*Microbiota/genetics
Metagenome
Saccharomyces cerevisiae
Tea/chemistry

@article {pmid37133385,
year = {2023},
author = {Podell, S and Oliver, A and Kelly, LW and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE},
title = {Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides.},
journal = {Applied and environmental microbiology},
volume = {89},
number = {5},
pages = {e0215422},
pmid = {37133385},
issn = {1098-5336},
mesh = {Animals ; Polysaccharides ; Sulfates ; Coral Reefs ; Fishes ; *Microbiota ; *Seaweed ; Bacteria/genetics ; },
abstract = {Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides. IMPORTANCE This work connects specific uncultured bacterial taxa with distinct polysaccharide digestion capabilities lacking in their marine vertebrate hosts, providing fresh insights into poorly understood processes for deconstructing complex sulfated polysaccharides and potential evolutionary mechanisms for microbial acquisition of expanded macroalgal utilization gene functions. Several thousand new marine-specific candidate enzyme sequences for polysaccharide utilization have been identified. These data provide foundational resources for future investigations into suppression of coral reef macroalgal overgrowth, fish host physiology, the use of macroalgal feedstocks in terrestrial and aquaculture animal feeds, and the bioconversion of macroalgae biomass into value-added commercial fuel and chemical products.},
}

Animals
Polysaccharides
Sulfates
Coral Reefs
Fishes
*Microbiota
*Seaweed
Bacteria/genetics

@article {pmid37254152,
year = {2023},
author = {Wang, K and Mehta, RS and Ma, W and Nguyen, LH and Wang, DD and Ghazi, AR and Yan, Y and Al-Shaar, L and Wang, Y and Hang, D and Fu, BC and Ogino, S and Rimm, EB and Hu, FB and Carmody, RN and Garrett, WS and Sun, Q and Chan, AT and Huttenhower, C and Song, M},
title = {The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {121},
pmid = {37254152},
issn = {2049-2618},
support = {R35 CA197735/NH/NIH HHS/United States ; K24 DK098311/NH/NIH HHS/United States ; R00 CA215314/NH/NIH HHS/United States ; },
mesh = {Female ; Humans ; Male ; Young Adult ; Body Weight ; Exercise/physiology ; Follow-Up Studies ; *Gastrointestinal Microbiome/genetics ; Obesity/metabolism ; Weight Gain ; Aged ; },
abstract = {BACKGROUND: The gut microbiome regulates host energy balance and adiposity-related metabolic consequences, but it remains unknown how the gut microbiome modulates body weight response to physical activity (PA).

METHODS: Nested in the Health Professionals Follow-up Study, a subcohort of 307 healthy men (mean[SD] age, 70[4] years) provided stool and blood samples in 2012-2013. Data from cohort long-term follow-ups and from the accelerometer, doubly labeled water, and plasma biomarker measurements during the time of stool collection were used to assess long-term and short-term associations of PA with adiposity. The gut microbiome was profiled by shotgun metagenomics and metatranscriptomics. A subcohort of 209 healthy women from the Nurses' Health Study II was used for validation.

RESULTS: The microbial species Alistipes putredinis was found to modify the association between PA and body weight. Specifically, in individuals with higher abundance of A. putredinis, each 15-MET-hour/week increment in long-term PA was associated with 2.26 kg (95% CI, 1.53-2.98 kg) less weight gain from age 21 to the time of stool collection, whereas those with lower abundance of A. putredinis only had 1.01 kg (95% CI, 0.41-1.61 kg) less weight gain (pinteraction = 0.019). Consistent modification associated with A. putredinis was observed for short-term PA in relation to BMI, fat mass%, plasma HbA1c, and 6-month weight change. This modification effect might be partly attributable to four metabolic pathways encoded by A. putredinis, including folate transformation, fatty acid β-oxidation, gluconeogenesis, and stearate biosynthesis.

CONCLUSIONS: A greater abundance of A. putredinis may strengthen the beneficial association of PA with body weight change, suggesting the potential of gut microbial intervention to improve the efficacy of PA in body weight management. Video Abstract.},
}

Female
Humans
Male
Young Adult
Body Weight
Exercise/physiology
Follow-Up Studies
*Gastrointestinal Microbiome/genetics
Obesity/metabolism
Weight Gain
Aged

@article {pmid37253538,
year = {2023},
author = {Mori, H and Kato, T and Ozawa, H and Sakamoto, M and Murakami, T and Taylor, TD and Toyoda, A and Ohkuma, M and Kurokawa, K and Ohno, H},
title = {Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.},
journal = {DNA research : an international journal for rapid publication of reports on genes and genomes},
volume = {30},
number = {3},
pages = {},
pmid = {37253538},
issn = {1756-1663},
mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Workflow ; *Microbiota/genetics ; Metagenome ; Metagenomics/methods ; },
abstract = {To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the influence of experimental and bioinformatics procedures on the 16S rRNA gene and shotgun metagenomic sequencing. We found that DNA extraction methods greatly affected the DNA yields and taxonomic composition of sequenced reads, and that some of the commonly used primers for 16S rRNA genes were prone to underestimate the abundance of some gut commensal taxa such as Erysipelotrichia, Verrucomicrobiota and Methanobacteriota. Binning of the assembled contigs of shotgun metagenomic sequences by MetaBAT2 produced phylogenetically consistent, less-contaminated bins with varied completeness. The ensemble approach of multiple binning tools by MetaWRAP can improve completeness but sometimes increases the contamination rate. Our benchmark study provides an important foundation for the interpretation of human gut microbiome data by providing means for standardization among gut microbiome data obtained with different methodologies and will facilitate further development of analytical methods.},
}

Humans
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Workflow
*Microbiota/genetics
Metagenome
Metagenomics/methods

@article {pmid37248474,
year = {2023},
author = {Stiller, J and Wilson, NG and Rouse, GW},
title = {Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture.},
journal = {BMC biology},
volume = {21},
number = {1},
pages = {129},
pmid = {37248474},
issn = {1741-7007},
mesh = {Humans ; Animals ; Phylogeny ; *Metagenomics ; Biodiversity ; *Smegmamorpha ; Australia ; Genetic Variation ; },
abstract = {BACKGROUND: Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture.

RESULTS: Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia.

CONCLUSIONS: We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.},
}

Humans
Animals
Phylogeny
*Metagenomics
Biodiversity
*Smegmamorpha
Australia
Genetic Variation

@article {pmid37244770,
year = {2023},
author = {Mincer, TJ and Bos, RP and Zettler, ER and Zhao, S and Asbun, AA and Orsi, WD and Guzzetta, VS and Amaral-Zettler, LA},
title = {Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat.},
journal = {Water research},
volume = {},
number = {},
pages = {120033},
doi = {10.1016/j.watres.2023.120033},
pmid = {37244770},
issn = {1879-2448},
abstract = {We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.},
}

@article {pmid37243505,
year = {2023},
author = {Bruggeling, CE and Te Groen, M and Garza, DR and van Heeckeren Tot Overlaer, F and Krekels, JPM and Sulaiman, BC and Karel, D and Rulof, A and Schaaphok, AR and Hornikx, DLAH and Nagtegaal, ID and Dutilh, BE and Hoentjen, F and Boleij, A},
title = {Bacterial oncotraits rather than spatial organization are associated with dysplasia in ulcerative colitis.},
journal = {Journal of Crohn's & colitis},
volume = {},
number = {},
pages = {},
doi = {10.1093/ecco-jcc/jjad092},
pmid = {37243505},
issn = {1876-4479},
abstract = {BACKGROUND AND AIMS: Colonic bacterial biofilms are frequently present in ulcerative colitis (UC) and may increase dysplasia risk through pathogens expressing oncotraits. This prospective cohort study aimed to determine (1) the association of oncotraits and longitudinal biofilm presence with dysplasia risk in UC, and (2) the relation of bacterial composition with biofilms and dysplasia risk.

METHODS: Feces and left- and right-sided colonic biopsies were collected from 80 UC patients and 35 controls. Oncotraits (FadA of Fusobacterium, BFT of Bacteroides fragilis, colibactin (ClbB) and Intimin (Eae) of Escherichia coli) were assessed in fecal DNA with multiplex qPCR. Biopsies were screened for biofilms (n=873) with 16S rRNA fluorescent in situ hybridization. Shotgun metagenomic sequencing (n=265), and ki67-immunohistochemistry were performed. Associations were determined with a mixed-effects regression model.

RESULTS: Biofilms were highly prevalent in UC patients (90.8%) with a median persistence of 3 years (IQR 2-5 years). Biofilm-positive biopsies showed increased epithelial hypertrophy (p=0.025), a reduced Shannon diversity independent of disease status (p=0.015), however, were not significantly associated with dysplasia in UC (aOR 1.45(95%CI0.63-3.40). In contrast, ClbB independently associated with dysplasia (aOR 7.16 (95%CI1.75-29.28), while FadA and Fusobacteriales were associated with a decreased dysplasia risk in UC (aOR 0.23 (95%CI0.06-0.83), and p<0.01).

CONCLUSIONS: Biofilms are a hallmark of UC, however, because of their high prevalence a poor biomarker for dysplasia. In contrast, colibactin presence and FadA absence independently associate with dysplasia in UC and might therefore be valuable biomarkers for future risk stratification and intervention strategies.},
}

@article {pmid37086993,
year = {2023},
author = {Yang, J and Yu, Q and Su, W and Wang, S and Wang, X and Han, Q and Qu, J and Li, H},
title = {Metagenomics reveals elevated temperature causes nitrogen accumulation mainly by inhibiting nitrate reduction process in polluted water.},
journal = {The Science of the total environment},
volume = {882},
number = {},
pages = {163631},
doi = {10.1016/j.scitotenv.2023.163631},
pmid = {37086993},
issn = {1879-1026},
mesh = {Animals ; *Nitrates ; Temperature ; Nitrogen/metabolism ; Metagenomics ; *Microbiota ; Water ; Glutamates ; Denitrification ; },
abstract = {Determining the response of functional genes and microbiota involved in the nitrogen (N) cycle to warming in the face of global climate change is a hotpot topic. However, whether and how elevated temperature affects the N-cycle genes in polluted water remains unclear. Based on metagenomics, we investigated the responses of the whole N-cycling genes and their microbial communities to the temperature gradients (23, 26, 29, 32, and 35 °C) using animal cadavers as an N-pollution model. We found that the abundance of gene families involved in glutamate metabolism, assimilatory nitrate reduction to nitrite (ANRN), and denitrification pathways decreased with temperature. Moreover, warming reduced the diversity of N-cycling microbial communities. Ecological network analysis indicated that elevated temperature intensified the mutual competition of N-cycle genes. The partial least squares path model (PLS-PM) showed that warming directly suppressed most N-cycle pathways, especially glutamate metabolism, denitrification, and ANRN pathways. Corpse decay also indirectly inhibited N-cycling via regulating N content and microbial communities. Our results highlight warming leads to N accumulation by inhibiting the ANRN and denitrification pathways, which may jeopardize ecological environment security. Our study is expected to provide valuable insights into the complex N-cycle process and N-pollution in warmer aquatic ecosystems.},
}

Animals
*Nitrates
Temperature
Nitrogen/metabolism
Metagenomics
*Microbiota
Water
Glutamates
Denitrification

@article {pmid37080313,
year = {2023},
author = {Ovis-Sánchez, JO and Perera-Pérez, VD and Buitrón, G and Quintela-Baluja, M and Graham, DW and Morales-Espinosa, R and Carrillo-Reyes, J},
title = {Exploring resistomes and microbiomes in pilot-scale microalgae-bacteria wastewater treatment systems for use in low-resource settings.},
journal = {The Science of the total environment},
volume = {882},
number = {},
pages = {163545},
doi = {10.1016/j.scitotenv.2023.163545},
pmid = {37080313},
issn = {1879-1026},
mesh = {Humans ; Waste Disposal, Fluid ; *Microalgae/metabolism ; Wastewater ; Bacteria/genetics ; Anti-Bacterial Agents/metabolism ; *Water Purification ; *Microbiota ; Genes, Bacterial ; },
abstract = {Antibiotic resistance genes (ARGs) released into the environment are an emerging human and environmental health concern, including ARGs spread in wastewater treatment effluents. In low-to-middle income countries (LMICs), an alternate wastewater treatment option instead of conventional systems are low-energy, high-rate algal ponds (HRAP) that use microalgae-bacteria aggregates (MABA) for waste degradation. Here we studied the robustness of ARG removal in MABA-based pilot-scale outdoor systems for 140 days of continuous operation. The HRAP system successfully removed 73 to 88 % chemical oxygen demand and up to 97.4 % ammonia, with aggregate size increasing over operating time. Fourteen ARG classes were identified in the HRAP influent, MABA, and effluent using metagenomics, with the HRAP process reducing total ARG abundances by up to 5-fold from influent to effluent. Parallel qPCR analyses showed the HRAP system significantly reduced exemplar ARGs (p < 0.05), with 1.2 to 4.9, 2.7 to 6.3, 0 to 1.5, and 1.2 to 4.8 log-removals for sul1, tetQ, blaKPC, and intl1 genes, respectively. Sequencing of influent, effluent and MABAs samples showed associated microbial communities differed significantly, with influent communities by Enterobacteriales (clinically relevant ARGs carrying bacteria), which were less evident in MABA and effluent. In this sense, such bacteria might be excluded from MABA due to their good settling properties and the presence of antimicrobial peptides. Microalgae-bacteria treatment systems steadily reduced ARGs from wastewater during operation time, using sunlight as the energetic driver, making them ideal for use in LMIC wastewater treatment applications.},
}

Humans
Waste Disposal, Fluid
*Microalgae/metabolism
Wastewater
Bacteria/genetics
Anti-Bacterial Agents/metabolism
*Water Purification
*Microbiota
Genes, Bacterial

@article {pmid37044345,
year = {2023},
author = {Sánchez-Reyes, A and Gaytán, I and Pulido-García, J and Burelo, M and Vargas-Suárez, M and Cruz-Gómez, MJ and Loza-Tavera, H},
title = {Genetic basis for the biodegradation of a polyether-polyurethane-acrylic copolymer by a landfill microbial community inferred by metagenomic deconvolution analysis.},
journal = {The Science of the total environment},
volume = {881},
number = {},
pages = {163367},
doi = {10.1016/j.scitotenv.2023.163367},
pmid = {37044345},
issn = {1879-1026},
mesh = {*Polyurethanes/chemistry ; Metagenome ; Plastics ; *Microbiota ; Biodegradation, Environmental ; Waste Disposal Facilities ; },
abstract = {Plastic accumulation in the world amounts to approximately 8300 million tons. Polyurethanes (PU) account for 7.7 % of total plastics production worldwide, and their diverse chemical composition makes them highly recalcitrant to biodegradation. Several works have reported polyurethane-degrading microbial communities. However, it is still necessary to learn more about the chemical, biochemical, and genetic bases linked to the polyurethanolytic phenotype and the microbial taxonomic determinants responsible for metabolizing the PU polymer and its associated chemical additives. To shed light on this problem, we applied physical, chemical, biochemical, metagenomic, and bioinformatic analyses to explore the biodegradation capability and related biochemical and genetic determinants of the BP6 microbial community that can grow in PolyLack, a commercial coating containing a polyether polyurethane acrylate (PE-PU-A) copolymer and several additives, as sole carbon source. We observed complete additives (isopropanol, N-methyl-2-pyrrolidone, 2-butoxyethanol, alkyl glycol ethers) biodegradation and the appearance of released polymer components (toluene diisocyanate (TDI) and methylene diphenyl diisocyanate (MDI) derivatives), and multiple degradation products since early cultivation times. The Hi-C metagenomic analysis identified a complex microbiome with 35 deconvolved Metagenome-Assembled Genomes (MAGs) - several new species - and biodegradation markers that suggest the coexistence of hydrolytic, oxidative, and reductive metabolic strategies for degrading the additives and the PU copolymer. This work also provides evidence of the metabolic capability the BP6 community has for biodegrading polyether polyurethane foams. Based on these analyses, we propose a novel metabolic pathway for 4,4'-methylenedianiline (MDA), an initial biodegradation intermediate of MDI-based PU, encoded in the complex BP6 community metagenome and suggest that this community is a potential biotechnological tool for PU bio-recycling.},
}

*Polyurethanes/chemistry
Metagenome
Plastics
*Microbiota
Biodegradation, Environmental
Waste Disposal Facilities

@article {pmid37240180,
year = {2023},
author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP},
title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.},
journal = {International journal of molecular sciences},
volume = {24},
number = {10},
pages = {},
pmid = {37240180},
issn = {1422-0067},
mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; },
abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.},
}

Humans
Multiomics
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
U937 Cells
*Periodontitis/microbiology
*Microbiota/genetics
Bacteria/metabolism
Cytokines/metabolism
RNA-Binding Proteins

@article {pmid37002975,
year = {2023},
author = {Stockdale, SR and Hill, C},
title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.},
journal = {Current opinion in microbiology},
volume = {73},
number = {},
pages = {102307},
doi = {10.1016/j.mib.2023.102307},
pmid = {37002975},
issn = {1879-0364},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; },
abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.},
}

Humans
*Gastrointestinal Microbiome/genetics
Plasmids/genetics
*Microbiota/genetics
Bacteria/genetics
Metagenomics

@article {pmid36931094,
year = {2023},
author = {Correia, GD and Marchesi, JR and MacIntyre, DA},
title = {Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods.},
journal = {Current opinion in microbiology},
volume = {73},
number = {},
pages = {102292},
doi = {10.1016/j.mib.2023.102292},
pmid = {36931094},
issn = {1879-0364},
mesh = {Female ; Humans ; *Microbiota/genetics ; Metagenomics/methods ; Host Microbial Interactions ; DNA ; },
abstract = {Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.},
}

Female
Humans
*Microbiota/genetics
Metagenomics/methods
Host Microbial Interactions
DNA

@article {pmid37239442,
year = {2023},
author = {Choudhury, N and Sahu, TK and Rao, AR and Rout, AK and Behera, BK},
title = {An Improved Machine Learning-Based Approach to Assess the Microbial Diversity in Major North Indian River Ecosystems.},
journal = {Genes},
volume = {14},
number = {5},
pages = {},
pmid = {37239442},
issn = {2073-4425},
mesh = {*Rivers ; Software ; Machine Learning ; Metagenome/genetics ; *Microbiota/genetics ; },
abstract = {The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics).},
}

*Rivers
Software
Machine Learning
Metagenome/genetics
*Microbiota/genetics

@article {pmid37237391,
year = {2023},
author = {Wang, Z and Peters, BA and Bryant, M and Hanna, DB and Schwartz, T and Wang, T and Sollecito, CC and Usyk, M and Grassi, E and Wiek, F and Peter, LS and Post, WS and Landay, AL and Hodis, HN and Weber, KM and French, A and Golub, ET and Lazar, J and Gustafson, D and Sharma, A and Anastos, K and Clish, CB and Burk, RD and Kaplan, RC and Knight, R and Qi, Q},
title = {Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {119},
pmid = {37237391},
issn = {2049-2618},
support = {R01HL140976/HL/NHLBI NIH HHS/United States ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *HIV Infections/complications/pathology ; *Carotid Stenosis/complications/pathology ; Proteomics ; *Carotid Artery Diseases/complications/pathology ; *Atherosclerosis/complications/pathology ; Carotid Arteries/metabolism/pathology ; Biomarkers/metabolism ; Inflammation/pathology ; },
abstract = {BACKGROUND: Alterations in gut microbiota have been implicated in HIV infection and cardiovascular disease. However, how gut microbial alterations relate to host inflammation and metabolite profiles, and their relationships with atherosclerosis, have not been well-studied, especially in the context of HIV infection. Here, we examined associations of gut microbial species and functional components measured by shotgun metagenomics with carotid artery plaque assessed by B-mode carotid artery ultrasound in 320 women with or at high risk of HIV (65% HIV +) from the Women's Interagency HIV Study. We further integrated plaque-associated microbial features with serum proteomics (74 inflammatory markers measured by the proximity extension assay) and plasma metabolomics (378 metabolites measured by liquid chromatography tandem mass spectrometry) in relation to carotid artery plaque in up to 433 women.

RESULTS: Fusobacterium nucleatum, a potentially pathogenic bacteria, was positively associated with carotid artery plaque, while five microbial species (Roseburia hominis, Roseburia inulinivorans, Johnsonella ignava, Odoribacter splanchnicus, Clostridium saccharolyticum) were inversely associated with plaque. Results were consistent between women with and without HIV. Fusobacterium nucleatum was positively associated with several serum proteomic inflammatory markers (e.g., CXCL9), and the other plaque-related species were inversely associated with proteomic inflammatory markers (e.g., CX3CL1). These microbial-associated proteomic inflammatory markers were also positively associated with plaque. Associations between bacterial species (especially Fusobacterium nucleatum) and plaque were attenuated after further adjustment for proteomic inflammatory markers. Plaque-associated species were correlated with several plasma metabolites, including the microbial metabolite imidazole-propionate (ImP), which was positively associated with plaque and several pro-inflammatory markers. Further analysis identified additional bacterial species and bacterial hutH gene (encoding enzyme histidine ammonia-lyase in ImP production) associated with plasma ImP levels. A gut microbiota score based on these ImP-associated species was positively associated with plaque and several pro-inflammatory markers.

CONCLUSION: Among women living with or at risk of HIV, we identified several gut bacterial species and a microbial metabolite ImP associated with carotid artery atherosclerosis, which might be related to host immune activation and inflammation. Video Abstract.},
}

Humans
Female
*Gastrointestinal Microbiome
*HIV Infections/complications/pathology
*Carotid Stenosis/complications/pathology
Proteomics
*Carotid Artery Diseases/complications/pathology
*Atherosclerosis/complications/pathology
Carotid Arteries/metabolism/pathology
Biomarkers/metabolism
Inflammation/pathology

@article {pmid37237317,
year = {2023},
author = {Coutinho, FH and Silveira, CB and Sebastián, M and Sánchez, P and Duarte, CM and Vaqué, D and Gasol, JM and Acinas, SG},
title = {Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {118},
pmid = {37237317},
issn = {2049-2618},
mesh = {Seawater/microbiology ; Water ; Genes, Viral ; *Viruses/genetics ; *Microbiota/genetics ; Oceans and Seas ; },
abstract = {BACKGROUND: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts.

RESULTS: We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 μm) and particle-attached (0.8-20 μm) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses.

CONCLUSIONS: These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities. Video Abstract.},
}

Seawater/microbiology
Water
Genes, Viral
*Viruses/genetics
*Microbiota/genetics
Oceans and Seas

@article {pmid37236370,
year = {2023},
author = {Řezanka, T and Kyselová, L and Murphy, DJ},
title = {Archaeal lipids.},
journal = {Progress in lipid research},
volume = {91},
number = {},
pages = {101237},
doi = {10.1016/j.plipres.2023.101237},
pmid = {37236370},
issn = {1873-2194},
abstract = {The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.},
}

@article {pmid37230981,
year = {2023},
author = {Feehily, C and O'Neill, IJ and Walsh, CJ and Moore, RL and Killeen, SL and Geraghty, AA and Lawton, EM and Byrne, D and Sanchez-Gallardo, R and Nori, SRC and Nielsen, IB and Wortmann, E and Matthews, E and O'Flaherty, R and Rudd, PM and Groeger, D and Shanahan, F and Saldova, R and McAuliffe, FM and Van Sinderen, D and Cotter, PD},
title = {Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach.},
journal = {Nature communications},
volume = {14},
number = {1},
pages = {3015},
pmid = {37230981},
issn = {2041-1723},
mesh = {Humans ; Infant ; Female ; Pregnancy ; *Bifidobacterium ; Mothers ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Parturition ; Feces/microbiology ; },
abstract = {A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.},
}

Humans
Infant
Female
Pregnancy
*Bifidobacterium
Mothers
*Gastrointestinal Microbiome/genetics
Metagenome/genetics
Parturition
Feces/microbiology

@article {pmid37228141,
year = {2023},
author = {Young, BD and Rosales, SM and Enochs, IC and Kolodziej, G and Formel, N and Moura, A and D'Alonso, GL and Traylor-Knowles, N},
title = {Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.},
journal = {PloS one},
volume = {18},
number = {5},
pages = {e0286293},
pmid = {37228141},
issn = {1932-6203},
mesh = {Animals ; Viverridae/genetics ; *Anthozoa/genetics/microbiology ; *Microbiota/genetics ; Gene Expression Profiling ; Serratia marcescens/genetics ; Coral Reefs ; },
abstract = {Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.},
}

Animals
Viverridae/genetics
*Anthozoa/genetics/microbiology
*Microbiota/genetics
Gene Expression Profiling
Serratia marcescens/genetics
Coral Reefs

@article {pmid37019075,
year = {2023},
author = {Pietruska, A and Bortoluzzi, C and Hauck, R},
title = {A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens.},
journal = {Poultry science},
volume = {102},
number = {6},
pages = {102652},
pmid = {37019075},
issn = {1525-3171},
mesh = {Animals ; *Eimeria ; Chickens/microbiology ; *Enteritis/veterinary ; *Poultry Diseases/microbiology ; *Clostridium Infections/veterinary/microbiology ; *Coccidiosis/veterinary/microbiology ; Clostridium perfringens ; *Microbiota ; },
abstract = {Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.},
}

Animals
*Eimeria
Chickens/microbiology
*Enteritis/veterinary
*Poultry Diseases/microbiology
*Clostridium Infections/veterinary/microbiology
*Coccidiosis/veterinary/microbiology
Clostridium perfringens
*Microbiota

@article {pmid36996985,
year = {2023},
author = {Yan, S and Zhang, Z and Wang, J and Xia, Y and Chen, S and Xie, S},
title = {River sediment microbial community composition and function impacted by thallium spill.},
journal = {The Science of the total environment},
volume = {880},
number = {},
pages = {163101},
doi = {10.1016/j.scitotenv.2023.163101},
pmid = {36996985},
issn = {1879-1026},
mesh = {Humans ; *Thallium/analysis ; Rivers ; Metals/analysis ; *Microbiota ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; },
abstract = {Thallium (Tl) is widely used in various industries, which increases the risk of leakage into the environment. Since Tl is highly toxic, it can do a great harm to human health and ecosystem. In order to explore the response of freshwater sediment microorganisms to sudden Tl spill, metagenomic technique was used to elucidate the changes of microbial community composition and functional genes in river sediments. Tl pollution could have profound impacts on microbial community composition and function. Proteobacteria remained the dominance in contaminated szediments, indicating that it had a strong resistance to Tl contamination, and Cyanobacteria also showed a certain resistance. Tl pollution also had a certain screening effect on resistance genes and affected the abundance of resistance genes. Metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) were enriched at the site near the spill site, where Tl concentration was relatively low among polluted sites. When Tl concentration was higher, the screening effect was not obvious and the resistance genes even became lower. Moreover, there was a significant correlation between MRGs and ARGs. In addition, co-occurrence network analysis showed that Sphingopyxis had the most links with resistance genes, indicating that it was the biggest potential host of resistance genes. This study provided new insight towards the shifts in the composition and function of microbial communities after sudden serious Tl contamination.},
}

Humans
*Thallium/analysis
Rivers
Metals/analysis
*Microbiota
Drug Resistance, Microbial/genetics
Genes, Bacterial
Anti-Bacterial Agents

@article {pmid36965198,
year = {2023},
author = {Ceylani, T and Allahverdi, H and Teker, HT},
title = {Role of age-related plasma in the diversity of gut bacteria.},
journal = {Archives of gerontology and geriatrics},
volume = {111},
number = {},
pages = {105003},
doi = {10.1016/j.archger.2023.105003},
pmid = {36965198},
issn = {1872-6976},
mesh = {Rats ; Humans ; Animals ; Feces/microbiology ; *Bacteria/genetics ; *Gastrointestinal Microbiome ; Bacteroidetes ; Plasma ; },
abstract = {Recent studies have demonstrated the efficacy of young blood plasma factors in reversing aging-related deformities. However, the impact of plasma exchange between young and old individuals on gut microbiota remains understudied. To investigate this, we evaluated the effects of plasma exchange between 5-week-old and 24-month-old rats on gut microbiota composition. In this study, old rats were administered 0.5 ml of young plasma, while young rats were administered 0.25 ml of old plasma daily for 30 days. Metagenome analysis was performed on the contents of the cecum after completing plasma transfer. Results showed that transferring young plasma to old rats significantly increased the alpha diversity indices (Shannon and Simpson values), while the Firmicutes to Bacteroidetes ratio decreased significantly. Conversely, transferring aged plasma to young rats led to a significant decrease in Shannon value and F/B ratio but no change in Simpson value. Plasma exchange also caused substantial changes in the top ten dominant genera and species found in the gut microbiota of young and old rats. After young blood plasma transfer, the dominant bacterial profile in the old gut microbiota shifted toward the bacterial profile found in the young control group. Notably, old plasma also altered the gut microbiota structure of young rats toward that of old rats. Our findings suggest that age-related changes in plasma play a crucial role in gut microbiota species diversity and their presence rates.},
}

Rats
Humans
Animals
Feces/microbiology
*Bacteria/genetics
*Gastrointestinal Microbiome
Bacteroidetes
Plasma

@article {pmid37234538,
year = {2023},
author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB},
title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1203870},
pmid = {37234538},
issn = {1664-302X},
}

@article {pmid37233257,
year = {2023},
author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N},
title = {Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {9},
number = {5},
pages = {},
pmid = {37233257},
issn = {2309-608X},
abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.},
}

@article {pmid37225687,
year = {2023},
author = {Zhao, F and Yang, L and Zhang, T and Zhuang, D and Wu, Q and Yu, J and Tian, C and Zhang, Z},
title = {Gut microbiome signatures of extreme environment adaption in Tibetan pig.},
journal = {NPJ biofilms and microbiomes},
volume = {9},
number = {1},
pages = {27},
pmid = {37225687},
issn = {2055-5008},
mesh = {Swine ; Animals ; *Gastrointestinal Microbiome ; Tibet ; Ultraviolet Rays ; Acclimatization ; Acetic Acid ; Extreme Environments ; Mammals ; },
abstract = {Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.},
}

Swine
Animals
*Gastrointestinal Microbiome
Tibet
Ultraviolet Rays
Acclimatization
Acetic Acid
Extreme Environments
Mammals

@article {pmid37223792,
year = {2023},
author = {Bertola, M and Righetti, L and Gazza, L and Ferrarini, A and Fornasier, F and Cirlini, M and Lolli, V and Galaverna, G and Visioli, G},
title = {Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines.},
journal = {Frontiers in plant science},
volume = {14},
number = {},
pages = {1172857},
pmid = {37223792},
issn = {1664-462X},
abstract = {Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.},
}

@article {pmid37221274,
year = {2023},
author = {Megremis, S and Constantinides, B and Xepapadaki, P and Yap, CF and Sotiropoulos, AG and Bachert, C and Finotto, S and Jartti, T and Tapinos, A and Vuorinen, T and Andreakos, E and Robertson, DL and Papadopoulos, NG},
title = {Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8319},
pmid = {37221274},
issn = {2045-2322},
mesh = {Child ; Humans ; Child, Preschool ; Eukaryota ; *Bacteriophages ; Virome ; Eukaryotic Cells ; *Asthma ; *Anelloviridae ; Asymptomatic Diseases ; },
abstract = {Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.},
}

Child
Humans
Child, Preschool
Eukaryota
*Bacteriophages
Virome
Eukaryotic Cells
*Asthma
*Anelloviridae
Asymptomatic Diseases

@article {pmid37217592,
year = {2023},
author = {Waldrop, MP and Chabot, CL and Liebner, S and Holm, S and Snyder, MW and Dillon, M and Dudgeon, SR and Douglas, TA and Leewis, MC and Walter Anthony, KM and McFarland, JW and Arp, CD and Bondurant, AC and Taş, N and Mackelprang, R},
title = {Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
pmid = {37217592},
issn = {1751-7370},
abstract = {Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.},
}

@article {pmid37215132,
year = {2023},
author = {Zhang, L and Wang, F and Jia, L and Yan, H and Gao, L and Tian, Y and Su, X and Zhang, X and Lv, C and Ma, Z and Xue, Y and Lin, Q and Wang, K},
title = {Edwardsiella piscicida infection reshapes the intestinal microbiome and metabolome of big-belly seahorses: mechanistic insights of synergistic actions of virulence factors.},
journal = {Frontiers in immunology},
volume = {14},
number = {},
pages = {1135588},
pmid = {37215132},
issn = {1664-3224},
mesh = {Animals ; Virulence Factors/metabolism ; *Gastrointestinal Microbiome ; Virulence ; *Smegmamorpha/metabolism ; Fishes/metabolism ; *Enteritis ; Metabolome ; },
abstract = {Uncovering the mechanism underlying the pathogenesis of Edwardsiella piscicida-induced enteritis is essential for global aquaculture. In the present study, we identified E. piscicida as a lethal pathogen of the big-belly seahorse (Hippocampus abdominalis) and revealed its pathogenic pattern and characteristics by updating our established bacterial enteritis model and evaluation system. Conjoint analysis of metagenomic and metabolomic data showed that 15 core virulence factors could mutually coordinate the remodeling of intestinal microorganisms and host metabolism and induce enteritis in the big-belly seahorse. Specifically, the Flagella, Type IV pili, and Lap could significantly increase the activities of the representative functional pathways of both flagella assembly and bacterial chemotaxis in the intestinal microbiota (P < 0.01) to promote pathogen motility, adherence, and invasion. Legiobactin, IraAB, and Hpt could increase ABC transporter activity (P < 0.01) to compete for host nutrition and promote self-replication. Capsule1, HP-NAP, and FarAB could help the pathogen to avoid phagocytosis. Upon entering epithelial cells and phagocytes, Bsa T3SS and Dot/Icm could significantly increase bacterial secretion system activity (P < 0.01) to promote the intracellular survival and replication of the pathogen and the subsequent invasion of the neighboring tissues. Finally, LPS3 could significantly increase lipopolysaccharide biosynthesis (P < 0.01) to release toxins and kill the host. Throughout the pathogenic process, BopD, PhoP, and BfmRS significantly activated the two-component system (P < 0.01) to coordinate with other VFs to promote deep invasion. In addition, the levels of seven key metabolic biomarkers, Taurine, L-Proline, Uridine, L-Glutamate, Glutathione, Xanthosine, and L-Malic acid, significantly decreased (P < 0.01), and they can be used for characterizing E. piscicida infection. Overall, the present study systematically revealed how a combination of virulence factors mediate E. piscicida-induced enteritis in fish for the first time, providing a theoretical reference for preventing and controlling this disease in the aquaculture of seahorses and other fishes.},
}

Animals
Virulence Factors/metabolism
*Gastrointestinal Microbiome
Virulence
*Smegmamorpha/metabolism
Fishes/metabolism
*Enteritis
Metabolome

@article {pmid37116481,
year = {2023},
author = {Manara, S and Selma-Royo, M and Huang, KD and Asnicar, F and Armanini, F and Blanco-Miguez, A and Cumbo, F and Golzato, D and Manghi, P and Pinto, F and Valles-Colomer, M and Amoroso, L and Corrias, MV and Ponzoni, M and Raffaetà, R and Cabrera-Rubio, R and Olcina, M and Pasolli, E and Collado, MC and Segata, N},
title = {Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.},
journal = {Current biology : CB},
volume = {33},
number = {10},
pages = {1939-1950.e4},
doi = {10.1016/j.cub.2023.04.011},
pmid = {37116481},
issn = {1879-0445},
mesh = {Female ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; Bacteria ; Milk, Human/microbiology ; Mothers ; *Gastrointestinal Microbiome ; Feces/microbiology ; },
abstract = {The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.},
}

Female
Humans
Infant
Infant, Newborn
*Microbiota
Bacteria
Milk, Human/microbiology
Mothers
*Gastrointestinal Microbiome
Feces/microbiology

@article {pmid37213492,
year = {2023},
author = {Zhang, X and Liang, Y and Zheng, K and Wang, Z and Dong, Y and Liu, Y and Ren, L and Wang, H and Han, Y and McMinn, A and Sung, YY and Mok, WJ and Wong, LL and He, J and Wang, M},
title = {Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1161265},
pmid = {37213492},
issn = {1664-302X},
abstract = {INTRODUCTION: Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed.

METHODS: Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method.

RESULTS AND DISCUSSION: Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.},
}

@article {pmid37210515,
year = {2023},
author = {Leleiwi, I and Rodriguez-Ramos, J and Shaffer, M and Sabag-Daigle, A and Kokkinias, K and Flynn, RM and Daly, RA and Kop, LFM and Solden, LM and Ahmer, BMM and Borton, MA and Wrighton, KC},
title = {Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {114},
pmid = {37210515},
issn = {2049-2618},
support = {R01AI143288/NH/NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; Disease Models, Animal ; Mice, Inbred CBA ; *Microbiota ; Inflammation ; Bacteroidetes ; },
abstract = {BACKGROUND: The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.

RESULTS: Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains.

CONCLUSIONS: This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.},
}

Humans
Animals
Mice
*Gastrointestinal Microbiome/genetics
Disease Models, Animal
Mice, Inbred CBA
*Microbiota
Inflammation
Bacteroidetes

@article {pmid37169197,
year = {2023},
author = {Wang, Y and Li, Q},
title = {Competition and interaction between DNRA and denitrification in composting ecosystems: Insights from metagenomic analysis.},
journal = {Bioresource technology},
volume = {381},
number = {},
pages = {129140},
doi = {10.1016/j.biortech.2023.129140},
pmid = {37169197},
issn = {1873-2976},
mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; *Composting ; *Microbiota ; Nitrogen ; Bacteria/genetics ; Oxidation-Reduction ; },
abstract = {This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO2[-]-N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.},
}

Nitrates
*Ammonium Compounds
Denitrification
*Composting
*Microbiota
Nitrogen
Bacteria/genetics
Oxidation-Reduction

@article {pmid37161271,
year = {2023},
author = {Chen, B and Zhang, Z and Zhang, Q and Xu, N and Lu, T and Wang, T and Hong, W and Fu, Z and Penuelas, J and Gillings, M and Qian, H},
title = {Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.},
journal = {Environmental science & technology},
volume = {57},
number = {20},
pages = {7698-7708},
doi = {10.1021/acs.est.3c01664},
pmid = {37161271},
issn = {1520-5851},
mesh = {Humans ; Antimicrobial Cationic Peptides/genetics/pharmacology/chemistry ; Antimicrobial Peptides ; *Anti-Infective Agents ; *Microbiota ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.},
}

Humans
Antimicrobial Cationic Peptides/genetics/pharmacology/chemistry
Antimicrobial Peptides
*Anti-Infective Agents
*Microbiota
*Gastrointestinal Microbiome
Anti-Bacterial Agents/pharmacology

@article {pmid37031344,
year = {2023},
author = {Liao, H and Liu, C and Ai, C and Gao, T and Yang, QE and Yu, Z and Gao, S and Zhou, S and Friman, VP},
title = {Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting.},
journal = {The ISME journal},
volume = {17},
number = {6},
pages = {916-930},
pmid = {37031344},
issn = {1751-7370},
mesh = {*Composting ; *Viruses/genetics ; Archaea ; Bacteria/genetics ; *Microbiota/genetics ; Nutrients ; },
abstract = {While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.},
}

*Composting
*Viruses/genetics
Archaea
Bacteria/genetics
*Microbiota/genetics
Nutrients

@article {pmid37208728,
year = {2023},
author = {Yu, J and Meng, J and Qin, Z and Yu, Y and Liang, Y and Wang, Y and Min, D},
title = {Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease.},
journal = {Journal of neuroinflammation},
volume = {20},
number = {1},
pages = {117},
pmid = {37208728},
issn = {1742-2094},
mesh = {Rats ; Animals ; *Parkinson Disease/metabolism ; Oxidopamine/toxicity ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/therapy/metabolism ; NAD ; Oxidative Stress ; },
abstract = {BACKGROUND: New data are accumulating on gut microbial dysbiosis in Parkinson's disease (PD), while the specific mechanism remains uncharacterized. This study aims to investigate the potential role and pathophysiological mechanism of dysbiosis of gut microbiota in 6-hydroxydopamine (6-OHDA)-induced PD rat models.

METHODS: The shotgun metagenome sequencing data of fecal samples from PD patients and healthy individuals were obtained from the Sequence Read Archive (SRA) database. The diversity, abundance, and functional composition of gut microbiota were further analyzed in these data. After the exploration of the functional pathway-related genes, KEGG and GEO databases were used to obtain PD-related microarray datasets for differential expression analysis. Finally, in vivo experiments were performed to confirm the roles of fecal microbiota transplantation (FMT) and upregulated NMNAT2 in neurobehavioral symptoms and oxidative stress response in 6-OHDA-lesioned rats.

RESULTS: Significant differences were found in the diversity, abundance, and functional composition of gut microbiota between PD patients and healthy individuals. Dysbiosis of gut microbiota could regulate NAD[+] anabolic pathway to affect the occurrence and development of PD. As a NAD[+] anabolic pathway-related gene, NMNAT2 was poorly expressed in the brain tissues of PD patients. More importantly, FMT or overexpression of NMNAT2 alleviated neurobehavioral deficits and reduced oxidative stress in 6-OHDA-lesioned rats.

CONCLUSIONS: Taken together, we demonstrated that dysbiosis of gut microbiota suppressed NMNAT2 expression, thus exacerbating neurobehavioral deficits and oxidative stress response in 6-OHDA-lesioned rats, which could be rescued by FMT or NMNAT2 restoration.},
}

Rats
Animals
*Parkinson Disease/metabolism
Oxidopamine/toxicity
*Gastrointestinal Microbiome/physiology
Dysbiosis/therapy/metabolism
NAD
Oxidative Stress

@article {pmid37208617,
year = {2023},
author = {Liao, F and Qian, J and Yang, R and Gu, W and Li, R and Yang, T and Fu, X and Yuan, B and Zhang, Y},
title = {Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health.},
journal = {BMC genomics},
volume = {24},
number = {1},
pages = {269},
pmid = {37208617},
issn = {1471-2164},
mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Viruses/genetics ; Bacteria/genetics ; DNA ; },
abstract = {BACKGROUND: Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study.

RESULTS: The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references.

CONCLUSIONS: In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.},
}

Animals
Humans
*Gastrointestinal Microbiome/genetics
Metagenomics
Phylogeny
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Viruses/genetics
Bacteria/genetics
DNA

@article {pmid37208450,
year = {2023},
author = {Mo, S and Yan, B and Gao, T and Li, J and Kashif, M and Song, J and Bai, L and Yu, D and Liao, J and Jiang, C},
title = {Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB.},
journal = {Scientific reports},
volume = {13},
number = {1},
pages = {8126},
pmid = {37208450},
issn = {2045-2322},
mesh = {*Microbiota ; Geologic Sediments ; Bacteria ; Archaea/genetics ; Sulfur/metabolism ; Phylogeny ; },
abstract = {Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB (https://smdb.gxu.edu.cn/)-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.},
}

*Microbiota
Geologic Sediments
Bacteria
Archaea/genetics
Sulfur/metabolism
Phylogeny

@article {pmid37207186,
year = {2023},
author = {Hao, SR and Zhou, YY and Zhang, X and Jiang, HY},
title = {Gut microbiome profiles may be related to atypical antipsychotic associated overweight in Asian children with psychiatric disorder: a preliminary study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1124846},
pmid = {37207186},
issn = {2235-2988},
mesh = {Humans ; Child ; Overweight/chemically induced/drug therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; *Antipsychotic Agents/adverse effects ; Cross-Sectional Studies ; *Mental Disorders ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; },
abstract = {OBJECTIVE: Atypical antipsychotics (APs) modify the gut microbiome, and weight gain in response to AP could be mediated by the gut microbiome. Thus, the present study aimed to explore the changes in the gut bacterial microbiome in AP-exposed children with obesity.

METHODS: To rule out the confounder of AP indication, the gut bacterial microbiome was compared between healthy controls (Con) and AP-exposed individuals with overweight (APO) or normal weight (APN). Fifty-seven AP-treated outpatients (21 APO and 36 APN) and 25 Con were included in this cross-sectional microbiota study.

RESULTS: AP users, regardless of body mass index, exhibited decreased microbial richness and diversity and a distinct metagenomic composition compared to the Con. Although no differences in the microbiota structure were observed between APO and APN groups, the APO group was characterised by a higher abundance of Megamonas and Lachnospira. Additionally, the differences in the microbial functions were observed between APO and APN groups.

CONCLUSIONS: The gut bacterial microbiota of APO children revealed taxonomic and functional differences compared to Con and APN. Further studies are needed to verify these findings and to explore the temporal and causal relationships between these variables.},
}

Humans
Child
Overweight/chemically induced/drug therapy/microbiology
*Gastrointestinal Microbiome/physiology
*Antipsychotic Agents/adverse effects
Cross-Sectional Studies
*Mental Disorders
Bacteria/genetics
RNA, Ribosomal, 16S/genetics
Feces/microbiology

@article {pmid37202728,
year = {2023},
author = {Xing, W and Qi, B and Chen, R and Ding, W and Zhang, F},
title = {Metagenomic analysis reveals taxonomic and functional diversity of microbial communities on the deteriorated wall paintings of Qinling Tomb in the Southern Tang Dynasty, China.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {140},
pmid = {37202728},
issn = {1471-2180},
mesh = {*Microbiota ; Metagenome ; *Cyanobacteria ; Proteobacteria ; China ; },
abstract = {The microbial colonization on ancient murals attracts more and more attention since the threaten by microorganisms was first reported in Lascaux, Spain. However, the biodeterioration or biodegradation of mural paintings resulted by microorganisms is not clear yet. Especially the biological function of microbial communities in different conditions remained largely unaddressed. The two mausoleums of the Southern Tang Dynasty are the largest group of emperor mausoleums during the Five Dynasties and Ten Kingdoms period in China, which are of great significance to the study of the architecture, imperial mausoleum systems and art in the Tang and Song Dynasties. To make clear the species composition and metabolic functions of different microbial communities (MID and BK), we analyzed the samples from the wall paintings in one of the two mausoleums of the Southern Tang Dynasty with metagenomics method. The result showed totally 55 phyla and 1729 genera were detected in the mural paintings. The two microbial community structure were similar with the dominance of Proteobacteria, Actinobacteria and Cyanobacteria. However, the species abundance presented a significant difference between two communities at genus level --- MID is Lysobacter, Luteimonas are predominant in MID while Sphingomonas and Streptomyces are popular in BK, which is partially attributed to the different substrate materials of murals. As a result, the two communities presented the different metabolic patterns that MID community was mainly participated in the formation of biofilm as well as the degradation of exogenous pollutants while the BK was predominantly related to the photosynthesis process and biosynthesis of secondary metabolites. Taken together, these findings indicated the effect of environmental factor on the taxonomic composition and functional diversity of the microbial populations. The installation of artificial lighting needs to be considered carefully in the future protection of cultural relics.},
}

*Microbiota
Metagenome
*Cyanobacteria
Proteobacteria
China

@article {pmid37202719,
year = {2023},
author = {Wang, XY and Meng, JX and Ren, WX and Ma, H and Liu, G and Liu, R and Geng, HL and Zhao, Q and Zhang, XX and Ni, HB},
title = {Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens.},
journal = {BMC microbiology},
volume = {23},
number = {1},
pages = {138},
pmid = {37202719},
issn = {1471-2180},
mesh = {Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Cyanobacteria/genetics ; },
abstract = {BACKGROUND: The gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.

RESULTS: Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host's feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.

CONCLUSIONS: Our findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.},
}

Animals
Female
*Gastrointestinal Microbiome/genetics
Chickens/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota
*Cyanobacteria/genetics

@article {pmid37195657,
year = {2023},
author = {Xue, W and Peng, P and Wen, X and Meng, H and Qin, Y and Deng, T and Guo, S and Chen, T and Li, X and Liang, J and Zhang, F and Xie, Z and Jin, M and Liang, Q and Wei, L},
title = {Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration.},
journal = {Investigative ophthalmology & visual science},
volume = {64},
number = {5},
pages = {11},
doi = {10.1167/iovs.64.5.11},
pmid = {37195657},
issn = {1552-5783},
mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Bacteria/genetics/metabolism ; Bacteroidetes ; *Macular Degeneration/genetics ; },
abstract = {PURPOSE: Alterations in the gut microbiota have been associated with age-related macular degeneration (AMD). However, the dysbiosis shared by different ethnicity and geographic groups, which may associate with the disease pathogenesis, remain underexplored. Here, we characterized dysbiosis of the gut microbiota in patients with AMD from Chinese and Swiss cohorts and identified cross-cohort signatures associated with AMD.

METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 30 patients with AMD and 30 healthy subjects. Published datasets with 138 samples from Swiss patients with AMD and healthy subjects were re-analyzed. Comprehensive taxonomic profiling was conducted by matching to the RefSeq genome database, metagenome-assembled genome (MAG) database, and Gut Virome Database (GVD). Functional profiling was performed by reconstruction of the MetaCyc pathways.

RESULTS: The α-diversity of the gut microbiota was decreased in patients with AMD according to taxonomic profiles generated using MAG but not RefSeq database as reference. The Firmicutes/Bacteroidetes ratio was also decreased in patients with AMD. Among AMD-associated bacteria shared between Chinese and Swiss cohorts, Ruminococcus callidus, Lactobacillus gasseri, and Prevotellaceae (f) uSGB 2135 were enriched in patients with AMD, whereas Bacteroidaceae (f) uSGB 1825 was depleted in patients with AMD and was negatively associated with hemorrhage size. Bacteroidaceae was one of the major hosts of phages associated with AMD. Three degradation pathways were reduced in AMD.

CONCLUSIONS: These results demonstrated that dysbiosis of the gut microbiota was associated with AMD. We identified cross-cohort gut microbial signatures involving bacteria, viruses, and metabolic pathways, which potentially serve as promising targets for the prevention or treatment of AMD.},
}

Humans
Metagenome
*Gastrointestinal Microbiome/genetics
Dysbiosis/microbiology
Bacteria/genetics/metabolism
Bacteroidetes
*Macular Degeneration/genetics

@article {pmid37195254,
year = {2023},
author = {Free, T},
title = {Long-read sequencing for the metagenomic analysis of microbiomes.},
journal = {BioTechniques},
volume = {74},
number = {4},
pages = {153-155},
doi = {10.2144/btn-2023-0028},
pmid = {37195254},
issn = {1940-9818},
mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Metagenome/genetics ; Sequence Analysis, DNA ; Metagenomics ; },
abstract = {One technology, long-read sequencing, and one research field, microbiome studies, have risen to prominence over the last decade. But how can one be used in the other? What changes are being wrought? And what limitations remain? [Formula: see text].},
}

*High-Throughput Nucleotide Sequencing
*Microbiota/genetics
Metagenome/genetics
Sequence Analysis, DNA
Metagenomics

@article {pmid37054839,
year = {2023},
author = {Chunxiao, D and Ma, F and Wu, W and Li, S and Yang, J and Chen, Z and Lian, S and Qu, Y},
title = {Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment.},
journal = {Environmental research},
volume = {229},
number = {},
pages = {115897},
doi = {10.1016/j.envres.2023.115897},
pmid = {37054839},
issn = {1096-0953},
mesh = {*Quorum Sensing/physiology ; Drug Resistance, Microbial ; Lactones/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Indoles/pharmacology ; },
abstract = {Indole is an essential signal molecule in microbial studies. However, its ecological role in biological wastewater treatments remains enigmatic. This study explores the links between indole and complex microbial communities using sequencing batch reactors exposed to 0, 15, and 150 mg/L indole concentrations. A concentration of 150 mg/L indole enriched indole degrader Burkholderiales, while pathogens, such as Giardia, Plasmodium, and Besnoitia were inhibited at 15 mg/L indole concentration. At the same time, indole reduced the abundance of predicted genes in the "signaling transduction mechanisms" pathway via the Non-supervised Orthologous Groups distributions analysis. Indole significantly decreased the concentration of homoserine lactones, especially C14-HSL. Furthermore, the quorum-sensing signaling acceptors containing LuxR, the dCACHE domain, and RpfC showed negative distributions with indole and indole oxygenase genes. Signaling acceptors' potential origins were mainly Burkholderiales, Actinobacteria, and Xanthomonadales. Meanwhile, concentrated indole (150 mg/L) increased the total abundance of antibiotic resistance genes by 3.52 folds, especially on aminoglycoside, multidrug, tetracycline, and sulfonamide. Based on Spearman's correlation analysis, the homoserine lactone degradation genes which were significantly impacted by indole negatively correlated with the antibiotic resistance gene abundance. This study brings new insights into the effect of indole signaling on in biological wastewater treatment plants.},
}

*Quorum Sensing/physiology
Drug Resistance, Microbial
Lactones/pharmacology
Anti-Bacterial Agents/pharmacology
*Microbiota
Indoles/pharmacology

@article {pmid37004601,
year = {2023},
author = {do Socorro Fôro Ramos, E and Bahia, SL and de Oliveira Ribeiro, G and Villanova, F and de Pádua Milagres, FA and Brustulin, R and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, É},
title = {Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis.},
journal = {Virus genes},
volume = {59},
number = {3},
pages = {464-472},
pmid = {37004601},
issn = {1572-994X},
mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Virome ; *Bacteriophages ; *Siphoviridae ; *Gastroenteritis ; *Staphylococcal Infections/microbiology ; },
abstract = {There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.},
}

Humans
*Methicillin-Resistant Staphylococcus aureus
Virome
*Bacteriophages
*Siphoviridae
*Gastroenteritis
*Staphylococcal Infections/microbiology

@article {pmid35485976,
year = {2023},
author = {Jiang, Y and Balaban, M and Zhu, Q and Mirarab, S},
title = {DEPP: Deep Learning Enables Extending Species Trees using Single Genes.},
journal = {Systematic biology},
volume = {72},
number = {1},
pages = {17-34},
pmid = {35485976},
issn = {1076-836X},
support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; 1R35GM142725/NH/NIH HHS/United States ; },
mesh = {Phylogeny ; *Deep Learning ; RNA, Ribosomal, 16S/genetics ; Algorithms ; *Microbiota/genetics ; },
abstract = {Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phylogeny. For example, they assume single-gene data (e.g., 16S rRNA amplicons) have evolved under the GTR model on a gene tree. Placement, however, often has a more ambitious goal: extending a (genome-wide) species tree given data from individual genes without knowing the evolutionary model. Addressing this challenging problem requires new directions. Here, we introduce Deep-learning Enabled Phylogenetic Placement (DEPP), an algorithm that learns to extend species trees using single genes without prespecified models. In simulations and on real data, we show that DEPP can match the accuracy of model-based methods without any prior knowledge of the model. We also show that DEPP can update the multilocus microbial tree-of-life with single genes with high accuracy. We further demonstrate that DEPP can combine 16S and metagenomic data onto a single tree, enabling community structure analyses that take advantage of both sources of data. [Deep learning; gene tree discordance; metagenomics; microbiome analyses; neural networks; phylogenetic placement.].},
}

Phylogeny
*Deep Learning
RNA, Ribosomal, 16S/genetics
Algorithms
*Microbiota/genetics

@article {pmid37194081,
year = {2023},
author = {Gallet, A and Halary, S and Duval, C and Huet, H and Duperron, S and Marie, B},
title = {Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {108},
pmid = {37194081},
issn = {2049-2618},
mesh = {Animals ; *Microcystis/physiology ; *Gastrointestinal Microbiome ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metabolome ; *Oryzias/physiology ; },
abstract = {BACKGROUND: Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level.

RESULTS: The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community.

CONCLUSION: Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.},
}

Animals
*Microcystis/physiology
*Gastrointestinal Microbiome
*Cyanobacteria/genetics
Lakes/microbiology
Metabolome
*Oryzias/physiology

@article {pmid37194043,
year = {2023},
author = {Yao, S and Jin, T and Zhang, L and Zhang, Y and Chen, R and Wang, Q and Lv, M and Hu, C and Ma, T and Xia, W},
title = {N/S element transformation modulating lithospheric microbial communities by single-species manipulation.},
journal = {Microbiome},
volume = {11},
number = {1},
pages = {107},
pmid = {37194043},
issn = {2049-2618},
mesh = {Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Petroleum/metabolism/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Sulfates ; },
abstract = {BACKGROUND: The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS: Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS: The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.},
}

Nitrates/metabolism
Phylogeny
RNA, Ribosomal, 16S/genetics
*Microbiota
*Petroleum/metabolism/microbiology
Sulfur/metabolism
Nitrogen/metabolism
Sulfates

@article {pmid37189387,
year = {2023},
author = {Aljuraiban, GS and Alfhili, MA and Aldhwayan, MM and Aljazairy, EA and Al-Musharaf, S},
title = {Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189387},
issn = {2218-273X},
mesh = {Humans ; Female ; *Insulin Resistance ; Saudi Arabia ; *Gastrointestinal Microbiome/genetics ; Body Fat Distribution ; Obesity ; Insulin ; },
abstract = {(1) Background: Gut microbiota dysbiosis may lead to diseases such as insulin resistance and obesity. We aimed to investigate the relationship between insulin resistance, body fat distribution, and gut microbiota composition. (2) Methods: The present study included 92 Saudi women (18-25 years) with obesity (body mass index (BMI) ≥ 30 kg/m[2], n = 44) and with normal weight (BMI 18.50-24.99 kg/m[2], n = 48). Body composition indices, biochemical data, and stool samples were collected. The whole-genome shotgun sequencing technique was used to analyze the gut microbiota. Participants were divided into subgroups stratified by the homeostatic model assessment for insulin resistance (HOMA-IR) and other adiposity indices. (3) Results: HOMA-IR was inversely correlated with Actinobacteria (r = -0.31, p = 0.003), fasting blood glucose was inversely correlated with Bifidobacterium kashiwanohense (r = -0.22, p = 0.03), and insulin was inversely correlated with Bifidobacterium adolescentis (r = -0.22, p = 0.04). There were significant differences in α- and β-diversities in those with high HOMA-IR and waist-hip ratio (WHR) compared to low HOMA-IR and WHR (p = 0.02, 0.03, respectively). (4) Conclusions: Our findings highlight the relationship between specific gut microbiota at different taxonomic levels and measures of glycemic control in Saudi Arabian women. Future studies are required to determine the role of the identified strains in the development of insulin resistance.},
}

Humans
Female
*Insulin Resistance
Saudi Arabia
*Gastrointestinal Microbiome/genetics
Body Fat Distribution
Obesity
Insulin

@article {pmid37148792,
year = {2023},
author = {Wang, Y and Tian, X and Song, T and Jiang, Z and Zhang, G and He, C and Li, P},
title = {Linking DOM characteristics to microbial community: The potential role of DOM mineralization for arsenic release in shallow groundwater.},
journal = {Journal of hazardous materials},
volume = {454},
number = {},
pages = {131566},
doi = {10.1016/j.jhazmat.2023.131566},
pmid = {37148792},
issn = {1873-3336},
mesh = {Dissolved Organic Matter ; *Arsenic/analysis ; *Groundwater/chemistry ; Carbon ; *Microbiota ; Nitrogen/analysis ; },
abstract = {Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N1/N2)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.},
}

Dissolved Organic Matter
*Arsenic/analysis
*Groundwater/chemistry
Carbon
*Microbiota
Nitrogen/analysis

@article {pmid37137392,
year = {2023},
author = {Jin, Y and Xiong, W and Liu, D and Wu, Z and Xiao, G and Wang, S and Su, H},
title = {Responses of straw foam-based aerobic granular sludge to atrazine: Insights from metagenomics and microbial community variations.},
journal = {Chemosphere},
volume = {331},
number = {},
pages = {138828},
doi = {10.1016/j.chemosphere.2023.138828},
pmid = {37137392},
issn = {1879-1298},
mesh = {Sewage/chemistry ; Waste Disposal, Fluid/methods ; *Atrazine ; Metagenomics ; Bioreactors/microbiology ; Aerobiosis ; *Microbiota ; Bacteria/genetics ; Nitrogen ; },
abstract = {Atrazine (ATZ) has caused serious environmental pollution, but the biodegradation of ATZ is relatively slow and inefficient. Herein, a straw foam-based aerobic granular sludge (SF-AGS) was developed, the spatially ordered architectures of which could greatly improve the drug tolerance and biodegradation efficiency of ATZ. The results showed that, in the presence of ATZ, chemical oxygen demand (COD), ammonium nitrogen (NH4[+]-N), total phosphorus (TP), and total nitrogen (TN) were effectively removed within 6 h, and the removal efficiencies were as high as 93.37%, 85.33%, 84.7%, and 70%, respectively. Furthermore, ATZ stimulated microbial consortia to secrete three times more extracellular polymers compared to without ATZ. Illumina MiSeq sequencing results showed that bacterial diversity and richness decreased, leading to significant changes in microbial population structure and composition. ATZ-resistant bacteria including Proteobacteria, Actinobacteria, and Burkholderia laid the biological basis for the stability of aerobic particles, efficient removal of pollutants, and degradation of ATZ. The study demonstrated that SF-AGS is feasible for ATZ-laden low-strength wastewater treatment.},
}

Sewage/chemistry
Waste Disposal, Fluid/methods
*Atrazine
Metagenomics
Bioreactors/microbiology
Aerobiosis
*Microbiota
Bacteria/genetics
Nitrogen

@article {pmid37100380,
year = {2023},
author = {Tang, H and Zhou, T and Jin, W and Zong, S and Mamtimin, T and Salama, ES and Jeon, BH and Liu, P and Han, H and Li, X},
title = {Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice.},
journal = {Life sciences},
volume = {324},
number = {},
pages = {121709},
doi = {10.1016/j.lfs.2023.121709},
pmid = {37100380},
issn = {1879-0631},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Azurin/adverse effects ; Carcinogenesis ; Cell Transformation, Neoplastic ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/metabolism ; Escherichia coli/genetics ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Colitis/chemically induced ; },
abstract = {AIMS: Preliminary studies have identified the use of probiotics as a potential treatment strategy against colorectal cancer (CRC). However, natural probiotics lack direct tumor-targeting and tumor-killing activity in the intestine. This study aimed to construct a tumor-targeting engineered probiotic to combat CRC.

MAIN METHODS: Standard adhesion assay was performed to analyze the adherence ability of tumor-binding protein HlpA to CT26 cells. CCK-8 assay, Hoechst 33258 staining and flow cytometry analysis were used for examining cytotoxicity of tumoricidal protein azurin toward CT26 cells. An engineered probiotic Ep-AH harboring azurin and hlpA genes was developed using Escherichia coli Nissle 1917 (EcN) chassis. Antitumor effects of Ep-AH were evaluated in the azoxymethane (AOM) and dextran sodium sulfate salt (DSS)-induced CRC mice. Moreover, analysis of gut microbiota was conducted via fecal 16S rRNA gene sequencing and shotgun metagenomic sequencing.

KEY FINDINGS: Azurin caused a dose-dependent increase of apoptosis in CT26 cells. Ep-AH treatment reversed weight loss (p < 0.001), fecal occult blood (p < 0.01), and shortening of colon length (p < 0.001) than model group, as well as reducing tumorigenesis by 36 % (p < 0.001). Both Ep-H and Ep-A (EcN expressing HlpA or azurin) were less effective than Ep-AH. Furthermore, Ep-AH enriched the members of beneficial bacteria (e.g., Blautia and Bifidobacterium) and reversed abnormal changes of genes associated with several metabolic pathways (e.g., lipopolysaccharide biosynthesis).

SIGNIFICANCE: These results demonstrated that Ep-AH had excellent therapeutic benefits on cancer remission and gut microbiota modulation. Our study provides an effective strategy for anti-CRC treatment.},
}

Animals
Mice
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Azurin/adverse effects
Carcinogenesis
Cell Transformation, Neoplastic
*Probiotics/therapeutic use
*Colorectal Neoplasms/metabolism
Escherichia coli/genetics
Dextran Sulfate/pharmacology
Disease Models, Animal
*Colitis/chemically induced

@article {pmid36694293,
year = {2023},
author = {Wang, G and Jin, Z and George, TS and Feng, G and Zhang, L},
title = {Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover.},
journal = {The New phytologist},
volume = {238},
number = {6},
pages = {2578-2593},
doi = {10.1111/nph.18772},
pmid = {36694293},
issn = {1469-8137},
mesh = {*Mycorrhizae/metabolism ; Phosphorus/metabolism ; Soil ; Phytic Acid/metabolism ; Fungi/metabolism ; *Microbiota ; Bacteria/metabolism ; Plant Roots/metabolism ; Soil Microbiology ; },
abstract = {The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH2 PO4 or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.},
}

*Mycorrhizae/metabolism
Phosphorus/metabolism
Soil
Phytic Acid/metabolism
Fungi/metabolism
*Microbiota
Bacteria/metabolism
Plant Roots/metabolism
Soil Microbiology

@article {pmid36082501,
year = {2023},
author = {Özdemir, A and Yozgat, A and Işgın-Atıcı, K and Avcı, E and Yıldız, BD and Gündoğdu, A and Nalbantoğlu, U and Turhan, T and Doğruman-Al, F and Büyüktuncer, Z},
title = {Potential associations between alterations in gut microbiome and obesity-related traits after the bariatric surgery.},
journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association},
volume = {36},
number = {3},
pages = {981-996},
doi = {10.1111/jhn.13087},
pmid = {36082501},
issn = {1365-277X},
mesh = {Humans ; *Obesity, Morbid/surgery ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Diet ; Cholesterol ; },
abstract = {BACKGROUND: This study aimed to examine the effects of both obesity and bariatric surgery on gut microbiome, dietary intake, as well as metabolic and inflammatory parameters.

METHODS: All participants (15 with morbid obesity who had bariatric surgery, 8 with morbid obesity and 11 non-obese) were followed up for a 6-month period with interviews at baseline (M0), at the end of 3 (M3) and 6 months (M6). Dietary assessment was done, and blood and faecal samples were collected.

RESULTS: Dietary energy and nutrient intakes as well as serum glucose levels, total cholesterol, low-density lipoprotein (LDL)-cholesterol and high sensitivity C-reactive protein (hs-CRP) levels decreased after surgery (p < 0.05, for each). Participants with morbid obesity had higher levels of Firmicutes and lower levels of Bacteroidetes at M0 compared to non-obese participants. The abundances of Bacteroidetes increased (p = 0.02), whereas that of Firmicutes decreased (p > 0.05) after the surgery, leading to a significant decrease in Firmicutes/Bacteroidetes ratio (p = 0.01). At sub-phylum level, the abundances of Lactobacillus and Bifidobacterium decreased, whereas those of Akkermansia increased after the surgery (p < 0.01, for each). Although participants who were morbidly obese had a distinct profile according to ß-diversity indices at M0, it became similar with the profile of non-obese participants (p > 0.05) at M3 and M6. Similarly, α-diversity indices were lower in subjects with morbid obesity at M0, but became similar to levels in non-obese controls at M6.

CONCLUSION: This study confirmed that bariatric surgery has substantial impacts on gut microbiome's composition and diversity, as well as anthropometrical measurements and biochemical parameters, which were associated with the alterations in dietary intake patterns.},
}

Humans
*Obesity, Morbid/surgery
*Gastrointestinal Microbiome
*Bariatric Surgery
Diet
Cholesterol

@article {pmid37189337,
year = {2023},
author = {Dossey, AT and Oppert, B and Chu, FC and Lorenzen, MD and Scheffler, B and Simpson, S and Koren, S and Johnston, JS and Kataoka, K and Ide, K},
title = {Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189337},
issn = {2218-273X},
mesh = {Animals ; *Gryllidae/genetics/metabolism ; Agriculture ; Crops, Agricultural ; Allergens/metabolism ; Genetic Engineering ; },
abstract = {Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.},
}

Animals
*Gryllidae/genetics/metabolism
Agriculture
Crops, Agricultural
Allergens/metabolism
Genetic Engineering

@article {pmid37189333,
year = {2023},
author = {Cres, CM and Tritt, A and Bouchard, KE and Zhang, Y},
title = {DL-TODA: A Deep Learning Tool for Omics Data Analysis.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189333},
issn = {2218-273X},
mesh = {Humans ; *Deep Learning ; Neural Networks, Computer ; Bacteria/genetics ; Metagenome ; *Microbiota/genetics ; Algorithms ; },
abstract = {Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.},
}

Humans
*Deep Learning
Neural Networks, Computer
Bacteria/genetics
Metagenome
*Microbiota/genetics
Algorithms

@article {pmid36631002,
year = {2023},
author = {Hsu, CL and Lang, S and Demir, M and Fouts, DE and Stärkel, P and Schnabl, B},
title = {Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome.},
journal = {Hepatology (Baltimore, Md.)},
volume = {77},
number = {6},
pages = {2073-2083},
pmid = {36631002},
issn = {1527-3350},
support = {P30 DK120515/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Non-alcoholic Fatty Liver Disease ; Virome ; Alcohol Drinking/adverse effects ; *Alcoholism ; Ethanol ; *Liver Diseases, Alcoholic ; },
abstract = {BACKGROUND AND AIMS: The prevalence of alcohol use disorder (AUD) and metabolic dysfunction-associated fatty liver disease (MAFLD) are increasing worldwide, leading to the increasing likelihood of both etiologies contributing to a patient's liver disease. However, the effects of modest alcohol use in NAFLD are controversial and more studies are needed. We compared the intestinal viromes of patients with AUD and NAFLD in order to evaluate the effect of alcohol consumption on the intestinal viromes of NAFLD patients by extracting virus-like particles and performing metagenomic sequencing.

APPROACH AND RESULTS: Viral nucleic acids were extracted from fecal samples and subjected to metagenomic sequencing. We demonstrate significant differences in the intestinal viromes of NAFLD and AUD patients, and that alcohol use in NAFLD patients reclassified to MAFLD accounted for significant differences in the intestinal viromes. The relative abundance of several Lactococcus phages was more similar between AUD patients and alcohol-consuming MAFLD patients than non-alcohol-consuming MAFLD patients and control subjects, and multivariate modeling using the most discriminating Lactococcus phages could better predict alcohol use in the MAFLD population than the alcohol-associated liver disease/NAFLD Index. Significant differences in the viral composition and diversity were also seen between MAFLD patients with low and moderate alcohol consumption compared with no alcohol consumption.

CONCLUSIONS: The intestinal virome of MAFLD patients who consume low to moderate amounts of alcohol are significantly different from those who do not, and many features of the intestinal virome of alcohol-consuming MAFLD patients resemble that of AUD patients.},
}

Humans
*Non-alcoholic Fatty Liver Disease
Virome
Alcohol Drinking/adverse effects
*Alcoholism
Ethanol
*Liver Diseases, Alcoholic

@article {pmid37189332,
year = {2023},
author = {Smith, L and Goldobina, E and Govi, B and Shkoporov, AN},
title = {Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?.},
journal = {Biomolecules},
volume = {13},
number = {4},
pages = {},
pmid = {37189332},
issn = {2218-273X},
support = {101001684/ERC_/European Research Council/International ; 220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Animals ; Humans ; *Bacteriophages/genetics ; Virome ; Metagenomics ; Genomics ; DNA ; Mammals/genetics ; },
abstract = {The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.},
}

Animals
Humans
*Bacteriophages/genetics
Virome
Metagenomics
Genomics
DNA
Mammals/genetics

@article {pmid37188713,
year = {2023},
author = {Orihara, K and Yahagi, K and Saito, Y and Watanabe, Y and Sasai, T and Hara, T and Tsukuda, N and Oki, K and Fujimoto, J and Matsuki, T},
title = {Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides.},
journal = {Gut microbes},
volume = {15},
number = {1},
pages = {2207455},
pmid = {37188713},
issn = {1949-0984},
mesh = {Infant ; Child ; Humans ; Phylogeny ; *Gastrointestinal Microbiome ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; alpha-L-Fucosidase/metabolism ; },
abstract = {Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.},
}

Infant
Child
Humans
Phylogeny
*Gastrointestinal Microbiome
Milk, Human/metabolism
Oligosaccharides/metabolism
alpha-L-Fucosidase/metabolism

@article {pmid37187470,
year = {2023},
author = {Wu, C and Yi, H and Hu, Y and Luo, D and Tang, Z and Wen, X and Zhang, Y and Tang, M and Zhang, L and Wu, S and Chen, M},
title = {Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1127916},
pmid = {37187470},
issn = {2235-2988},
mesh = {Humans ; Antitubercular Agents/pharmacology/therapeutic use ; Rifampin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Tryptophan ; *Tuberculosis, Multidrug-Resistant/drug therapy ; *Tuberculosis/drug therapy ; *Mycobacterium tuberculosis ; },
abstract = {OBJECTIVE: To determine the effects of second-line anti-tuberculosis (TB) drugs on the composition and functions of intestinal microbiota in patients with rifampicin-resistant TB (RR-TB).

METHODS: In this cross-sectional study, stool samples and relevant clinical information were collected from patients with RR-TB admitted to the Drug-resistant Specialty Department at Hunan Chest Hospital (Hunan Institute For Tuberculosis Control). The composition and functions of intestinal microbiota were analyzed using metagenomic sequencing and bioinformatics methods.

RESULTS: Altered structural composition of the intestinal microbiota was found when patients from the control, intensive phase treatment, and continuation phase treatment groups were compared (P<0.05). Second-line anti-TB treatment resulted in a decrease in the relative abundance of species, such as Prevotella copri, compared with control treatment. However, the relative abundance of Escherichia coli, Salmonella enterica, and 11 other conditionally pathogenic species increased significantly in the intensive phase treatment group. Based on differential functional analysis, some metabolism-related functions, such as the biosynthesises of phenylalanine, tyrosine, and tryptophan, were significantly inhibited during second-line anti-TB drug treatment, while other functions, such as phenylalanine metabolism, were significantly promoted during the intensive phase of treatment.

CONCLUSION: Second-line anti-TB drug treatment caused changes in the structural composition of the intestinal microbiota in patients with RR-TB. In particular, this treatment induced a significant increase in the relative abundance of 11 conditionally pathogenic species, including Escherichia coli. Functional analysis revealed significantly decreased biosynthesises of phenylalanine, tyrosine, and tryptophan and significantly increased phenylalanine metabolism.},
}

Humans
Antitubercular Agents/pharmacology/therapeutic use
Rifampin/pharmacology/therapeutic use
*Gastrointestinal Microbiome
Cross-Sectional Studies
Tryptophan
*Tuberculosis, Multidrug-Resistant/drug therapy
*Tuberculosis/drug therapy
*Mycobacterium tuberculosis

@article {pmid37186231,
year = {2023},
author = {Stach, TL and Sieber, G and Shah, M and Simon, SA and Soares, A and Bornemann, TLV and Plewka, J and Künkel, J and Becker, C and Meyer, F and Boenigk, J and Probst, AJ},
title = {Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater.},
journal = {MicrobiologyOpen},
volume = {12},
number = {2},
pages = {e1347},
pmid = {37186231},
issn = {2045-8827},
mesh = {*Ecosystem ; Rivers/microbiology ; Wastewater ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; },
abstract = {Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.},
}

*Ecosystem
Rivers/microbiology
Wastewater
RNA, Ribosomal, 16S/genetics
Bacteria/genetics
*Microbiota/genetics

@article {pmid37180439,
year = {2023},
author = {Niu, C and Tu, Y and Jin, Q and Chen, Z and Yuan, K and Wang, M and Zhang, P and Luo, J and Li, H and Yang, Y and Liu, X and Mao, M and Dong, T and Tan, W and Hu, X and Pan, Y and Hou, L and Ma, R and Huang, Z},
title = {Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {13},
number = {},
pages = {1157368},
pmid = {37180439},
issn = {2235-2988},
mesh = {Humans ; *Mycobiome ; Fungi/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Saliva ; *Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed "oral-gut-liver axis" concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible "oral-gut-liver" axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.},
}

Humans
*Mycobiome
Fungi/genetics
*Gastrointestinal Microbiome
Feces/microbiology
Saliva
*Non-alcoholic Fatty Liver Disease

@article {pmid37121198,
year = {2023},
author = {Li, L and Yan, W and Zhang, B and Zhang, H and Geng, R and Sun, S and Guan, X},
title = {Coupling of selenate reduction and pyrrhotite oxidation by indigenous microbial consortium in natural aquifer.},
journal = {Water research},
volume = {238},
number = {},
pages = {119987},
doi = {10.1016/j.watres.2023.119987},
pmid = {37121198},
issn = {1879-2448},
mesh = {Selenic Acid ; *Microbial Consortia ; Ferric Compounds ; Oxidation-Reduction ; Ferrous Compounds ; *Groundwater ; },
abstract = {Pyrrhotite is ubiquitously found in natural environment and involved in diverse (bio)processes. However, the pyrrhotite-driven bioreduction of toxic selenate [Se(VI)] remains largely unknown. This study demonstrates that Se(VI) is successfully bioreduced under anaerobic condition with the participation of pyrrhotite for the first time. Completely removal of Se(VI) was achieved at initial concentration of 10 mg/L Se(VI) and 0.56 mL/min flow rate in continuous column experiment with indigenous microbial consortium and pyrrhotite. Variation in hydrochemistry and hydrodynamics affected Se(VI) removal performance. Se(VI) was reduced to insoluble Se(0) while elements in pyrrhotite were oxidized to Fe(III) and SO4[2-]. Breakthrough study indicated that biotic activity contributed 81.4 ± 1.07% to Se(VI) transformation. Microbial community analysis suggested that chemoautotrophic genera (e.g., Thiobacillus) could realize pyrrhotite oxidation and Se(VI) reduction independently, while heterotrophic genera (e.g., Bacillus, Pseudomonas) contributed to Se(VI) detoxification by utilizing metabolic intermediates generated through Fe(II) and S(-II) oxidation, which were further verified by pure culture tests. Metagenomic and qPCR analyses indicated genes encoding enzymes for Se(VI) reduction (e.g., serA, napA and srdBAC), S oxidation (e.g., soxB) and Fe oxidation (e.g., mtrA) were upregulated. The elevated electron transporters (e.g., nicotinamide adenine dinucleotide, cytochrome c) promoted electron transfer from pyrrhotite to Se(VI). This study gains insights into Se biogeochemistry under the effect of Fe(II)-bearing minerals and provides a sustainable strategy for Se(VI) bioremediation in natural aquifer.},
}

Selenic Acid
*Microbial Consortia
Ferric Compounds
Oxidation-Reduction
Ferrous Compounds
*Groundwater

@article {pmid37041035,
year = {2023},
author = {Sun, Y and Cheng, Z and Li, X and Yang, Q and Zhao, B and Wu, Z and Xia, Y},
title = {Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.},
journal = {Genome research},
volume = {33},
number = {4},
pages = {612-621},
doi = {10.1101/gr.277266.122},
pmid = {37041035},
issn = {1549-5469},
mesh = {Humans ; *Nanopores ; *Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.},
}

Humans
*Nanopores
*Microbiota/genetics
Metagenome
Metagenomics