@article {pmid34671161,
year = {2021},
author = {Wang, Y and Pedersen, MW and Alsos, IG and De Sanctis, B and Racimo, F and Prohaska, A and Coissac, E and Owens, HL and Merkel, MKF and Fernandez-Guerra, A and Rouillard, A and Lammers, Y and Alberti, A and Denoeud, F and Money, D and Ruter, AH and McColl, H and Larsen, NK and Cherezova, AA and Edwards, ME and Fedorov, GB and Haile, J and Orlando, L and Vinner, L and Korneliussen, TS and Beilman, DW and Bjørk, AA and Cao, J and Dockter, C and Esdale, J and Gusarova, G and Kjeldsen, KK and Mangerud, J and Rasic, JT and Skadhauge, B and Svendsen, JI and Tikhonov, A and Wincker, P and Xing, Y and Zhang, Y and Froese, DG and Rahbek, C and Nogues, DB and Holden, PB and Edwards, NR and Durbin, R and Meltzer, DJ and Kjær, KH and Möller, P and Willerslev, E},
title = {Late Quaternary dynamics of Arctic biota from ancient environmental genomics.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {34671161},
issn = {1476-4687},
abstract = {During the last glacial-interglacial cycle, Arctic biotas experienced substantial climatic changes, yet the nature, extent and rate of their responses are not fully understood1-8. Here we report a large-scale environmental DNA metagenomic study of ancient plant and mammal communities, analysing 535 permafrost and lake sediment samples from across the Arctic spanning the past 50,000 years. Furthermore, we present 1,541 contemporary plant genome assemblies that were generated as reference sequences. Our study provides several insights into the long-term dynamics of the Arctic biota at the circumpolar and regional scales. Our key findings include: (1) a relatively homogeneous steppe-tundra flora dominated the Arctic during the Last Glacial Maximum, followed by regional divergence of vegetation during the Holocene epoch; (2) certain grazing animals consistently co-occurred in space and time; (3) humans appear to have been a minor factor in driving animal distributions; (4) higher effective precipitation, as well as an increase in the proportion of wetland plants, show negative effects on animal diversity; (5) the persistence of the steppe-tundra vegetation in northern Siberia enabled the late survival of several now-extinct megafauna species, including the woolly mammoth until 3.9 ± 0.2 thousand years ago (ka) and the woolly rhinoceros until 9.8 ± 0.2 ka; and (6) phylogenetic analysis of mammoth environmental DNA reveals a previously unsampled mitochondrial lineage. Our findings highlight the power of ancient environmental metagenomics analyses to advance understanding of population histories and long-term ecological dynamics.},
}

@article {pmid34649602,
year = {2021},
author = {Liu, L and Wang, Y and Yang, Y and Wang, D and Cheng, SH and Zheng, C and Zhang, T},
title = {Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {205},
pmid = {34649602},
issn = {2049-2618},
mesh = {Genome, Bacterial/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; *Sewage ; },
abstract = {BACKGROUND: Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems.

RESULTS: Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs.

CONCLUSION: Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into "complete metagenomics". The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment. Video Abstract.},
}

Genome, Bacterial/genetics
Humans
Metagenome/genetics
Metagenomics
*Microbiota/genetics
*Sewage

@article {pmid34641974,
year = {2021},
author = {Muller, E and Algavi, YM and Borenstein, E},
title = {A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {203},
pmid = {34641974},
issn = {2049-2618},
support = {U19 AG057377/AG/NIA NIH HHS/United States ; U19AG057377/NH/NIH HHS/United States ; R01DK095869/NH/NIH HHS/United States ; },
mesh = {Bile Acids and Salts ; Dysbiosis ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics ; *Microbiota ; },
abstract = {BACKGROUND: Microbiome-metabolome studies of the human gut have been gaining popularity in recent years, mostly due to accumulating evidence of the interplay between gut microbes, metabolites, and host health. Statistical and machine learning-based methods have been widely applied to analyze such paired microbiome-metabolome data, in the hope of identifying metabolites that are governed by the composition of the microbiome. Such metabolites can be likely modulated by microbiome-based interventions, offering a route for promoting gut metabolic health. Yet, to date, it remains unclear whether findings of microbially associated metabolites in any single study carry over to other studies or cohorts, and how robust and universal are microbiome-metabolites links.

RESULTS: In this study, we addressed this challenge by performing a comprehensive meta-analysis to identify human gut metabolites that can be predicted based on the composition of the gut microbiome across multiple studies. We term such metabolites "robustly well-predicted". To this end, we processed data from 1733 samples from 10 independent human gut microbiome-metabolome studies, focusing initially on healthy subjects, and implemented a machine learning pipeline to predict metabolite levels in each dataset based on the composition of the microbiome. Comparing the predictability of each metabolite across datasets, we found 97 robustly well-predicted metabolites. These include metabolites involved in important microbial pathways such as bile acid transformations and polyamines metabolism. Importantly, however, other metabolites exhibited large variation in predictability across datasets, suggesting a cohort- or study-specific relationship between the microbiome and the metabolite. Comparing taxonomic contributors to different models, we found that some robustly well-predicted metabolites were predicted by markedly different sets of taxa across datasets, suggesting that some microbially associated metabolites may be governed by different members of the microbiome in different cohorts. We finally examined whether models trained on a control group of a given study successfully predicted the metabolite's level in the disease group of the same study, identifying several metabolites where the model was not transferable, indicating a shift in microbial metabolism in disease-associated dysbiosis.

CONCLUSIONS: Combined, our findings provide a better understanding of the link between the microbiome and metabolites and allow researchers to put identified microbially associated metabolites within the context of other studies. Video abstract.},
}

Bile Acids and Salts
Dysbiosis
*Gastrointestinal Microbiome/genetics
Humans
Metabolome
Metabolomics
*Microbiota

@article {pmid34641955,
year = {2021},
author = {Arikawa, K and Ide, K and Kogawa, M and Saeki, T and Yoda, T and Endoh, T and Matsuhashi, A and Takeyama, H and Hosokawa, M},
title = {Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {202},
pmid = {34641955},
issn = {2049-2618},
mesh = {Genome, Microbial ; Humans ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Phylogeny ; },
abstract = {BACKGROUND: Obtaining high-quality (HQ) reference genomes from microbial communities is crucial for understanding the phylogeny and function of uncultured microbes in complex microbial ecosystems. Despite improvements in bioinformatic approaches to generate curated metagenome-assembled genomes (MAGs), existing metagenome binners obtain population consensus genomes but they are nowhere comparable to genomes sequenced from isolates in terms of strain level resolution. Here, we present a framework for the integration of single-cell genomics and metagenomics, referred to as single-cell (sc) metagenomics, to reconstruct strain-resolved genomes from microbial communities at once.

RESULTS: Our sc-metagenomics integration framework, termed SMAGLinker, uses single-cell amplified genomes (SAGs) generated using microfluidic technology as binning guides and integrates them with metagenome-assembled genomes (MAGs) to recover improved draft genomes. We compared sc-metagenomics with the metagenomics-alone approach using conventional metagenome binners. The sc-metagenomics approach showed precise contig binning and higher recovery rates (>97%) of rRNA and plasmids than conventional metagenomics in genome reconstruction from the cell mock community. In human microbiota samples, sc-metagenomics recovered the largest number of genomes with a total of 103 gut microbial genomes (21 HQ, with 65 showing >90% completeness) and 45 skin microbial genomes (10 HQ, with 40 showing >90% completeness), respectively. Conventional metagenomics recovered one Staphylococcus hominis genome, whereas sc-metagenomics recovered two S. hominis genomes from identical skin microbiota sample. Single-cell sequencing revealed that these S. hominis genomes were derived from two distinct strains harboring specifically different plasmids. We found that all conventional S. hominis MAGs had a substantial lack or excess of genome sequences and contamination from other Staphylococcus species (S. epidermidis).

CONCLUSIONS: SMAGLinker enabled us to obtain strain-resolved genomes in the mock community and human microbiota samples by assigning metagenomic sequences correctly and covering both highly conserved genes such as rRNA genes and unique extrachromosomal elements, including plasmids. SMAGLinker will provide HQ genomes that are difficult to obtain using metagenomics alone and will facilitate the understanding of microbial ecosystems by elucidating detailed metabolic pathways and horizontal gene transfer networks. SMAGLinker is available at https://github.com/kojiari/smaglinker . Video abstract.},
}

Genome, Microbial
Humans
Metagenome
*Metagenomics
*Microbiota/genetics
Phylogeny

@article {pmid34576010,
year = {2021},
author = {Pistone, D and Meroni, G and Panelli, S and D'Auria, E and Acunzo, M and Pasala, AR and Zuccotti, GV and Bandi, C and Drago, L},
title = {A Journey on the Skin Microbiome: Pitfalls and Opportunities.},
journal = {International journal of molecular sciences},
volume = {22},
number = {18},
pages = {},
pmid = {34576010},
issn = {1422-0067},
mesh = {Dysbiosis/*microbiology/therapy ; Humans ; Metagenomics/methods ; *Microbiota ; Probiotics/therapeutic use ; Skin/*microbiology ; Skin Diseases/*microbiology/therapy ; },
abstract = {The human skin microbiota is essential for maintaining homeostasis and ensuring barrier functions. Over the years, the characterization of its composition and taxonomic diversity has reached outstanding goals, with more than 10 million bacterial genes collected and cataloged. Nevertheless, the study of the skin microbiota presents specific challenges that need to be addressed in study design. Benchmarking procedures and reproducible and robust analysis workflows for increasing comparability among studies are required. For various reasons and because of specific technical problems, these issues have been investigated in gut microbiota studies, but they have been largely overlooked for skin microbiota. After a short description of the skin microbiota, the review tackles methodological aspects and their pitfalls, covering NGS approaches and high throughput culture-based techniques. Recent insights into the "core" and "transient" types of skin microbiota and how the manipulation of these communities can prevent or combat skin diseases are also covered. Finally, this review includes an overview of the main dermatological diseases, the changes in the microbiota composition associated with them, and the recommended skin sampling procedures. The last section focuses on topical and oral probiotics to improve and maintain skin health, considering their possible applications for skin diseases.},
}

Dysbiosis/*microbiology/therapy
Humans
Metagenomics/methods
*Microbiota
Probiotics/therapeutic use
Skin/*microbiology
Skin Diseases/*microbiology/therapy

@article {pmid34548111,
year = {2021},
author = {Wang, L and Huang, G and Hou, R and Qi, D and Wu, Q and Nie, Y and Zuo, Z and Ma, R and Zhou, W and Ma, Y and Hu, Y and Yang, Z and Yan, L and Wei, F},
title = {Multi-omics reveals the positive leverage of plant secondary metabolites on the gut microbiota in a non-model mammal.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {192},
pmid = {34548111},
issn = {2049-2618},
mesh = {Animals ; Diet ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Ursidae ; },
abstract = {BACKGROUND: Flavonoids are important plant secondary metabolites (PSMs) that have been widely used for their health-promoting effects. However, little is known about overall flavonoid metabolism and the interactive effects between flavonoids and the gut microbiota. The flavonoid-rich bamboo and the giant panda provide an ideal system to bridge this gap.

RESULTS: Here, integrating metabolomic and metagenomic approaches, and in vitro culture experiment, we identified 97 flavonoids in bamboo and most of them have not been identified previously; the utilization of more than 70% flavonoid monomers was attributed to gut microbiota; the variation of flavonoid in bamboo leaves and shoots shaped the seasonal microbial fluctuation. The greater the flavonoid content in the diet was, the lower microbial diversity and virulence factor, but the more cellulose-degrading species.

CONCLUSIONS: Our study shows an unprecedented landscape of beneficial PSMs in a non-model mammal and reveals that PSMs remodel the gut microbiota conferring host adaptation to diet transition in an ecological context, providing a novel insight into host-microbe interaction. Video abstract.},
}

Animals
Diet
*Gastrointestinal Microbiome/genetics
Metagenome
Metagenomics
*Ursidae

@article {pmid34526096,
year = {2021},
author = {Gao, M and Xiong, C and Gao, C and Tsui, CKM and Wang, MM and Zhou, X and Zhang, AM and Cai, L},
title = {Disease-induced changes in plant microbiome assembly and functional adaptation.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {187},
pmid = {34526096},
issn = {2049-2618},
mesh = {Bacteria/genetics ; *Microbiota/genetics ; Plant Roots ; Rhizosphere ; *Soil Microbiology ; },
abstract = {BACKGROUND: The plant microbiome is an integral part of the host and increasingly recognized as playing fundamental roles in plant growth and health. Increasing evidence indicates that plant rhizosphere recruits beneficial microbes to the plant to suppress soil-borne pathogens. However, the ecological processes that govern plant microbiome assembly and functions in the below- and aboveground compartments under pathogen invasion are not fully understood. Here, we studied the bacterial and fungal communities associated with 12 compartments (e.g., soils, roots, stems, and fruits) of chili pepper (Capsicum annuum L.) using amplicons (16S and ITS) and metagenomics approaches at the main pepper production sites in China and investigated how Fusarium wilt disease (FWD) affects the assembly, co-occurrence patterns, and ecological functions of plant-associated microbiomes.

RESULTS: The amplicon data analyses revealed that FWD affected less on the microbiome of pepper reproductive organs (fruit) than vegetative organs (root and stem), with the strongest impact on the upper stem epidermis. Fungal intra-kingdom networks were less stable and their communities were more sensitive to FWD than the bacterial communities. The analysis of microbial interkingdom network further indicated that FWD destabilized the network and induced the ecological importance of fungal taxa. Although the diseased plants were more susceptible to colonization by other pathogenic fungi, their below- and aboveground compartments can also recruit potential beneficial bacteria. Some of the beneficial bacterial taxa enriched in the diseased plants were also identified as core taxa for plant microbiomes and hub taxa in networks. On the other hand, metagenomic analysis revealed significant enrichment of several functional genes involved in detoxification, biofilm formation, and plant-microbiome signaling pathways (i.e., chemotaxis) in the diseased plants.

CONCLUSIONS: Together, we demonstrate that a diseased plant could recruit beneficial bacteria and mitigate the changes in reproductive organ microbiome to facilitate host or its offspring survival. The host plants may attract the beneficial microbes through the modulation of plant-microbiome signaling pathways. These findings significantly advance our understanding on plant-microbiome interactions and could provide fundamental and important data for harnessing the plant microbiome in sustainable agriculture. Video abstract.},
}

Bacteria/genetics
*Microbiota/genetics
Plant Roots
Rhizosphere
*Soil Microbiology

@article {pmid34393020,
year = {2021},
author = {Robertson, RC and Church, JA and Edens, TJ and Mutasa, K and Min Geum, H and Baharmand, I and Gill, SK and Ntozini, R and Chasekwa, B and Carr, L and Majo, FD and Kirkpatrick, BD and Lee, B and Moulton, LH and Humphrey, JH and Prendergast, AJ and Manges, AR and , },
title = {The fecal microbiome and rotavirus vaccine immunogenicity in rural Zimbabwean infants.},
journal = {Vaccine},
volume = {39},
number = {38},
pages = {5391-5400},
pmid = {34393020},
issn = {1873-2518},
support = {203905/Z/16/Z//Wellcome Trust/United Kingdom ; 206455/Z/17/Z//Wellcome Trust/United Kingdom ; 093768/Z/10/Z//Wellcome Trust/United Kingdom ; 108065/Z/15/Z//Wellcome Trust/United Kingdom ; R01 HD060338/HD/NICHD NIH HHS/United States ; },
mesh = {Antibodies, Viral ; *Gastrointestinal Microbiome ; Humans ; Immunogenicity, Vaccine ; Immunoglobulin A ; Infant ; *Rotavirus/genetics ; *Rotavirus Infections/prevention & control ; *Rotavirus Vaccines ; },
abstract = {BACKGROUND: Oral rotavirus vaccine (RVV) immunogenicity is considerably lower in low- versus high-income populations; however, the mechanisms underlying this remain unclear. Previous evidence suggests that the gut microbiota may contribute to differences in oral vaccine efficacy.

METHODS: We performed whole metagenome shotgun sequencing on stool samples and measured anti-rotavirus immunoglobulin A in plasma samples from a subset of infants enrolled in a cluster randomized 2 × 2 factorial trial of improved water, sanitation and hygiene and infant feeding in rural Zimbabwe (SHINE trial: NCT01824940). We examined taxonomic microbiome composition and functional metagenome features using random forest models, differential abundance testing and regression analyses to explored associations with RVV immunogenicity.

RESULTS: Among 158 infants with stool samples and anti-rotavirus IgA titres, 34 were RVV seroconverters. The median age at stool collection was 43 days (IQR: 35-68), corresponding to a median of 4 days before the first RVV dose. The infant microbiome was dominated by Bifidobacterium longum. The gut microbiome differed significantly between early (≤42 days) and later samples (>42 days) however, we observed no meaningful differences in alpha diversity, beta diversity, species composition or functional metagenomic features by RVV seroconversion status. Bacteroides thetaiotaomicron was the only species associated with anti-rotavirus IgA titre. Random forest models poorly classified seroconversion status by both composition and functional microbiome variables.

CONCLUSIONS: RVV immunogenicity is low in this rural Zimbabwean setting, however it was not associated with the composition or function of the early-life gut microbiome in this study. Further research is warranted to examine the mechanisms of poor oral RVV efficacy in low-income countries.},
}

Antibodies, Viral
*Gastrointestinal Microbiome
Humans
Immunogenicity, Vaccine
Immunoglobulin A
Infant
*Rotavirus/genetics
*Rotavirus Infections/prevention & control
*Rotavirus Vaccines

@article {pmid34352595,
year = {2021},
author = {Lin, W and Djukovic, A and Mathur, D and Xavier, JB},
title = {Listening in on the conversation between the human gut microbiome and its host.},
journal = {Current opinion in microbiology},
volume = {63},
number = {},
pages = {150-157},
doi = {10.1016/j.mib.2021.07.009},
pmid = {34352595},
issn = {1879-0364},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolomics ; Metagenomics ; *Microbiota ; },
abstract = {The gut microbiome is an ecosystem. Natural selection favored microbes fit for the gut, which can utilize and convert molecules produced by the host for their own benefit. But natural selection also favored the host's mechanisms to sense and respond to the microbial ecosystem for its own benefit. We can listen in on the host-microbiome 'conversation' in the simultaneous responses of the microbiome and the host to strong perturbations. In laboratory animals a perturbation can be done for research; in human patients a perturbation can be caused by disease or therapy. Advances in metagenomics, metabolomics and computation amplify our means to listen in on the conversation between the gut microbiome and its host.},
}

Animals
*Gastrointestinal Microbiome/genetics
Humans
Metabolomics
Metagenomics
*Microbiota

@article {pmid34273006,
year = {2021},
author = {Dalal, N and Jalandra, R and Bayal, N and Yadav, AK and Harshulika, and Sharma, M and Makharia, GK and Kumar, P and Singh, R and Solanki, PR and Kumar, A},
title = {Gut microbiota-derived metabolites in CRC progression and causation.},
journal = {Journal of cancer research and clinical oncology},
volume = {147},
number = {11},
pages = {3141-3155},
pmid = {34273006},
issn = {1432-1335},
mesh = {Animals ; Colorectal Neoplasms/*microbiology/pathology ; Disease Progression ; Gastrointestinal Microbiome/*physiology ; Gram-Negative Bacteria/metabolism ; Gram-Positive Bacteria/metabolism ; Humans ; Metagenomics ; },
abstract = {BACKGROUND: Based on recent research reports, dysbiosis and improper concentrations of microbial metabolites in the gut may result into the carcinogenesis of colorectal cancer. Recent advancement also highlights the involvement of bacteria and their secreted metabolites in the cancer causation. Gut microbial metabolites are functional output of the host-microbiota interactions and produced by anaerobic fermentation of food components in the diet. They contribute to influence variety of biological mechanisms including inflammation, cell signaling, cell-cycle disruption which are majorly disrupted in carcinogenic activities.

PURPOSE: In this review, we intend to discuss recent updates and possible molecular mechanisms to provide the role of bacterial metabolites, gut bacteria and diet in the colorectal carcinogenesis. Recent evidences have proposed the role of bacteria, such as Fusobacterium nucleaturm, Streptococcus bovis, Helicobacter pylori, Bacteroides fragilis and Clostridium septicum, in the carcinogenesis of CRC. Metagenomic study confirmed that these bacteria are in increased abundance in CRC patient as compared to healthy individuals and can cause inflammation and DNA damage which can lead to development of cancer. These bacteria produce metabolites, such as secondary bile salts from primary bile salts, hydrogen sulfide, trimethylamine-N-oxide (TMAO), which are likely to promote inflammation and subsequently cancer development.

CONCLUSION: Recent studies suggest that gut microbiota-derived metabolites have a role in CRC progression and causation and hence, could be implicated in CRC diagnosis, prognosis and therapy.},
}

Animals
Colorectal Neoplasms/*microbiology/pathology
Disease Progression
Gastrointestinal Microbiome/*physiology
Gram-Negative Bacteria/metabolism
Gram-Positive Bacteria/metabolism
Humans
Metagenomics

@article {pmid34119873,
year = {2021},
author = {Batool, M and Blazier, JC and Rogovska, YV and Wang, J and Liu, S and Nebogatkin, IV and Rogovskyy, AS},
title = {Metagenomic analysis of individually analyzed ticks from Eastern Europe demonstrates regional and sex-dependent differences in the microbiota of Ixodes ricinus.},
journal = {Ticks and tick-borne diseases},
volume = {12},
number = {5},
pages = {101768},
doi = {10.1016/j.ttbdis.2021.101768},
pmid = {34119873},
issn = {1877-9603},
mesh = {Animals ; Bacteria/genetics/*isolation & purification ; Female ; Geography ; Ixodes/*microbiology ; Male ; *Metagenome ; Metagenomics ; *Microbiota ; Sex Factors ; Ukraine ; },
abstract = {Understanding the microbial ecology of disease vectors may be useful for development of novel strategies aimed at preventing transmission of vector-borne pathogens. Although Ixodes ricinus is one of the most important tick vectors, the microbiota of this tick has been examined for only limited parts of the globe. To date, the microbiota of I. ricinus ticks collected from Eastern Europe has not been defined. The objective of this study was to compare microbiota of I. ricinus ticks within (males vs. females) and between collection sites that represented three administrative regions of Ukraine, Dnipropetrovs'k (D), Kharkiv (K), and Poltava (P). A total of 89 questing I. ricinus adults were collected from region D (number of ticks, n = 29; 14 males and 15 females), region K (n = 30; 15 males and 15 females) and region P (n = 30; 15 males and 15 females). Each tick was subjected to metagenomic analysis by targeting the V6 region of 16S rRNA gene through the Illumina 4000 Hiseq sequencing. The alpha diversity analysis demonstrated that, regardless of tick sex, patterns of bacterial diversity in ticks from regions K and P were similar, whereas the microbiota of region D ticks was quite distinct. A number of inter-regional differences were detected by most beta diversity metrics for both males and females. The inter-regional variations were also supported by the principal coordinate analysis based on the unweighted UniFrac metrics with three region-specific clusters of female ticks and one distinct cluster of region D males. Lastly, numerous region- and sex-specific differences were also identified in the relative abundance of various bacterial taxa. Collectively, the present findings demonstrate that the microbiota of the I. ricinus tick can exhibit a high degree of variation between tick sexes and geographical regions.},
}

Animals
Bacteria/genetics/*isolation & purification
Female
Geography
Ixodes/*microbiology
Male
*Metagenome
Metagenomics
*Microbiota
Sex Factors
Ukraine

@article {pmid34114607,
year = {2021},
author = {Aevarsson, A and Kaczorowska, AK and Adalsteinsson, BT and Ahlqvist, J and Al-Karadaghi, S and Altenbuchner, J and Arsin, H and Átlasson, ÚÁ and Brandt, D and Cichowicz-Cieślak, M and Cornish, KAS and Courtin, J and Dabrowski, S and Dahle, H and Djeffane, S and Dorawa, S and Dusaucy, J and Enault, F and Fedøy, AE and Freitag-Pohl, S and Fridjonsson, OH and Galiez, C and Glomsaker, E and Guérin, M and Gundesø, SE and Gudmundsdóttir, EE and Gudmundsson, H and Håkansson, M and Henke, C and Helleux, A and Henriksen, JR and Hjörleifdóttir, S and Hreggvidsson, GO and Jasilionis, A and Jochheim, A and Jónsdóttir, I and Jónsdóttir, LB and Jurczak-Kurek, A and Kaczorowski, T and Kalinowski, J and Kozlowski, LP and Krupovic, M and Kwiatkowska-Semrau, K and Lanes, O and Lange, J and Lebrat, J and Linares-Pastén, J and Liu, Y and Lorentsen, SA and Lutterman, T and Mas, T and Merré, W and Mirdita, M and Morzywołek, A and Ndela, EO and Karlsson, EN and Olgudóttir, E and Pedersen, C and Perler, F and Pétursdóttir, SK and Plotka, M and Pohl, E and Prangishvili, D and Ray, JL and Reynisson, B and Róbertsdóttir, T and Sandaa, RA and Sczyrba, A and Skírnisdóttir, S and Söding, J and Solstad, T and Steen, IH and Stefánsson, SK and Steinegger, M and Overå, KS and Striberny, B and Svensson, A and Szadkowska, M and Tarrant, EJ and Terzian, P and Tourigny, M and Bergh, TVD and Vanhalst, J and Vincent, J and Vroling, B and Walse, B and Wang, L and Watzlawick, H and Welin, M and Werbowy, O and Wons, E and Zhang, R},
title = {Going to extremes - a metagenomic journey into the dark matter of life.},
journal = {FEMS microbiology letters},
volume = {368},
number = {12},
pages = {},
doi = {10.1093/femsle/fnab067},
pmid = {34114607},
issn = {1574-6968},
mesh = {Bioprospecting/organization & administration ; Computational Biology ; Databases, Genetic ; Europe ; Genome, Viral/*genetics ; Hydrothermal Vents/virology ; *Metagenomics ; Viral Proteins/chemistry/genetics/metabolism ; Virome/genetics ; Viruses/classification/genetics ; },
abstract = {The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.},
}

Bioprospecting/organization & administration
Computational Biology
Databases, Genetic
Europe
Genome, Viral/*genetics
Hydrothermal Vents/virology
*Metagenomics
Viral Proteins/chemistry/genetics/metabolism
Virome/genetics
Viruses/classification/genetics

@article {pmid33944776,
year = {2021},
author = {Beghini, F and McIver, LJ and Blanco-Míguez, A and Dubois, L and Asnicar, F and Maharjan, S and Mailyan, A and Manghi, P and Scholz, M and Thomas, AM and Valles-Colomer, M and Weingart, G and Zhang, Y and Zolfo, M and Huttenhower, C and Franzosa, EA and Segata, N},
title = {Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {33944776},
issn = {2050-084X},
support = {R01 CA230551/CA/NCI NIH HHS/United States ; C10674/A27140/CRUK_/Cancer Research UK/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U54 DE023798/DE/NIDCR NIH HHS/United States ; R01 HG005220/HG/NHGRI NIH HHS/United States ; },
mesh = {Bacteria/*classification/*genetics/metabolism ; Computational Biology/*methods ; Humans ; *Metagenome ; Metagenomics/methods ; Microbiota/*genetics/*physiology ; *Phylogeny ; Research Personnel ; Ruminococcus/classification/genetics ; Workflow ; },
abstract = {Culture-independent analyses of microbial communities have progressed dramatically in the last decade, particularly due to advances in methods for biological profiling via shotgun metagenomics. Opportunities for improvement continue to accelerate, with greater access to multi-omics, microbial reference genomes, and strain-level diversity. To leverage these, we present bioBakery 3, a set of integrated, improved methods for taxonomic, strain-level, functional, and phylogenetic profiling of metagenomes newly developed to build on the largest set of reference sequences now available. Compared to current alternatives, MetaPhlAn 3 increases the accuracy of taxonomic profiling, and HUMAnN 3 improves that of functional potential and activity. These methods detected novel disease-microbiome links in applications to CRC (1262 metagenomes) and IBD (1635 metagenomes and 817 metatranscriptomes). Strain-level profiling of an additional 4077 metagenomes with StrainPhlAn 3 and PanPhlAn 3 unraveled the phylogenetic and functional structure of the common gut microbe Ruminococcus bromii, previously described by only 15 isolate genomes. With open-source implementations and cloud-deployable reproducible workflows, the bioBakery 3 platform can help researchers deepen the resolution, scale, and accuracy of multi-omic profiling for microbial community studies.},
}

Bacteria/*classification/*genetics/metabolism
Computational Biology/*methods
Humans
*Metagenome
Metagenomics/methods
Microbiota/*genetics/*physiology
*Phylogeny
Research Personnel
Ruminococcus/classification/genetics
Workflow

@article {pmid33917566,
year = {2021},
author = {Mazier, W and Le Corf, K and Martinez, C and Tudela, H and Kissi, D and Kropp, C and Coubard, C and Soto, M and Elustondo, F and Rawadi, G and Claus, SP},
title = {A New Strain of Christensenella minuta as a Potential Biotherapy for Obesity and Associated Metabolic Diseases.},
journal = {Cells},
volume = {10},
number = {4},
pages = {},
pmid = {33917566},
issn = {2073-4409},
mesh = {Animals ; Biodiversity ; *Biological Therapy ; Biomarkers/metabolism ; Clostridiales/classification/*isolation & purification ; Diet ; Disease Models, Animal ; Epithelial Cells/metabolism ; Feces/microbiology ; Gastrointestinal Microbiome ; Humans ; Lipid Metabolism ; Liver/metabolism ; Male ; Metabolic Diseases/*microbiology/*therapy ; Mice, Inbred C57BL ; Obesity/*microbiology/*therapy ; Phylogeny ; },
abstract = {Obesity is associated with gut microbiota dysbiosis, characterized by a high Firmicutes/Bacteroidetes ratio. Gut-dwelling bacteria of the Christensenellaceae family have been proposed to act as keystones of the human gut ecosystem and to prevent adipogenesis. The objectives of the present study were to demonstrate the antiobesity potential of a new strain of Christensenella minuta in preclinical models and explore related mechanisms of action. The antiobesity potential of C. minuta DSM33407 was assessed in a diet-induced obesity mouse model. Changes in hepatic lipid metabolism were explored using targeted transcriptomics. Effects on gut microbiota were further assessed in a humanized Simulator of the Human Intestinal Microbial Ecosystem (SHIME®) model inoculated with obese fecal samples. Shotgun metagenomics was applied to study microbial community structures in both models. C. minuta DSM33407 protected from diet-induced obesity and regulated associated metabolic markers such as glycemia and leptin. It also regulated hepatic lipid metabolism through a strong inhibition of de novo lipogenesis and maintained gut epithelial integrity. In the humanized SHIME® model, these effects were associated with modulations of the intestinal microbiota characterized by a decreased Firmicutes/Bacteroidetes ratio. These data indicate that C. minuta DSM33407 is a convincing therapeutic candidate for the management of obesity and associated metabolic disorders.},
}

Animals
Biodiversity
*Biological Therapy
Biomarkers/metabolism
Clostridiales/classification/*isolation & purification
Diet
Disease Models, Animal
Epithelial Cells/metabolism
Feces/microbiology
Gastrointestinal Microbiome
Humans
Lipid Metabolism
Liver/metabolism
Male
Metabolic Diseases/*microbiology/*therapy
Mice, Inbred C57BL
Obesity/*microbiology/*therapy
Phylogeny

@article {pmid33762692,
year = {2021},
author = {Palkova, L and Tomova, A and Repiska, G and Babinska, K and Bokor, B and Mikula, I and Minarik, G and Ostatnikova, D and Soltys, K},
title = {Evaluation of 16S rRNA primer sets for characterisation of microbiota in paediatric patients with autism spectrum disorder.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6781},
pmid = {33762692},
issn = {2045-2322},
mesh = {Autism Spectrum Disorder/diagnosis/*etiology ; Biodiversity ; Child ; Child, Preschool ; Computational Biology/methods ; Humans ; Male ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; *RNA, Ribosomal, 16S ; },
abstract = {intestinal microbiota is becoming a significant marker that reflects differences between health and disease status also in terms of gut-brain axis communication. Studies show that children with autism spectrum disorder (ASD) often have a mix of gut microbes that is distinct from the neurotypical children. Various assays are being used for microbiota investigation and were considered to be universal. However, newer studies showed that protocol for preparing DNA sequencing libraries is a key factor influencing results of microbiota investigation. The choice of DNA amplification primers seems to be the crucial for the outcome of analysis. In our study, we have tested 3 primer sets to investigate differences in outcome of sequencing analysis of microbiota in children with ASD. We found out that primers detected different portion of bacteria in samples especially at phylum level; significantly higher abundance of Bacteroides and lower Firmicutes were detected using 515f/806r compared to 27f/1492r and 27f*/1495f primers. So, the question is whether a gold standard of Firmicutes/Bacteroidetes ratio is a valuable and reliable universal marker, since two primer sets towards 16S rRNA can provide opposite information. Moreover, significantly higher relative abundance of Proteobacteria was detected using 27f/1492r. The beta diversity of sample groups differed remarkably and so the number of observed bacterial genera.},
}

Autism Spectrum Disorder/diagnosis/*etiology
Biodiversity
Child
Child, Preschool
Computational Biology/methods
Humans
Male
Metagenome
Metagenomics/methods
*Microbiota/genetics
*RNA, Ribosomal, 16S

@article {pmid33758359,
year = {2021},
author = {Rojas-Jaimes, J and Lindo-Seminario, D and Correa-Núñez, G and Diringer, B},
title = {Characterization of the bacterial microbiome of Rhipicephalus (Boophilus) microplus collected from Pecari tajacu "Sajino" Madre de Dios, Peru.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6661},
pmid = {33758359},
issn = {2045-2322},
mesh = {Animals ; *Bacteria/classification ; Biodiversity ; Cattle ; Ecosystem ; Farms ; Female ; Male ; *Microbiota ; Peru ; Rhipicephalus/*microbiology ; },
abstract = {Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The bacterial microbiome of adult (males and females) and nymph Rhipicephalus microplus ticks collected from a collared peccary, Pecari tajacu, captured in the rural area of Botijón Village in the Amazon region of Madre de Dios, Peru, was evaluated using metagenomics. The Chao1 and Shannon-Weaver analyses indicated greater bacterial richness and diversity in female ticks (GARH; 375-4.15) and nymph ticks (GARN; 332-4.75) compared to that in male ticks (GARM; 215-3.20). Taxonomic analyses identified 185 operational taxonomic units representing 147 bacterial genera. Of the 25 most prevalent genera, Salmonella (17.5%) and Vibrio (15.0%) showed the highest relative abundance followed by several other potentially pathogenic genera, such as Paracoccus (7.8%), Staphylococcus (6.8%), Pseudomonas (6.6%), Corynebacterium (5.0%), Cloacibacterium (3.6%), and Acinetobacter (2.5%). In total, 19.7% of the detected genera are shared by GARH, GARM, and GARN, and they can be considered as the core microbiome of R. microplus. To the best of our knowledge, this study is the first to characterize the microbiome of ticks collected from P. tajacu and to report the presence of Salmonella and Vibrio in R. microplus. The pathogenic potential and the role of these bacteria in the physiology of R. microplus should be further investigated due to the possible implications for public health and animal health in populations neighboring the habitat of P. tajacu.},
}

Animals
*Bacteria/classification
Biodiversity
Cattle
Ecosystem
Farms
Female
Male
*Microbiota
Peru
Rhipicephalus/*microbiology

@article {pmid33758228,
year = {2021},
author = {Appiah, SA and Foxx, CL and Langgartner, D and Palmer, A and Zambrano, CA and Braumüller, S and Schaefer, EJ and Wachter, U and Elam, BL and Radermacher, P and Stamper, CE and Heinze, JD and Salazar, SN and Luthens, AK and Arnold, AL and Reber, SO and Huber-Lang, M and Lowry, CA and Halbgebauer, R},
title = {Evaluation of the gut microbiome in association with biological signatures of inflammation in murine polytrauma and shock.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {6665},
pmid = {33758228},
issn = {2045-2322},
support = {R21 MH116263/MH/NIMH NIH HHS/United States ; R01 AT010005/AT/NCCIH NIH HHS/United States ; R41 AT011390/AT/NCCIH NIH HHS/United States ; },
mesh = {Animals ; Biodiversity ; *Biomarkers ; Disease Models, Animal ; Enzyme-Linked Immunosorbent Assay ; *Gastrointestinal Microbiome ; Inflammation/diagnosis/*etiology/*metabolism ; Male ; Metagenomics ; Mice ; Multiple Trauma/*complications/etiology ; RNA, Ribosomal, 16S ; ROC Curve ; Shock/*complications/etiology ; Supervised Machine Learning ; },
abstract = {Severe injuries are frequently accompanied by hemorrhagic shock and harbor an increased risk for complications. Local or systemic inflammation after trauma/hemorrhage may lead to a leaky intestinal epithelial barrier and subsequent translocation of gut microbiota, potentially worsening outcomes. To evaluate the extent with which trauma affects the gut microbiota composition, we performed a post hoc analysis of a murine model of polytrauma and hemorrhage. Four hours after injury, organs and plasma samples were collected, and the diversity and composition of the cecal microbiome were evaluated using 16S rRNA gene sequencing. Although cecal microbial alpha diversity and microbial community composition were not found to be different between experimental groups, norepinephrine support in shock animals resulted in increased alpha diversity, as indicated by higher numbers of distinct microbial features. We observed that the concentrations of proinflammatory mediators in plasma and intestinal tissue were associated with measures of microbial alpha and beta diversity and the presence of specific microbial drivers of inflammation, suggesting that the composition of the gut microbiome at the time of trauma, or shortly after trauma exposure, may play an important role in determining physiological outcomes. In conclusion, we found associations between measures of gut microbial alpha and beta diversity and the severity of systemic and local gut inflammation. Furthermore, our data suggest that four hours following injury is too early for development of global changes in the alpha diversity or community composition of the intestinal microbiome. Future investigations with increased temporal-spatial resolution are needed in order to fully elucidate the effects of trauma and shock on the gut microbiome, biological signatures of inflammation, and proximal and distal outcomes.},
}

Animals
Biodiversity
*Biomarkers
Disease Models, Animal
Enzyme-Linked Immunosorbent Assay
*Gastrointestinal Microbiome
Inflammation/diagnosis/*etiology/*metabolism
Male
Metagenomics
Mice
Multiple Trauma/*complications/etiology
RNA, Ribosomal, 16S
ROC Curve
Shock/*complications/etiology
Supervised Machine Learning

@article {pmid33639859,
year = {2021},
author = {Stevens, V and Thijs, S and Vangronsveld, J},
title = {Diversity and plant growth-promoting potential of (un)culturable bacteria in the Hedera helix phylloplane.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {66},
pmid = {33639859},
issn = {1471-2180},
support = {08M03VGRJ//Universiteit Hasselt Methusalem/ ; G0D0916N//Fonds Wetenschappelijk Onderzoek/ ; 1166918N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Bacteria/*classification/*genetics/isolation & purification ; Biodegradation, Environmental ; Culture Media/chemistry ; Hedera/*growth & development/*microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Microbiota ; *Plant Development ; Plant Leaves/microbiology ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: A diverse community of microbes naturally exists on the phylloplane, the surface of leaves. It is one of the most prevalent microbial habitats on earth and bacteria are the most abundant members, living in communities that are highly dynamic. Today, one of the key challenges for microbiologists is to develop strategies to culture the vast diversity of microorganisms that have been detected in metagenomic surveys.

RESULTS: We isolated bacteria from the phylloplane of Hedera helix (common ivy), a widespread evergreen, using five growth media: Luria-Bertani (LB), LB01, yeast extract-mannitol (YMA), yeast extract-flour (YFlour), and YEx. We also included a comparison with the uncultured phylloplane, which we showed to be dominated by Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes. Inter-sample (beta) diversity shifted from LB and LB01 containing the highest amount of resources to YEx, YMA, and YFlour which are more selective. All growth media equally favoured Actinobacteria and Gammaproteobacteria, whereas Bacteroidetes could only be found on LB01, YEx, and YMA. LB and LB01 favoured Firmicutes and YFlour was most selective for Betaproteobacteria. At the genus level, LB favoured the growth of Bacillus and Stenotrophomonas, while YFlour was most selective for Burkholderia and Curtobacterium. The in vitro plant growth promotion (PGP) profile of 200 isolates obtained in this study indicates that previously uncultured bacteria from the phylloplane may have potential applications in phytoremediation and other plant-based biotechnologies.

CONCLUSIONS: This study gives first insights into the total bacterial community of the H. helix phylloplane, including an evaluation of its culturability using five different growth media. We further provide a collection of 200 bacterial isolates underrepresented in current databases, including the characterization of PGP profiles. Here we highlight the potential of simple strategies to obtain higher microbial diversity from environmental samples and the use of high-throughput sequencing to guide isolate selection from a variety of growth media.},
}

Bacteria/*classification/*genetics/isolation & purification
Biodegradation, Environmental
Culture Media/chemistry
Hedera/*growth & development/*microbiology
High-Throughput Nucleotide Sequencing
Metagenomics
*Microbiota
*Plant Development
Plant Leaves/microbiology
RNA, Ribosomal, 16S

@article {pmid33596852,
year = {2021},
author = {Straub, TJ and Chou, WC and Manson, AL and Schreiber, HL and Walker, BJ and Desjardins, CA and Chapman, SB and Kaspar, KL and Kahsai, OJ and Traylor, E and Dodson, KW and Hullar, MAJ and Hultgren, SJ and Khoo, C and Earl, AM},
title = {Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {53},
pmid = {33596852},
issn = {1471-2180},
support = {HHSN272200900018C/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U01 AI095542/AI/NIAID NIH HHS/United States ; R01 DK121822/DK/NIDDK NIH HHS/United States ; },
mesh = {Adult ; Bacteria/classification/*drug effects/genetics ; Beverages ; Double-Blind Method ; Feces/microbiology ; Female ; Gastrointestinal Microbiome/*drug effects/*genetics/physiology ; Humans ; Metagenome ; Metagenomics/methods ; Middle Aged ; Plant Extracts/*administration & dosage ; Reinfection/microbiology/prevention & control ; Urinary Tract Infections/microbiology/prevention & control ; Vaccinium macrocarpon/*chemistry ; },
abstract = {BACKGROUND: Urinary tract infections (UTIs) affect 15 million women each year in the United States, with > 20% experiencing frequent recurrent UTIs. A recent placebo-controlled clinical trial found a 39% reduction in UTI symptoms among recurrent UTI sufferers who consumed a daily cranberry beverage for 24 weeks. Using metagenomic sequencing of stool from a subset of these trial participants, we assessed the impact of cranberry consumption on the gut microbiota, a reservoir for UTI-causing pathogens such as Escherichia coli, which causes > 80% of UTIs.

RESULTS: The overall taxonomic composition, community diversity, carriage of functional pathways and gene families, and relative abundances of the vast majority of observed bacterial taxa, including E. coli, were not changed significantly by cranberry consumption. However, one unnamed Flavonifractor species (OTU41), which represented ≤1% of the overall metagenome, was significantly less abundant in cranberry consumers compared to placebo at trial completion. Given Flavonifractor's association with negative human health effects, we sought to determine OTU41 characteristic genes that may explain its differential abundance and/or relationship to key host functions. Using comparative genomic and metagenomic techniques, we identified genes in OTU41 related to transport and metabolism of various compounds, including tryptophan and cobalamin, which have been shown to play roles in host-microbe interactions.

CONCLUSION: While our results indicated that cranberry juice consumption had little impact on global measures of the microbiome, we found one unnamed Flavonifractor species differed significantly between study arms. This suggests further studies are needed to assess the role of cranberry consumption and Flavonifractor in health and wellbeing in the context of recurrent UTI.

TRIAL REGISTRATION: Clinical trial registration number: ClinicalTrials.gov NCT01776021 .},
}

Adult
Bacteria/classification/*drug effects/genetics
Beverages
Double-Blind Method
Feces/microbiology
Female
Gastrointestinal Microbiome/*drug effects/*genetics/physiology
Humans
Metagenome
Metagenomics/methods
Middle Aged
Plant Extracts/*administration & dosage
Reinfection/microbiology/prevention & control
Urinary Tract Infections/microbiology/prevention & control
Vaccinium macrocarpon/*chemistry

@article {pmid33547887,
year = {2021},
author = {Avitia, M and Barrón-Sandoval, A and Hernández-Terán, A and Benítez, M and A Barron-Gafford, G and Dontsova, K and A Pavao-Zuckerman, M and E Escalante, A},
title = {Soil microbial composition and carbon mineralization are associated with vegetation type and temperature regime in mesocosms of a semiarid ecosystem.},
journal = {FEMS microbiology letters},
volume = {368},
number = {4},
pages = {},
doi = {10.1093/femsle/fnab012},
pmid = {33547887},
issn = {1574-6968},
mesh = {Carbon/analysis/*metabolism ; *Ecosystem ; *Microbiota ; Plants/classification/metabolism/microbiology ; Soil/chemistry ; *Soil Microbiology ; Temperature ; },
abstract = {Transition from historic grasslands to woody plants in semiarid regions has led to questions about impacts on soil functioning, where microorganisms play a primary role. Understanding the relationship between microbes, plant diversity and soil functioning is relevant to assess such impacts. We evaluate the effect that plant type change in semiarid ecosystems has for microbial diversity and composition, and how this is related to carbon mineralization (CMIN) as a proxy for soil functioning. We followed a mesocosm experiment during 2 years within the Biosphere 2 facility in Oracle, AZ, USA. Two temperature regimes were established with two types of plants (grass or mesquite). Soil samples were analyzed for physicochemical and functional parameters, as well as microbial community composition using 16S rRNA amplicon metagenomics (Illumina MiSeq). Our results show the combined role of plant type and temperature regime in CMIN, where CMIN in grass has lower values at elevated temperatures compared with the opposite trend in mesquite. We also found a strong correlation of microbial composition with plant type but not with temperature regime. Overall, we provide evidence of the major effect of plant type in the specific composition of microbial communities as a potential result of the shrub encroachment.},
}

Carbon/analysis/*metabolism
*Ecosystem
*Microbiota
Plants/classification/metabolism/microbiology
Soil/chemistry
*Soil Microbiology
Temperature

@article {pmid33376062,
year = {2021},
author = {Brubaker, L and Luu, S and Hoffman, K and Wood, A and Navarro Cagigas, M and Yao, Q and Petrosino, J and Fisher, W and Van Buren, G},
title = {Microbiome changes associated with acute and chronic pancreatitis: A systematic review.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {21},
number = {1},
pages = {1-14},
pmid = {33376062},
issn = {1424-3911},
support = {T32 HL139425/HL/NHLBI NIH HHS/United States ; U01 DK108326/DK/NIDDK NIH HHS/United States ; },
mesh = {Gastrointestinal Microbiome/*physiology ; Humans ; Pancreatitis/metabolism/*microbiology ; Pancreatitis, Chronic/metabolism/microbiology ; },
abstract = {BACKGROUND: Altered intestinal microbiota has been reported in pancreatic disorders, however, it remains unclear whether these changes alter the course of disease in patients with acute (AP) and chronic pancreatitis (CP), or whether these disease states alter the environment to enable pathogenic microbial composition changes to occur. We undertook a systematic review to characterize the gut microbiome in pancreatitis patients.

METHODS: MEDLINE and EMBASE were searched for studies on microbiota in pancreatitis published from January 1, 2000 to June 5, 2020. Animal studies, reviews, case reports, and non-English articles were excluded. A frequency analysis was performed for outcomes reported in ≥2 studies and studies were analyzed for risk of bias and quality of evidence.

RESULTS: 22 papers met inclusion criteria; 15 included AP, 7 included CP. No studies were appropriately designed to assess whether alterations in the gut microbiome exacerbate pancreatitis or develop as a result of pancreatitis. We did identify several patterns of microbiome changes that are associated with pancreatitis. The gut microbiome demonstrated decreased alpha diversity in 3/3 A P studies and 3/3 C P studies. Beta diversity analysis revealed differences in bacterial community composition in the gut microbiome in 2/2 A P studies and 3/3 C P studies. Functionally, gut microbiome changes were associated with infectious pathways in AP and CP. Several studies suffered from high risk of bias and inadequate quality.

CONCLUSIONS: Detecting differences in microbial composition associated with AP and CP may represent a diagnostic tool. Appropriately controlled longitudinal studies are needed to determine whether microbiome changes are causative or reactive in pancreatitis.},
}

Gastrointestinal Microbiome/*physiology
Humans
Pancreatitis/metabolism/*microbiology
Pancreatitis, Chronic/metabolism/microbiology

@article {pmid34663463,
year = {2021},
author = {Trubl, G and Kimbrel, JA and Liquet-Gonzalez, J and Nuccio, EE and Weber, PK and Pett-Ridge, J and Jansson, JK and Waldrop, MP and Blazewicz, SJ},
title = {Active virus-host interactions at sub-freezing temperatures in Arctic peat soil.},
journal = {Microbiome},
volume = {9},
number = {1},
pages = {208},
pmid = {34663463},
issn = {2049-2618},
mesh = {Freezing ; *Microbiota ; *Soil ; Soil Microbiology ; Temperature ; },
abstract = {BACKGROUND: Winter carbon loss in northern ecosystems is estimated to be greater than the average growing season carbon uptake and is primarily driven by microbial decomposers. Viruses modulate microbial carbon cycling via induced mortality and metabolic controls, but it is unknown whether viruses are active under winter conditions (anoxic and sub-freezing temperatures).

RESULTS: We used stable isotope probing (SIP) targeted metagenomics to reveal the genomic potential of active soil microbial populations under simulated winter conditions, with an emphasis on viruses and virus-host dynamics. Arctic peat soils from the Bonanza Creek Long-Term Ecological Research site in Alaska were incubated under sub-freezing anoxic conditions with H218O or natural abundance water for 184 and 370 days. We sequenced 23 SIP-metagenomes and measured carbon dioxide (CO2) efflux throughout the experiment. We identified 46 bacterial populations (spanning 9 phyla) and 243 viral populations that actively took up 18O in soil and respired CO2 throughout the incubation. Active bacterial populations represented only a small portion of the detected microbial community and were capable of fermentation and organic matter degradation. In contrast, active viral populations represented a large portion of the detected viral community and one third were linked to active bacterial populations. We identified 86 auxiliary metabolic genes and other environmentally relevant genes. The majority of these genes were carried by active viral populations and had diverse functions such as carbon utilization and scavenging that could provide their host with a fitness advantage for utilizing much-needed carbon sources or acquiring essential nutrients.

CONCLUSIONS: Overall, there was a stark difference in the identity and function of the active bacterial and viral community compared to the unlabeled community that would have been overlooked with a non-targeted standard metagenomic analysis. Our results illustrate that substantial active virus-host interactions occur in sub-freezing anoxic conditions and highlight viruses as a major community-structuring agent that likely modulates carbon loss in peat soils during winter, which may be pivotal for understanding the future fate of arctic soils' vast carbon stocks. Video abstract.},
}

Freezing
*Microbiota
*Soil
Soil Microbiology
Temperature

@article {pmid34635053,
year = {2021},
author = {Bao, L and Zhang, C and Lyu, J and Yan, C and Cao, R and Pan, M and Li, Y},
title = {Beware of pharyngeal Fusobacterium nucleatum in COVID-19.},
journal = {BMC microbiology},
volume = {21},
number = {1},
pages = {277},
pmid = {34635053},
issn = {1471-2180},
mesh = {Adult ; Biomarkers/analysis ; COVID-19/*microbiology/virology ; Carrier State/microbiology ; Coinfection/microbiology/virology ; Dysbiosis ; Feces/*microbiology ; Female ; Fusobacterium Infections/*microbiology/virology ; Fusobacterium nucleatum/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenomics ; Microbiota ; Middle Aged ; Pharynx/*microbiology/virology ; Sex Factors ; },
abstract = {BACKGROUND: Fusobacterium nucleatum (F. n) is an important opportunistic pathogen causing oral and gastrointestinal disease. Faecalibacterium prausnitzii (F. p) is a next-generation probiotic and could serve as a biomarker of gut eubiosis/dysbiosis to some extent. Alterations in the human oral and gut microbiomes are associated with viral respiratory infection. The aim of this study was to characterise the oral and fecal bacterial biomarker (i.e., F. n and F. p) in COVID-19 patients by qPCR and investigate the pharyngeal microbiome of COVID-19 patients through metagenomic next-generation sequencing (mNGS).

RESULTS: Pharyngeal F. n was significantly increased in COVID-19 patients, and it was higher in male than female patients. Increased abundance of pharyngeal F. n was associated with a higher risk of a positive SARS-CoV-2 test (adjusted OR = 1.32, 95% CI = 1.06 ~ 1.65, P < 0.05). A classifier to distinguish COVID-19 patients from the healthy controls based on the pharyngeal F. n was constructed and achieved an area under the curve (AUC) of 0.843 (95% CI = 0.688 ~ 0.940, P < 0.001). However, the level of fecal F. n and fecal F. p remained unaltered between groups. Besides, mNGS showed that the pharyngeal swabs of COVID-19 patients were dominated by opportunistic pathogens.

CONCLUSIONS: Pharyngeal but not fecal F. n was significantly increased in COVID-19 patients, clinicians should pay careful attention to potential coinfection. Pharyngeal F. n may serve as a promising candidate indicator for COVID-19.},
}

Adult
Biomarkers/analysis
COVID-19/*microbiology/virology
Carrier State/microbiology
Coinfection/microbiology/virology
Dysbiosis
Feces/*microbiology
Female
Fusobacterium Infections/*microbiology/virology
Fusobacterium nucleatum/*genetics
High-Throughput Nucleotide Sequencing
Humans
Male
Metagenomics
Microbiota
Middle Aged
Pharynx/*microbiology/virology
Sex Factors

@article {pmid34621696,
year = {2021},
author = {Belstrøm, D and Constancias, F and Markvart, M and Sikora, M and Sørensen, CE and Givskov, M},
title = {Transcriptional Activity of Predominant Streptococcus Species at Multiple Oral Sites Associate With Periodontal Status.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {752664},
pmid = {34621696},
issn = {2235-2988},
mesh = {Humans ; Metagenome ; Metagenomics ; *Microbiota ; Saliva ; Streptococcus/genetics ; },
abstract = {Background: Streptococcus species are predominant members of the oral microbiota in both health and diseased conditions. The purpose of the present study was to explore if different ecological characteristics, such as oxygen availability and presence of periodontitis, associates with transcriptional activity of predominant members of genus Streptococcus. We tested the hypothesis that genetically closely related Streptococcus species express different transcriptional activities in samples collected from environments with critically different ecological conditions determined by site and inflammatory status.

Methods: Metagenomic and metatranscriptomic data was retrieved from 66 oral samples, subgingival plaque (n=22), tongue scrapings (n=22) and stimulated saliva (n=22) collected from patients with periodontitis (n=11) and orally healthy individuals (n=11). Species-specific transcriptional activity was computed as Log2(RNA/DNA), and transcriptional activity of predominant Streptococcus species was compared between multiple samples collected from different sites in the same individual, and between individuals with different oral health status.

Results: The predominant Streptococcus species were identified with a site-specific colonization pattern of the tongue and the subgingival plaque. A total of 11, 4 and 2 pathways expressed by S. parasanguinis, S. infantis and S. salivarius, respectively, were recorded with significantly higher transcriptional activity in saliva than in tongue biofilm in healthy individuals. In addition, 18 pathways, including pathways involved in synthesis of peptidoglycan, amino acid biosynthesis, glycolysis and purine nucleotide biosynthesis expressed by S. parasanguinis and 3 pathways expressed by S. salivarius were identified with significantly less transcriptional activity in patients with periodontitis.

Conclusion: Data from the present study significantly demonstrates the association of site-specific ecological conditions and presence of periodontitis with transcriptional activity of the predominant Streptococcus species of the oral microbiota. In particular, pathways expressed by S. parasanguinis being involved in peptidoglycan, amino acid biosynthesis, glycolysis, and purine nucleotide biosynthesis were identified to be significantly associated with oral site and/or inflammation status.},
}

Humans
Metagenome
Metagenomics
*Microbiota
Saliva
Streptococcus/genetics

@article {pmid34589441,
year = {2021},
author = {Ding, L and Liu, Y and Wu, X and Wu, M and Luo, X and Ouyang, H and Xia, J and Liu, X and Ding, T},
title = {Pathogen Metagenomics Reveals Distinct Lung Microbiota Signatures Between Bacteriologically Confirmed and Negative Tuberculosis Patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {708827},
pmid = {34589441},
issn = {2235-2988},
mesh = {Ascomycota ; Bronchoalveolar Lavage Fluid ; Haemophilus parainfluenzae ; Humans ; Kluyveromyces ; Lung ; Metagenomics ; *Microbiota ; *Mycobacterium tuberculosis/genetics ; Staphylococcus aureus ; *Tuberculosis/microbiology ; },
abstract = {Understanding the dynamics of lung microbiota in tuberculosis patients, especially those who cannot be confirmed bacteriologically in clinical practice, is imperative for accurate diagnosis and effective treatment. This study aims to characterize the distinct lung microbial features between bacteriologically confirmed and negative tuberculosis patients to understand the influence of microbiota on tuberculosis patients. We collected specimens of bronchoalveolar lavage fluid from 123 tuberculosis patients. Samples were subjected to metagenomic next-generation sequencing to reveal the lung microbial signatures. By combining conventional bacterial detection and metagenomic sequencing, 101/123 (82%) tuberculosis patients were bacteriologically confirmed. In addition to Mycobacterium tuberculosis, Staphylococcus aureus, Kluyveromyces lactis, and Pyricularia pennisetigena were also enriched in the bacteriological confirmation group. In contrast, Haemophilus parainfluenzae was enriched in the bacteriologically negative group. Besides, microbial interaction exhibits a different state between bacteriologically confirmed and negative tuberculosis patients. Mycobacterium tuberculosis was confirmed correlated with clinical characteristics such as albumin and chest cavities. Our study comprehensively demonstrates the correlation between unique features of lung microbial dynamics and the clinical characteristics of tuberculosis patients, suggesting the importance of studying the pulmonary microbiome in tuberculosis disease and providing new insights for future precision diagnosis and treatment.},
}

Ascomycota
Bronchoalveolar Lavage Fluid
Haemophilus parainfluenzae
Humans
Kluyveromyces
Lung
Metagenomics
*Microbiota
*Mycobacterium tuberculosis/genetics
Staphylococcus aureus
*Tuberculosis/microbiology

@article {pmid34568090,
year = {2021},
author = {Yu, J and Zhang, H and Chen, L and Ruan, Y and Chen, Y and Liu, Q},
title = {Disease-Associated Gut Microbiota Reduces the Profile of Secondary Bile Acids in Pediatric Nonalcoholic Fatty Liver Disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {698852},
pmid = {34568090},
issn = {2235-2988},
mesh = {Bile Acids and Salts ; Child ; Chromatography, Liquid ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease ; Tandem Mass Spectrometry ; },
abstract = {Children with nonalcoholic fatty liver disease (NAFLD) display an altered gut microbiota compared with healthy children. However, little is known about the fecal bile acid profiles and their association with gut microbiota dysbiosis in pediatric NAFLD. A total of 68 children were enrolled in this study, including 32 NAFLD patients and 36 healthy children. Fecal samples were collected and analyzed by metagenomic sequencing to determine the changes in the gut microbiota of children with NAFLD, and an ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) system was used to quantify the concentrations of primary and secondary bile acids. The associations between the gut microbiota and concentrations of primary and secondary bile acids in the fecal samples were then analyzed. We found that children with NAFLD exhibited reduced levels of secondary bile acids and alterations in bile acid biotransforming-related bacteria in the feces. Notably, the decrease in Eubacterium and Ruminococcaceae bacteria, which express bile salt hydrolase and 7α-dehydroxylase, was significantly positively correlated with the level of fecal lithocholic acid (LCA). However, the level of fecal LCA was negatively associated with the abundance of the potential pathogen Escherichia coli that was enriched in children with NAFLD. Pediatric NAFLD is characterized by an altered profile of gut microbiota and fecal bile acids. This study demonstrates that the disease-associated gut microbiota is linked with decreased concentrations of secondary bile acids in the feces. The disease-associated gut microbiota likely inhibits the conversion of primary to secondary bile acids.},
}

Bile Acids and Salts
Child
Chromatography, Liquid
Feces
*Gastrointestinal Microbiome
Humans
*Non-alcoholic Fatty Liver Disease
Tandem Mass Spectrometry

@article {pmid34568084,
year = {2021},
author = {Oh, KY and Lee, S and Lee, MS and Lee, MJ and Shim, E and Hwang, YH and Ha, JG and Yang, YS and Hwang, IT and Park, JS},
title = {Composition of Vaginal Microbiota in Pregnant Women With Aerobic Vaginitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {677648},
pmid = {34568084},
issn = {2235-2988},
mesh = {Case-Control Studies ; Dysbiosis ; Female ; Humans ; *Microbiota ; Pregnancy ; Pregnant Women ; Vagina ; *Vaginitis ; },
abstract = {Vaginal dysbiosis, such as bacterial vaginosis (BV) and aerobic vaginitis (AV), is an important cause of premature birth in pregnant women. However, there is very little research on vaginal microbial distribution in AV compared to that in BV. This study aimed to analyze the composition of the vaginal microbiota of pregnant women with AV using microbial community analysis and identify the causative organism using each criterion of the AV scoring system. Also, we compared the quantification of aerobic bacteria using quantitative polymerase chain reaction (qPCR) and their relative abundances (RA) using metagenomics. This prospective case-control study included 228 pregnant Korean women from our previous study. A wet mount test was conducted on 159 women to diagnose AV using the AV scoring system. Vaginal samples were analyzed using metagenomics, Gram staining for Nugent score determination, conventional culture, and qPCR for Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae. The relative abundances (RAs) of eleven species showed significant differences among the three groups (Normal flora (NF), mild AV, and moderate AV). Three species including Lactobacillus crispatus were significantly lower in the AV groups than in the NF group, while eight species were higher in the AV groups, particularly moderate AV. The decrease in the RA of L. crispatus was common in three criteria of the AV scoring system (Lactobacillary, WBC, and background flora grades), while it did not show a significant difference among the three grade groups of the toxic leukocyte criterion. Also, the RAs of anaerobes, such as Gardnerella and Megasphaera, were higher in the AV groups, particularly moderate AV, while the RAs of aerobes were very low (RA < 0.01). Therefore, qPCR was performed for aerobes (Staphylococcus spp., Streptococcus spp., and Enterobacteriaceae); however, their quantification did not show a higher level in the AV groups when compared to that in the NF group. Therefore, AV might be affected by the RA of Lactobacillus spp. and the main anaerobes, such as Gardnerella spp. Activation of leukocytes under specific conditions might convert them to toxic leukocytes, despite high levels of L. crispatus. Thus, the pathogenesis of AV can be evaluated under such conditions.},
}

Case-Control Studies
Dysbiosis
Female
Humans
*Microbiota
Pregnancy
Pregnant Women
Vagina
*Vaginitis

@article {pmid34507779,
year = {2021},
author = {Jia, Y and Niu, CT and Xu, X and Zheng, FY and Liu, CF and Wang, JJ and Lu, ZM and Xu, ZH and Li, Q},
title = {Metabolic potential of microbial community and distribution mechanism of Staphylococcus species during broad bean paste fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {148},
number = {},
pages = {110533},
doi = {10.1016/j.foodres.2021.110533},
pmid = {34507779},
issn = {1873-7145},
mesh = {Fermentation ; *Fermented Foods and Beverages ; *Microbiota ; Staphylococcus ; *Vicia faba ; },
abstract = {Although the microbial diversity and structure in bean-based fermented foods have been widely studied, systematic studies on functional microbiota and mechanism of community forms in multi-microbial fermentation systems were still lacking. In this work, the metabolic pathway and functional potential of microbial community in broad bean paste (BBP) were investigated by metagenomics approach, and Staphylococcus, Bacillus, Weissella, Aspergillus and Zygosaccharomyces were found to be the potential predominant populations responsible for substrate alteration and flavor biosynthesis. Among them, Staphylococcus was the most abundant and widespread functional microbe, and closely related Staphylococcus species were diverse and ubiquitously distributed, with the opportunistic pathogen S. gallinarum being the most abundant Staphylococcus specie isolated from BBP. To explain the dominance status of S. gallinarum and species distributions of Staphylococcus genus, we tested the effects of abiotic and biotic factors on three Staphylococcus species using a tractable BBP model, demonstrating that adaptation to environmental conditions (environmental parameters and other functional microbes) led to the dominant position and species coexistence of Staphylococcus, and congeneric competition among Staphylococcus species further shaped ecological distributions of closely related Staphylococcus species. In general, this work revealed the metabolic potential of microbial community and distribution mechanism of Staphylococcus species during BBP fermentation, which could help traditional factories to more precisely control the safety and quality of bean-based fermented foods.},
}

Fermentation
*Fermented Foods and Beverages
*Microbiota
Staphylococcus
*Vicia faba

@article {pmid34507766,
year = {2021},
author = {Liu, D and Zhang, C and Zhang, J and Xin, X and Liao, X},
title = {Metagenomics reveals the formation mechanism of flavor metabolites during the spontaneous fermentation of potherb mustard (Brassica juncea var. multiceps).},
journal = {Food research international (Ottawa, Ont.)},
volume = {148},
number = {},
pages = {110622},
doi = {10.1016/j.foodres.2021.110622},
pmid = {34507766},
issn = {1873-7145},
mesh = {Fermentation ; *Lactobacillales/genetics ; Metagenomics ; *Microbiota ; Mustard Plant/genetics ; },
abstract = {Fermented vegetable flavors are closely associated with microbial metabolism. Here, shifts in flavor metabolites and their correlations to the structure and function of fermentative microbial communities were explored during the spontaneous fermentation process of potherb mustard (Brassica juncea var. multiceps), a traditionally fermented vegetable from China. Halophilic bacteria (HAB, i.e., Halomonas, Salinivibrio, and Vibrio) and lactic acid bacteria (LAB, i.e., Lactobacillus-related genera and Weissella) became highly abundant after potherb mustard fermentation. Further, HAB and LAB abundances exhibited significant, positive correlations with metabolites important in fermented potherb mustard flavoring (e.g., organic acids, amino acids, alcohols, aldehydes, and nitriles). Metagenomic analysis indicated that Halomonas, Salinivibrio, Weissella, and Lactobacillus-related genera were likely actively engaged in pyruvate metabolism (ko00620) and citrate cycle (TCA cycle, ko00020), leading to higher lactic and acetic acid concentrations, along with lower pH, which would affect levels of volatile isothiocyanates and nitriles that contribute to flavoring of fermented potherb mustard. Further, HAB and LAB were the primary populations inferred to be responsible for amino acid and fatty acid metabolism in addition to the biosynthesis of numerous volatile flavor compounds. This study highlights the predominance and importance of LAB and HAB during spontaneous fermentation of potherb mustard and provides new insights into their roles in this process.},
}

Fermentation
*Lactobacillales/genetics
Metagenomics
*Microbiota
Mustard Plant/genetics

@article {pmid34490138,
year = {2021},
author = {Lyu, X and Zheng, H and Wang, X and Zhang, H and Gao, L and Xun, Z and Zhang, Q and He, X and Hua, H and Yan, Z and Chen, F},
title = {Oral Microbiota Composition and Function Changes During Chronic Erythematous Candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {11},
number = {},
pages = {691092},
pmid = {34490138},
issn = {2235-2988},
mesh = {*Candidiasis, Oral ; Humans ; Metagenomics ; *Microbiota ; *Micrococcaceae ; },
abstract = {Oral microbiota is constantly changing with the host state, whereas the oral microbiome of chronic erythematous candidiasis remains poorly understood. The aim of this study was to compare oral microbial signatures and functional profiling between chronic erythematous candidiasis and healthy subjects. Using shotgun metagenomic sequencing, we analyzed the microbiome in 12 chronic erythematous candidiasis, 12 healthy subjects, and 2 chronic erythematous candidiasis cured by antifungal therapy. We found that the salivary microbiota of chronic erythematous candidiasis was significantly different from that of healthy subjects. Among them, Rothia mucilaginosa and Streptococcus mitis were the most abundant disease-enriched species (Mann-Whitney U-test, P < 0.05). In addition, co-occurrence network analysis showed that C. albicans formed densely connected modules with oral bacterial species and was mainly positive connected to Streptococcus species. Furthermore, we investigated the functional potentials of the microbiome and identified a set of microbial marker genes associated with chronic erythematous candidiasis. Some of these genes enriching in chronic erythematous candidiasis are involved in eukaryotic ribosome, putative glutamine transport system, and cytochrome bc1 complex respiratory unit. Altogether, this study revealed the changes of oral microbial composition, the co-occurrence between C. albicans and oral bacteria, as well as the changes of microbial marker genes during chronic erythematous candidiasis, which provides evidence of oral microbiome as a target for the treatment and prevention of chronic erythematous candidiasis.},
}

*Candidiasis, Oral
Humans
Metagenomics
*Microbiota
*Micrococcaceae

@article {pmid34481302,
year = {2021},
author = {Aguinaga, OE and White, KN and Dean, AP and Pittman, JK},
title = {Addition of organic acids to acid mine drainage polluted wetland sediment leads to microbial community structure and functional changes and improved water quality.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {290},
number = {},
pages = {118064},
doi = {10.1016/j.envpol.2021.118064},
pmid = {34481302},
issn = {1873-6424},
mesh = {Acids ; *Microbiota ; Mining ; Water Quality ; *Wetlands ; },
abstract = {Acid mine drainage (AMD) is a serious environmental problem worldwide that requires efficient and sustainable remediation technologies including the use of biological mechanisms. A key challenge for AMD bioremediation is to provide optimal conditions for microbial-mediated immobilisation of trace metals. Although organic carbon and oxygen can enhance treatment efficiency, the effect on microbial communities is unclear. In this study, surface sediments from a natural wetland with proven efficiency for AMD bioremediation were artificially exposed to oxygen (by aeration) and/or organic carbon (in the form of mixed organic acids) and incubated under laboratory conditions. In addition to measuring changes in water chemistry, a metagenomics approach was used to determine changes in sediment bacterial, archaeal and fungal community structure, and functional gene abundance. The addition of organic carbon produced major changes in the abundance of microorganisms related to iron and sulfur metabolism (including Geobacter and Pelobacter) and increased levels of particulate metals via sulfate reduction. Aeration resulted in an increase in Sideroxydans abundance but no significant changes in metal chemistry were observed. The study concludes that the utilisation of organic carbon by microorganisms is more important for achieving efficient AMD treatment than the availability of oxygen, yet the combination of oxygen with organic carbon addition did not inhibit the improvements to water quality.},
}

Acids
*Microbiota
Mining
Water Quality
*Wetlands

@article {pmid34407780,
year = {2021},
author = {Kværner, AS and Birkeland, E and Bucher-Johannessen, C and Vinberg, E and Nordby, JI and Kangas, H and Bemanian, V and Ellonen, P and Botteri, E and Natvig, E and Rognes, T and Hovig, E and Lyle, R and Ambur, OH and de Vos, WM and Bultman, S and Hjartåker, A and Landberg, R and Song, M and Blix, HS and Ursin, G and Randel, KR and de Lange, T and Hoff, G and Holme, Ø and Berstad, P and Rounge, TB},
title = {The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants.},
journal = {BMC cancer},
volume = {21},
number = {1},
pages = {930},
pmid = {34407780},
issn = {1471-2407},
mesh = {Aged ; Case-Control Studies ; Colonoscopy ; Colorectal Neoplasms/*diagnosis/epidemiology/microbiology ; Early Detection of Cancer/*methods ; Female ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Humans ; Incidence ; *Life Style ; Male ; Middle Aged ; Norway/epidemiology ; Occult Blood ; Prognosis ; Prospective Studies ; ROC Curve ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions.

METHODS: The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50-74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period.

DISCUSSION: The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01538550 .},
}

Aged
Case-Control Studies
Colonoscopy
Colorectal Neoplasms/*diagnosis/epidemiology/microbiology
Early Detection of Cancer/*methods
Female
Follow-Up Studies
*Gastrointestinal Microbiome
Humans
Incidence
*Life Style
Male
Middle Aged
Norway/epidemiology
Occult Blood
Prognosis
Prospective Studies
ROC Curve

@article {pmid34367134,
year = {2021},
author = {Hetemäki, I and Jian, C and Laakso, S and Mäkitie, O and Pajari, AM and de Vos, WM and Arstila, TP and Salonen, A},
title = {Fecal Bacteria Implicated in Biofilm Production Are Enriched and Associate to Gastrointestinal Symptoms in Patients With APECED - A Pilot Study.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {668219},
pmid = {34367134},
issn = {1664-3224},
mesh = {Adult ; Aged ; Antibodies, Fungal/metabolism ; Bacteria/genetics/*growth & development/immunology/metabolism ; Biofilms/*growth & development ; Case-Control Studies ; Dysbiosis ; Feces/*microbiology ; Female ; Finland ; Gastrointestinal Diseases/diagnosis/immunology/metabolism/*microbiology ; *Gastrointestinal Microbiome ; Genetic Predisposition to Disease ; Host-Pathogen Interactions ; Humans ; Immunoglobulin G/metabolism ; Intestines/*microbiology ; Lipopolysaccharides/metabolism ; Male ; Metagenome ; Middle Aged ; *Mutation ; Pilot Projects ; Polyendocrinopathies, Autoimmune/complications/diagnosis/genetics/immunology ; Saccharomyces cerevisiae/genetics/immunology ; Transcription Factors/*genetics ; Young Adult ; },
abstract = {Backgrounds and Aims: APECED is a rare autoimmune disease caused by mutations in the Autoimmune Regulator gene. A significant proportion of patients also have gastrointestinal symptoms, including malabsorption, chronic diarrhea, and obstipation. The pathological background of the gastrointestinal symptoms remains incompletely understood and involves multiple factors, with autoimmunity being the most common underlying cause. Patients with APECED have increased immune responses against gut commensals. Our objective was to evaluate whether the intestinal microbiota composition, predicted functions or fungal abundance differ between Finnish patients with APECED and healthy controls, and whether these associate to the patients' clinical phenotype and gastrointestinal symptoms.

Methods: DNA was isolated from fecal samples from 15 patients with APECED (median age 46.4 years) together with 15 samples from body mass index matched healthy controls. DNA samples were subjected to analysis of the gut microbiota using 16S rRNA gene amplicon sequencing, imputed metagenomics using the PICRUSt2 algorithm, and quantitative PCR for fungi. Extensive correlations of the microbiota with patient characteristics were determined.

Results: Analysis of gut microbiota indicated that both alpha- and beta-diversity were altered in patients with APECED compared to healthy controls. The fraction of Faecalibacterium was reduced in patients with APECED while that of Atopobium spp. and several gram-negative genera previously implicated in biofilm formation, e.g. Veillonella, Prevotella, Megasphaera and Heamophilus, were increased in parallel to lipopolysaccharide (LPS) synthesis in imputed metagenomics. The differences in gut microbiota were linked to patient characteristics, especially the presence of anti-Saccharomyces cerevisiae antibodies (ASCA) and severity of gastrointestinal symptoms.

Conclusions: Gut microbiota of patients with APECED is altered and enriched with predominantly gram-negative bacterial taxa that may promote biofilm formation and lead to increased exposure to LPS in the patients. The most pronounced alterations in the microbiota were associated with more severe gastrointestinal symptoms.},
}

Adult
Aged
Antibodies, Fungal/metabolism
Bacteria/genetics/*growth & development/immunology/metabolism
Biofilms/*growth & development
Case-Control Studies
Dysbiosis
Feces/*microbiology
Female
Finland
Gastrointestinal Diseases/diagnosis/immunology/metabolism/*microbiology
*Gastrointestinal Microbiome
Genetic Predisposition to Disease
Host-Pathogen Interactions
Humans
Immunoglobulin G/metabolism
Intestines/*microbiology
Lipopolysaccharides/metabolism
Male
Metagenome
Middle Aged
*Mutation
Pilot Projects
Polyendocrinopathies, Autoimmune/complications/diagnosis/genetics/immunology
Saccharomyces cerevisiae/genetics/immunology
Transcription Factors/*genetics
Young Adult

@article {pmid34216067,
year = {2021},
author = {Kwon, MJ and Tripathi, BM and Göckede, M and Shin, SC and Myeong, NR and Lee, YK and Kim, M},
title = {Disproportionate microbial responses to decadal drainage on a Siberian floodplain.},
journal = {Global change biology},
volume = {27},
number = {20},
pages = {5124-5140},
doi = {10.1111/gcb.15785},
pmid = {34216067},
issn = {1365-2486},
mesh = {Carbon Cycle ; Carbon Dioxide/analysis ; Methane ; *Microbiota ; *Permafrost ; Soil ; },
abstract = {Permafrost thaw induces soil hydrological changes which in turn affects carbon cycle processes in the Arctic terrestrial ecosystems. However, hydrological impacts of thawing permafrost on microbial processes and greenhouse gas (GHG) dynamics are poorly understood. This study examined changes in microbial communities using gene and genome-centric metagenomics on an Arctic floodplain subject to decadal drainage, and linked them to CO2 and CH4 flux and soil chemistry. Decadal drainage led to significant changes in the abundance, taxonomy, and functional potential of microbial communities, and these modifications well explained the changes in CO2 and CH4 fluxes between ecosystem and atmosphere-increased fungal abundances potentially increased net CO2 emission rates and highly reduced CH4 emissions in drained sites corroborated the marked decrease in the abundance of methanogens and methanotrophs. Interestingly, various microbial taxa disproportionately responded to drainage: Methanoregula, one of the key players in methanogenesis under saturated conditions, almost disappeared, and also Methylococcales methanotrophs were markedly reduced in response to drainage. Seven novel methanogen population genomes were recovered, and the metabolic reconstruction of highly correlated population genomes revealed novel syntrophic relationships between methanogenic archaea and syntrophic partners. These results provide a mechanistic view of microbial processes regulating GHG dynamics in the terrestrial carbon cycle, and disproportionate microbial responses to long-term drainage provide key information for understanding the effects of warming-induced soil drying on microbial processes in Arctic wetland ecosystems.},
}

Carbon Cycle
Carbon Dioxide/analysis
Methane
*Microbiota
*Permafrost
Soil

@article {pmid34143768,
year = {2021},
author = {Prost, V and Gazut, S and Brüls, T},
title = {A zero inflated log-normal model for inference of sparse microbial association networks.},
journal = {PLoS computational biology},
volume = {17},
number = {6},
pages = {e1009089},
pmid = {34143768},
issn = {1553-7358},
mesh = {Algorithms ; Computational Biology ; Computer Simulation ; Metagenome ; Metagenomics/statistics & numerical data ; Microbial Consortia/genetics/physiology ; *Microbiota/genetics/physiology ; *Models, Biological ; Multivariate Analysis ; Normal Distribution ; Synthetic Biology ; },
abstract = {The advent of high-throughput metagenomic sequencing has prompted the development of efficient taxonomic profiling methods allowing to measure the presence, abundance and phylogeny of organisms in a wide range of environmental samples. Multivariate sequence-derived abundance data further has the potential to enable inference of ecological associations between microbial populations, but several technical issues need to be accounted for, like the compositional nature of the data, its extreme sparsity and overdispersion, as well as the frequent need to operate in under-determined regimes. The ecological network reconstruction problem is frequently cast into the paradigm of Gaussian Graphical Models (GGMs) for which efficient structure inference algorithms are available, like the graphical lasso and neighborhood selection. Unfortunately, GGMs or variants thereof can not properly account for the extremely sparse patterns occurring in real-world metagenomic taxonomic profiles. In particular, structural zeros (as opposed to sampling zeros) corresponding to true absences of biological signals fail to be properly handled by most statistical methods. We present here a zero-inflated log-normal graphical model (available at https://github.com/vincentprost/Zi-LN) specifically aimed at handling such "biological" zeros, and demonstrate significant performance gains over state-of-the-art statistical methods for the inference of microbial association networks, with most notable gains obtained when analyzing taxonomic profiles displaying sparsity levels on par with real-world metagenomic datasets.},
}

Algorithms
Computational Biology
Computer Simulation
Metagenome
Metagenomics/statistics & numerical data
Microbial Consortia/genetics/physiology
*Microbiota/genetics/physiology
*Models, Biological
Multivariate Analysis
Normal Distribution
Synthetic Biology

@article {pmid34085924,
year = {2021},
author = {Hughes, ER and Winter, MG and Alves da Silva, L and Muramatsu, MK and Jimenez, AG and Gillis, CC and Spiga, L and Chanin, RB and Santos, RL and Zhu, W and Winter, SE},
title = {Reshaping of bacterial molecular hydrogen metabolism contributes to the outgrowth of commensal E. coli during gut inflammation.},
journal = {eLife},
volume = {10},
number = {},
pages = {},
pmid = {34085924},
issn = {2050-084X},
support = {R01 AI118807/AI/NIAID NIH HHS/United States ; R21 AI128151/AI/NIAID NIH HHS/United States ; T32 AI007520/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Cecum/metabolism/*microbiology/pathology ; Colitis/*chemically induced/metabolism/*microbiology/pathology ; Colon/metabolism/*microbiology/pathology ; Databases, Genetic ; Dextran Sulfate ; Disease Models, Animal ; Dysbiosis ; Escherichia coli/genetics/growth & development/*metabolism ; Escherichia coli Infections/metabolism/*microbiology/pathology ; Escherichia coli Proteins/genetics/metabolism ; Female ; *Gastrointestinal Microbiome ; Humans ; Hydrogen/*metabolism ; Hydrogenase/genetics/metabolism ; Interleukin-10/genetics/metabolism ; Male ; Metagenome ; Metagenomics ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; Mice, Knockout ; Piroxicam ; },
abstract = {The composition of gut-associated microbial communities changes during intestinal inflammation, including an expansion of Enterobacteriaceae populations. The mechanisms underlying microbiota changes during inflammation are incompletely understood. Here, we analyzed previously published metagenomic datasets with a focus on microbial hydrogen metabolism. The bacterial genomes in the inflamed murine gut and in patients with inflammatory bowel disease contained more genes encoding predicted hydrogen-utilizing hydrogenases compared to communities found under non-inflamed conditions. To validate these findings, we investigated hydrogen metabolism of Escherichia coli, a representative Enterobacteriaceae, in mouse models of colitis. E. coli mutants lacking hydrogenase-1 and hydrogenase-2 displayed decreased fitness during colonization of the inflamed cecum and colon. Utilization of molecular hydrogen was in part dependent on respiration of inflammation-derived electron acceptors. This work highlights the contribution of hydrogenases to alterations of the gut microbiota in the context of non-infectious colitis.},
}

Animals
Cecum/metabolism/*microbiology/pathology
Colitis/*chemically induced/metabolism/*microbiology/pathology
Colon/metabolism/*microbiology/pathology
Databases, Genetic
Dextran Sulfate
Disease Models, Animal
Dysbiosis
Escherichia coli/genetics/growth & development/*metabolism
Escherichia coli Infections/metabolism/*microbiology/pathology
Escherichia coli Proteins/genetics/metabolism
Female
*Gastrointestinal Microbiome
Humans
Hydrogen/*metabolism
Hydrogenase/genetics/metabolism
Interleukin-10/genetics/metabolism
Male
Metagenome
Metagenomics
Mice, Inbred BALB C
Mice, Inbred C57BL
Mice, Knockout
Piroxicam

@article {pmid33995413,
year = {2021},
author = {Alam, MS and Gangiredla, J and Hasan, NA and Barnaba, T and Tartera, C},
title = {Aging-Induced Dysbiosis of Gut Microbiota as a Risk Factor for Increased Listeria monocytogenes Infection.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {672353},
pmid = {33995413},
issn = {1664-3224},
mesh = {Aging/*physiology ; Animals ; Dysbiosis/*microbiology ; Female ; Gastrointestinal Microbiome/*physiology ; Listeria monocytogenes ; Listeriosis/*microbiology ; Mice ; Mice, Inbred C57BL ; Risk Factors ; },
abstract = {Invasive foodborne Listeria monocytogenes infection causes gastroenteritis, septicemia, meningitis, and chorioamnionitis, and is associated with high case-fatality rates in the elderly. It is unclear how aging alters gut microbiota, increases risk of listeriosis, and causes dysbiosis post-infection. We used a geriatric murine model of listeriosis as human surrogate of listeriosis for aging individuals to study the effect of aging and L. monocytogenes infection. Aging and listeriosis-induced perturbation of gut microbiota and disease severity were compared between young-adult and old mice. Young-adult and old mice were dosed intragastrically with L. monocytogenes. Fecal pellets were collected pre- and post-infection for microbiome analysis. Infected old mice had higher Listeria colonization in liver, spleen, and feces. Metagenomics analyses of fecal DNA-sequences showed increase in α-diversity as mice aged, and infection reduced its diversity. The relative abundance of major bacterial phylum like, Bacteroidetes and Firmicutes remained stable over aging or infection, while the Verrucomicrobia phylum was significantly reduced only in infected old mice. Old mice showed a marked reduction in Clostridaiceae and Lactobacillaceae bacteria even before infection when compared to uninfected young-adult mice. L. monocytogenes infection increased the abundance of Porphyromonadaceae and Prevotellaceae in young-adult mice, while members of the Ruminococcaceae and Lachnospiraceae family were significantly increased in old mice. The abundance of the genera Blautia and Alistipes were significantly reduced post-infection in young-adult and in old mice as compared to their uninfected counterparts. Butyrate producing, immune-modulating bacterial species, like Pseudoflavonifractor and Faecalibacterium were significantly increased only in old infected mice, correlating with increased intestinal inflammatory mRNA up-regulation from old mice tissue. Histologic analyses of gastric tissues showed extensive lesions in the Listeria-infected old mice, more so in the non-glandular region and fundus than in the pylorus. Commensal species like Lactobacillus, Clostridiales, and Akkermansia were only abundant in infected young-adult mice but their abundance diminished in the infected old mice. Listeriosis in old mice enhances the abundance of butyrate-producing inflammatory members of the Ruminococcaceae/Lachnospiraceae bacteria while reducing/eliminating beneficial commensals in the gut. Results of this study indicate that, aging may affect the composition of gut microbiota and increase the risk of invasive L. monocytogenes infection.},
}

Aging/*physiology
Animals
Dysbiosis/*microbiology
Female
Gastrointestinal Microbiome/*physiology
Listeria monocytogenes
Listeriosis/*microbiology
Mice
Mice, Inbred C57BL
Risk Factors

@article {pmid33956889,
year = {2021},
author = {Thapa, S and Venkatachalam, A and Khan, N and Naqvi, M and Balderas, M and Runge, JK and Haag, A and Hoch, KM and Glaze, DG and Luna, RA and Motil, KJ},
title = {Assessment of the gut bacterial microbiome and metabolome of girls and women with Rett Syndrome.},
journal = {PloS one},
volume = {16},
number = {5},
pages = {e0251231},
pmid = {33956889},
issn = {1932-6203},
mesh = {Adolescent ; Adult ; Child ; Child, Preschool ; Feces/chemistry/microbiology ; Female ; Gas Chromatography-Mass Spectrometry ; Gastrointestinal Diseases/etiology/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Metabolome ; Phenotype ; RNA, Ribosomal, 16S/genetics ; Rett Syndrome/complications/metabolism/*microbiology ; Sequence Analysis, DNA ; Severity of Illness Index ; Young Adult ; },
abstract = {BACKGROUND: Gastrointestinal problems affect the health and quality of life of individuals with Rett syndrome (RTT) and pose a medical hardship for their caregivers. We hypothesized that the variability in the RTT phenotype contributes to the dysbiosis of the gut microbiome and metabolome in RTT, predisposing these individuals to gastrointestinal dysfunction.

OBJECTIVES: We characterized the gut bacterial microbiome and metabolome in girls and young women with RTT (n = 44) and unaffected controls (n = 21), and examined the relation between the composition of the microbiome and variations in the RTT phenotype.

METHODS: Demographics and clinical information, including growth and anthropometric measurements, pubertal status, symptoms, clinical severity score, bowel movement, medication use, and dietary intakes were collected from the participants. Fecal samples were collected for analysis of the gut microbiome using Illumina MiSeq-based next-generation sequencing of the 16S rRNA gene followed by bioinformatics analysis of microbial composition, diversity, and community structure. Selected end-products of microbial protein metabolism were characterized by liquid chromatography-mass spectrometry.

RESULTS: The gut bacterial microbiome differed within the RTT cohort based on pubertal status (p<0.02) and clinical severity scores (p<0.02) of the individuals and the type of diet (p<0.01) consumed. Although the composition of the gut microbiome did not differ between RTT and unaffected individuals, concentrations of protein end-products of the gut bacterial metabolome, including γ-aminobutyric acid (GABA) (p<0.001), tyrosine (p<0.02), and glutamate (p<0.06), were lower in the RTT cohort. Differences in the microbiome within RTT groups, based on symptomatic anxiety, hyperventilation, abdominal distention, or changes in stool frequency and consistency, were not detected.

CONCLUSIONS: Although variability in the RTT phenotype contributes to the dysbiosis of the gut microbiome, we presently cannot infer causality between gut bacterial dysbiosis and gastrointestinal dysfunction. Nevertheless, alterations in the gut metabolome may provide clues to the pathophysiology of gastrointestinal problems in RTT.},
}

Adolescent
Adult
Child
Child, Preschool
Feces/chemistry/microbiology
Female
Gas Chromatography-Mass Spectrometry
Gastrointestinal Diseases/etiology/metabolism/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Metabolome
Phenotype
RNA, Ribosomal, 16S/genetics
Rett Syndrome/complications/metabolism/*microbiology
Sequence Analysis, DNA
Severity of Illness Index
Young Adult

@article {pmid33936102,
year = {2021},
author = {El-Far, M and Durand, M and Turcotte, I and Larouche-Anctil, E and Sylla, M and Zaidan, S and Chartrand-Lefebvre, C and Bunet, R and Ramani, H and Sadouni, M and Boldeanu, I and Chamberland, A and Lesage, S and Baril, JG and Trottier, B and Thomas, R and Gonzalez, E and Filali-Mouhim, A and Goulet, JP and Martinson, JA and Kassaye, S and Karim, R and Kizer, JR and French, AL and Gange, SJ and Ancuta, P and Routy, JP and Hanna, DB and Kaplan, RC and Chomont, N and Landay, AL and Tremblay, CL},
title = {Upregulated IL-32 Expression And Reduced Gut Short Chain Fatty Acid Caproic Acid in People Living With HIV With Subclinical Atherosclerosis.},
journal = {Frontiers in immunology},
volume = {12},
number = {},
pages = {664371},
pmid = {33936102},
issn = {1664-3224},
support = {PJT 148482//CIHR/Canada ; R01 AG054324/AG/NIA NIH HHS/United States ; K01 HL137557/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL148094/HL/NHLBI NIH HHS/United States ; },
mesh = {Atherosclerosis/*complications/diagnosis/etiology/metabolism ; Biomarkers ; Caproates/*metabolism ; Electrocardiography ; Fatty Acids, Volatile/*metabolism ; Female ; Gastrointestinal Microbiome ; Gastrointestinal Tract/*metabolism ; *Gene Expression Regulation ; HIV Infections/*complications/diagnosis ; Humans ; Interleukins/*genetics/metabolism ; Macrophages/immunology/metabolism ; Male ; Metagenome ; Metagenomics/methods ; Monocytes/immunology/metabolism ; T-Lymphocytes/immunology/metabolism ; Tomography, X-Ray Computed ; },
abstract = {Despite the success of antiretroviral therapy (ART), people living with HIV (PLWH) are still at higher risk for cardiovascular diseases (CVDs) that are mediated by chronic inflammation. Identification of novel inflammatory mediators with the inherent potential to be used as CVD biomarkers and also as therapeutic targets is critically needed for better risk stratification and disease management in PLWH. Here, we investigated the expression and potential role of the multi-isoform proinflammatory cytokine IL-32 in subclinical atherosclerosis in PLWH (n=49 with subclinical atherosclerosis and n=30 without) and HIV- controls (n=25 with subclinical atherosclerosis and n=24 without). While expression of all tested IL-32 isoforms (α, β, γ, D, ϵ, and θ) was significantly higher in peripheral blood from PLWH compared to HIV- controls, IL-32D and IL-32θ isoforms were further upregulated in HIV+ individuals with coronary artery atherosclerosis compared to their counterparts without. Upregulation of these two isoforms was associated with increased plasma levels of IL-18 and IL-1β and downregulation of the atheroprotective protein TRAIL, which together composed a unique atherosclerotic inflammatory signature specific for PLWH compared to HIV- controls. Logistic regression analysis demonstrated that modulation of these inflammatory variables was independent of age, smoking, and statin treatment. Furthermore, our in vitro functional data linked IL-32 to macrophage activation and production of IL-18 and downregulation of TRAIL, a mechanism previously shown to be associated with impaired cholesterol metabolism and atherosclerosis. Finally, increased expression of IL-32 isoforms in PLWH with subclinical atherosclerosis was associated with altered gut microbiome (increased pathogenic bacteria; Rothia and Eggerthella species) and lower abundance of the gut metabolite short-chain fatty acid (SCFA) caproic acid, measured in fecal samples from the study participants. Importantly, caproic acid diminished the production of IL-32, IL-18, and IL-1β in human PBMCs in response to bacterial LPS stimulation. In conclusion, our studies identified an HIV-specific atherosclerotic inflammatory signature including specific IL-32 isoforms, which is regulated by the SCFA caproic acid and that may lead to new potential therapies to prevent CVD in ART-treated PLWH.},
}

Atherosclerosis/*complications/diagnosis/etiology/metabolism
Biomarkers
Caproates/*metabolism
Electrocardiography
Fatty Acids, Volatile/*metabolism
Female
Gastrointestinal Microbiome
Gastrointestinal Tract/*metabolism
*Gene Expression Regulation
HIV Infections/*complications/diagnosis
Humans
Interleukins/*genetics/metabolism
Macrophages/immunology/metabolism
Male
Metagenome
Metagenomics/methods
Monocytes/immunology/metabolism
T-Lymphocytes/immunology/metabolism
Tomography, X-Ray Computed

@article {pmid33838112,
year = {2021},
author = {Chen, L and Wang, D and Garmaeva, S and Kurilshikov, A and Vich Vila, A and Gacesa, R and Sinha, T and , and Segal, E and Weersma, RK and Wijmenga, C and Zhernakova, A and Fu, J},
title = {The long-term genetic stability and individual specificity of the human gut microbiome.},
journal = {Cell},
volume = {184},
number = {9},
pages = {2302-2315.e12},
doi = {10.1016/j.cell.2021.03.024},
pmid = {33838112},
issn = {1097-4172},
mesh = {Adult ; Aged ; Aged, 80 and over ; Bacteria/classification/*genetics/isolation & purification/metabolism ; Bacterial Proteins/genetics/*metabolism ; Drug Resistance, Microbial ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; Genomic Instability ; Humans ; Longitudinal Studies ; Male ; *Metabolome ; *Metagenome ; *Microbiota ; Middle Aged ; Phenotype ; Polymorphism, Single Nucleotide ; Virulence Factors/genetics/metabolism ; Young Adult ; },
abstract = {By following up the gut microbiome, 51 human phenotypes and plasma levels of 1,183 metabolites in 338 individuals after 4 years, we characterize microbial stability and variation in relation to host physiology. Using these individual-specific and temporally stable microbial profiles, including bacterial SNPs and structural variations, we develop a microbial fingerprinting method that shows up to 85% accuracy in classifying metagenomic samples taken 4 years apart. Application of our fingerprinting method to the independent HMP cohort results in 95% accuracy for samples taken 1 year apart. We further observe temporal changes in the abundance of multiple bacterial species, metabolic pathways, and structural variation, as well as strain replacement. We report 190 longitudinal microbial associations with host phenotypes and 519 associations with plasma metabolites. These associations are enriched for cardiometabolic traits, vitamin B, and uremic toxins. Finally, mediation analysis suggests that the gut microbiome may influence cardiometabolic health through its metabolites.},
}

Adult
Aged
Aged, 80 and over
Bacteria/classification/*genetics/isolation & purification/metabolism
Bacterial Proteins/genetics/*metabolism
Drug Resistance, Microbial
Feces/microbiology
Female
*Gastrointestinal Microbiome
Genomic Instability
Humans
Longitudinal Studies
Male
*Metabolome
*Metagenome
*Microbiota
Middle Aged
Phenotype
Polymorphism, Single Nucleotide
Virulence Factors/genetics/metabolism
Young Adult

@article {pmid33790324,
year = {2021},
author = {Saxena, R and Mittal, P and Clavaud, C and Dhakan, DB and Roy, N and Breton, L and Misra, N and Sharma, VK},
title = {Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {7220},
pmid = {33790324},
issn = {2045-2322},
mesh = {Administration, Topical ; Adult ; Coconut Oil/*administration & dosage ; *Dandruff/drug therapy/microbiology ; Female ; Humans ; Longitudinal Studies ; Microbiota/*drug effects ; Middle Aged ; Scalp/*microbiology ; },
abstract = {Dandruff is a recurrent chronic scalp disorder, affecting majority of the population worldwide. Recently a metagenomic study of the Indian scalp microbiome described an imperative role of bacterial commensals in providing essential vitamins and amino acids to the scalp. Coconut oil and its formulations are commonly applied on the scalp in several parts of the world to maintain scalp health. Thus, in this study we examined the effect of topical application of coconut oil on the scalp microbiome (bacterial and fungal) at the taxonomic and functional levels and their correlation with scalp physiological parameters. A 16-weeks-long time-course study was performed including 12-weeks of treatment and 4-weeks of relapse phase on a cohort of 140 (70 healthy and 70 dandruff) Indian women, resulting in ~ 900 metagenomic samples. After the treatment phase, an increase in the abundance of Cutibacterium acnes and Malassezia globosa in dandruff scalp was observed, which were negatively correlated to dandruff parameters. At the functional level, an enrichment of healthy scalp-related bacterial pathways, such as biotin metabolism and decrease in the fungal pathogenesis pathways was observed. The study provides novel insights on the effect of coconut oil in maintaining a healthy scalp and in modulating the scalp microbiome.},
}

Administration, Topical
Adult
Coconut Oil/*administration & dosage
*Dandruff/drug therapy/microbiology
Female
Humans
Longitudinal Studies
Microbiota/*drug effects
Middle Aged
Scalp/*microbiology

@article {pmid33753486,
year = {2021},
author = {Geng, J and Ji, B and Li, G and López-Isunza, F and Nielsen, J},
title = {CODY enables quantitatively spatiotemporal predictions on in vivo gut microbial variability induced by diet intervention.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {118},
number = {13},
pages = {},
pmid = {33753486},
issn = {1091-6490},
mesh = {Adult ; Biological Variation, Individual ; Colon/microbiology/*physiology ; Cross-Sectional Studies ; Datasets as Topic ; Feces/microbiology ; Feeding Behavior/*physiology ; Gastrointestinal Microbiome/*physiology ; Humans ; Hydrodynamics ; Infant ; Longitudinal Studies ; Metabolomics ; Metagenomics ; *Models, Biological ; Obesity/blood/*diet therapy/metabolism/microbiology ; Spatio-Temporal Analysis ; },
abstract = {Microbial variations in the human gut are harbored in temporal and spatial heterogeneity, and quantitative prediction of spatiotemporal dynamic changes in the gut microbiota is imperative for development of tailored microbiome-directed therapeutics treatments, e.g. precision nutrition. Given the high-degree complexity of microbial variations, subject to the dynamic interactions among host, microbial, and environmental factors, identifying how microbiota colonize in the gut represents an important challenge. Here we present COmputing the DYnamics of microbiota (CODY), a multiscale framework that integrates species-level modeling of microbial dynamics and ecosystem-level interactions into a mathematical model that characterizes spatial-specific in vivo microbial residence in the colon as impacted by host physiology. The framework quantifies spatiotemporal resolution of microbial variations on species-level abundance profiles across site-specific colon regions and in feces, independent of a priori knowledge. We demonstrated the effectiveness of CODY using cross-sectional data from two longitudinal metagenomics studies-the microbiota development during early infancy and during short-term diet intervention of obese adults. For each cohort, CODY correctly predicts the microbial variations in response to diet intervention, as validated by available metagenomics and metabolomics data. Model simulations provide insight into the biogeographical heterogeneity among lumen, mucus, and feces, which provides insight into how host physical forces and spatial structure are shaping microbial structure and functionality.},
}

Adult
Biological Variation, Individual
Colon/microbiology/*physiology
Cross-Sectional Studies
Datasets as Topic
Feces/microbiology
Feeding Behavior/*physiology
Gastrointestinal Microbiome/*physiology
Humans
Hydrodynamics
Infant
Longitudinal Studies
Metabolomics
Metagenomics
*Models, Biological
Obesity/blood/*diet therapy/metabolism/microbiology
Spatio-Temporal Analysis

@article {pmid33502259,
year = {2021},
author = {Mesnage, R and Teixeira, M and Mandrioli, D and Falcioni, L and Ducarmon, QR and Zwittink, RD and Mazzacuva, F and Caldwell, A and Halket, J and Amiel, C and Panoff, JM and Belpoggi, F and Antoniou, MN},
title = {Use of Shotgun Metagenomics and Metabolomics to Evaluate the Impact of Glyphosate or Roundup MON 52276 on the Gut Microbiota and Serum Metabolome of Sprague-Dawley Rats.},
journal = {Environmental health perspectives},
volume = {129},
number = {1},
pages = {17005},
pmid = {33502259},
issn = {1552-9924},
mesh = {Acinetobacter ; Animals ; Blood/*metabolism ; *Gastrointestinal Microbiome/drug effects ; Glycine/*analogs & derivatives/toxicity ; *Herbicides/toxicity ; Metabolome/drug effects ; *Metabolomics ; *Metagenomics ; Rats ; Rats, Sprague-Dawley ; },
abstract = {BACKGROUND: There is intense debate on whether glyphosate can inhibit the shikimate pathway of gastrointestinal microorganisms, with potential health implications.

OBJECTIVES: We tested whether glyphosate or its representative EU herbicide formulation Roundup MON 52276 affects the rat gut microbiome.

METHODS: We combined cecal microbiome shotgun metagenomics with serum and cecum metabolomics to assess the effects of glyphosate [0.5, 50, 175mg/kg body weight (BW) per day] or MON 52276 at the same glyphosate-equivalent doses, in a 90-d toxicity test in rats.

RESULTS: Glyphosate and MON 52276 treatment resulted in ceca accumulation of shikimic acid and 3-dehydroshikimic acid, suggesting inhibition of 5-enolpyruvylshikimate-3-phosphate synthase of the shikimate pathway in the gut microbiome. Cysteinylglycine, γ-glutamylglutamine, and valylglycine levels were elevated in the cecal microbiome following glyphosate and MON 52276 treatments. Altered cecum metabolites were not differentially expressed in serum, suggesting that the glyphosate and MON 52276 impact on gut microbial metabolism had limited consequences on physiological biochemistry. Serum metabolites differentially expressed with glyphosate treatment were associated with nicotinamide, branched-chain amino acid, methionine, cysteine, and taurine metabolism, indicative of a response to oxidative stress. MON 52276 had similar, but more pronounced, effects than glyphosate on the serum metabolome. Shotgun metagenomics of the cecum showed that treatment with glyphosate and MON 52276 resulted in higher levels of Eggerthella spp., Shinella zoogleoides, Acinetobacter johnsonii, and Akkermansia muciniphila. Shinella zoogleoides was higher only with MON 52276 exposure. In vitro culture assays with Lacticaseibacillus rhamnosus strains showed that Roundup GT plus inhibited growth at concentrations at which MON 52276 and glyphosate had no effect.

DISCUSSION: Our study highlights the power of multi-omics approaches to investigate the toxic effects of pesticides. Multi-omics revealed that glyphosate and MON 52276 inhibited the shikimate pathway in the rat gut microbiome. Our findings could be used to develop biomarkers for epidemiological studies aimed at evaluating the effects of glyphosate herbicides on humans. https://doi.org/10.1289/EHP6990.},
}

Acinetobacter
Animals
Blood/*metabolism
*Gastrointestinal Microbiome/drug effects
Glycine/*analogs & derivatives/toxicity
*Herbicides/toxicity
Metabolome/drug effects
*Metabolomics
*Metagenomics
Rats
Rats, Sprague-Dawley

@article {pmid32340697,
year = {2020},
author = {Dumas, E and Venken, K and Rosenbaum, JT and Elewaut, D},
title = {Intestinal Microbiota, HLA-B27, and Spondyloarthritis: Dangerous Liaisons.},
journal = {Rheumatic diseases clinics of North America},
volume = {46},
number = {2},
pages = {213-224},
doi = {10.1016/j.rdc.2020.01.007},
pmid = {32340697},
issn = {1558-3163},
mesh = {Disease Progression ; *Gastrointestinal Microbiome/genetics/immunology ; *HLA-B27 Antigen/genetics/immunology ; Humans ; *Spondylarthritis/complications/genetics/immunology ; },
abstract = {Spondyloarthritis, although primarily a joint-centered disease, is associated with extra-articular features, such as gut inflammation, psoriasis, and/or uveitis. Evidence points to underlying genetic predisposing factors and/or environmental factors. This is most clear in the gut, with progress through 16S and metagenomics sequencing studies and the results of functional studies in preclinical arthritis models. Translation of these findings to the clinic is making progress based on encouraging results of fecal microbial transplant studies in several human diseases. This review elaborates on novel trends in host-microbial interplay in spondyloarthritis, focusing on microbiota, immune dysregulation, and disease progression, and modulation by HLA-B27.},
}

Disease Progression
*Gastrointestinal Microbiome/genetics/immunology
*HLA-B27 Antigen/genetics/immunology
Humans
*Spondylarthritis/complications/genetics/immunology

@article {pmid34537552,
year = {2021},
author = {Jia, J and Liang, C and Wu, X and Xiong, L and Bao, P and Chen, Q and Yan, P},
title = {Effect of high proportion concentrate dietary on Ashdan Yak jejunal barrier and microbial function in cold season.},
journal = {Research in veterinary science},
volume = {140},
number = {},
pages = {259-267},
doi = {10.1016/j.rvsc.2021.09.010},
pmid = {34537552},
issn = {1532-2661},
mesh = {Animals ; Cattle ; Diet/veterinary ; Digestion ; *Jejunum ; Male ; *Microbiota ; Seasons ; },
abstract = {The intestinal health of ruminants plays a vital role in absorbing and metabolizing nutrients. In order to explore the jejunal barrier and microbiota dysfunction of Ashdan yaks, animals were fed with a high proportion of concentrated feeds in cold season. In present study, twelve Ashdan male yaks were arbitrarily separated into two categories, namely FF and CF. Compositional and functional differences in their jejunum barrier and microbiota between the FF and CF yaks were compared using metagenomics and proteomics methods. The results showed that the activity of jejunum digestive protease and microbe metabolite of forage-fed yaks were more conducive to healthy cultivation than the concentrate-fed yaks. 57 differentially expressed proteins (DEPs) were recognized using label-free MS, those could conclude to 2 principal classes: structural proteins and inflammatory factors, and 14 proteins were relatively active in those principal classes. Firmicutes were the dominant bacterial phylum in the jejunum microbiota of both the forage-fed group (24.33%) and concentrate-fed group (23.16%). As compared to forage-fed group, the concentrate-fed group showed enhanced alpha diversity and reduced beta diversity of the jejunal microbiota. The long-term high-proportion concentrate feeding inhibited the growth of Actinobacteria, Proteo-bacteria, Ascomycota, Bacteroidetes and stimulated the growth of Streptophyta, Cyanobacteria, Fusobacteria and Chlamydiae. The concentrate-fed group showed increase in the abundance of immune system process, along with decrease in the metabolic process, especially the binding process. Interestingly, the proteomics and metagenomics results were both inclined to the enrichment of jejunum mechanical barrier and inflammatory response. Overall, the study suggested that the long-term high-proportion concentrate feeding affected the expressions of specific jejunum proteins and composition of microbiota, which damaged the jejunum barrier and the function of microbiota in yaks.},
}

Animals
Cattle
Diet/veterinary
Digestion
*Jejunum
Male
*Microbiota
Seasons

@article {pmid34444993,
year = {2021},
author = {Tso, L and Bonham, KS and Fishbein, A and Rowland, S and Klepac-Ceraj, V},
title = {Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Human Milk Oligosaccharide Metabolizing Genes.},
journal = {Nutrients},
volume = {13},
number = {8},
pages = {},
pmid = {34444993},
issn = {2072-6643},
support = {UG3 OD023313/GF/NIH HHS/United States ; },
mesh = {Bacterial Proteins/classification/genetics ; *Bifidobacterium longum/genetics/metabolism ; Breast Feeding ; Cohort Studies ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; Genes, Bacterial/genetics ; Humans ; Infant ; Infant, Newborn ; Milk, Human/*chemistry ; Oligosaccharides/*metabolism ; },
abstract = {Bifidobacterium longum subsp. infantis (B. infantis) is one of a few microorganisms capable of metabolizing human breast milk and is a pioneer colonizer in the guts of breastfed infants. One current challenge is differentiating B. infantis from its close relatives, B. longum and B. suis. All three organisms are classified in the same species group but only B. infantis can metabolize human milk oligosaccharides (HMOs). We compared HMO-metabolizing genes across different Bifidobacterium genomes and developed B. infantis-specific primers to determine if the genes alone or the primers can be used to quickly characterize B. infantis. We showed that B. infantis is uniquely identified by the presence of five HMO-metabolizing gene clusters, tested for its prevalence in infant gut metagenomes, and validated the results using the B. infantis-specific primers. We observed that only 15 of 203 (7.4%) children under 2 years old from a cohort of US children harbored B. infantis. These results highlight the importance of developing and improving approaches to identify B. infantis. A more accurate characterization may provide insights into regional differences of B. infantis prevalence in infant gut microbiota.},
}

Bacterial Proteins/classification/genetics
*Bifidobacterium longum/genetics/metabolism
Breast Feeding
Cohort Studies
Feces/microbiology
Gastrointestinal Microbiome/*genetics
Genes, Bacterial/genetics
Humans
Infant
Infant, Newborn
Milk, Human/*chemistry
Oligosaccharides/*metabolism

@article {pmid34405262,
year = {2021},
author = {Ghosh, S and Pramanik, S},
title = {Structural diversity, functional aspects and future therapeutic applications of human gut microbiome.},
journal = {Archives of microbiology},
volume = {203},
number = {9},
pages = {5281-5308},
pmid = {34405262},
issn = {1432-072X},
support = {BT/PR31826BIC/101/1211/2019//Department of Biotechnology , Ministry of Science and Technology/ ; },
mesh = {*Cyanobacteria ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S ; },
abstract = {The research on human gut microbiome, regarded as the black box of the human body, is still at the stage of infancy as the functional properties of the complex gut microbiome have not yet been understood. Ongoing metagenomic studies have deciphered that the predominant microbial communities belong to eubacterial phyla Firmicutes, Bacteroidetes, Proteobacteria, Fusobacteria, Cyanobacteria, Verrucomicrobia and archaebacterial phylum Euryarchaeota. The indigenous commensal microbial flora prevents opportunistic pathogenic infection and play undeniable roles in digestion, metabolite and signaling molecule production and controlling host's cellular health, immunity and neuropsychiatric behavior. Besides maintaining intestinal health via short-chain fatty acid (SCFA) production, gut microbes also aid in neuro-immuno-endocrine modulatory molecule production, immune cell differentiation and glucose and lipid metabolism. Interdependence of diet and intestinal microbial diversity suggests the effectiveness of pre- and pro-biotics in maintenance of gut and systemic health. Several companies worldwide have started potentially exploiting the microbial contribution to human health and have translated their use in disease management and therapeutic applications. The present review discusses the vast diversity of microorganisms playing intricate roles in human metabolism. The contribution of the intestinal microbiota to regulate systemic activities including gut-brain-immunity crosstalk has been focused. To the best of our knowledge, this review is the first of its kind to collate and discuss the companies worldwide translating the multi-therapeutic potential of human intestinal microbiota, based on the multi-omics studies, i.e. metagenomics and metabolomics, as ready solutions for several metabolic and systemic disorders.},
}

*Cyanobacteria
*Gastrointestinal Microbiome
Humans
Metagenomics
*Microbiota
RNA, Ribosomal, 16S

@article {pmid34233671,
year = {2021},
author = {Liu, P and Jiang, Y and Gu, S and Xue, Y and Yang, H and Li, Y and Wang, Y and Yan, C and Jia, P and Lin, X and Qi, G},
title = {Metagenome-wide association study of gut microbiome revealed potential microbial marker set for diagnosis of pediatric myasthenia gravis.},
journal = {BMC medicine},
volume = {19},
number = {1},
pages = {159},
pmid = {34233671},
issn = {1741-7015},
mesh = {Adult ; Bacteroides ; Child ; Clostridiales ; Feces ; Firmicutes ; Fusobacterium ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Myasthenia Gravis/diagnosis ; Prevotella ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Myasthenia gravis (MG) is an acquired immune-mediated disorder of the neuromuscular junction that causes fluctuating skeletal muscle weakness and fatigue. Pediatric MG and adult MG have many different characteristics, and current MG diagnostic methods for children are not quite fit. Previous studies indicate that alterations in the gut microbiota may be associated with adult MG. However, it has not been determined whether the gut microbiota are altered in pediatric MG patients.

METHODS: Our study recruited 53 pediatric MG patients and 46 age- and gender-matched healthy controls (HC). We sequenced the fecal samples of recruited individuals using whole-genome shotgun sequencing and analyzed the data with in-house bioinformatics pipeline.

RESULTS: We built an MG disease classifier based on the abundance of five species, Fusobacterium mortiferum, Prevotella stercorea, Prevotella copri, Megamonas funiformis, and Megamonas hypermegale. The classifier obtained 94% area under the curve (AUC) in cross-validation and 84% AUC in the independent validation cohort. Gut microbiome analysis revealed the presence of human adenovirus F/D in 10 MG patients. Significantly different pathways and gene families between MG patients and HC belonged to P. copri, Clostridium bartlettii, and Bacteroides massiliensis. Based on functional annotation, we found that the gut microbiome affects the production of short-chain fatty acids (SCFAs), and we confirmed the decrease in SCFA levels in pediatric MG patients via serum tests.

CONCLUSIONS: The study indicated that altered fecal microbiota might play vital roles in pediatric MG's pathogenesis by reducing SCFAs. The microbial markers might serve as novel diagnostic methods for pediatric MG.},
}

Adult
Bacteroides
Child
Clostridiales
Feces
Firmicutes
Fusobacterium
*Gastrointestinal Microbiome
Humans
Metagenome
*Myasthenia Gravis/diagnosis
Prevotella
RNA, Ribosomal, 16S

@article {pmid34215422,
year = {2021},
author = {Kothe, CI and Bolotin, A and Kraïem, BF and Dridi, B and , and Renault, P},
title = {Unraveling the world of halophilic and halotolerant bacteria in cheese by combining cultural, genomic and metagenomic approaches.},
journal = {International journal of food microbiology},
volume = {358},
number = {},
pages = {109312},
doi = {10.1016/j.ijfoodmicro.2021.109312},
pmid = {34215422},
issn = {1879-3460},
mesh = {Animals ; Bacteria/genetics ; Brevibacterium ; Cattle ; *Cheese/analysis ; Metagenome ; Metagenomics ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Staphylococcus ; },
abstract = {Halophilic/halotolerant bacteria are generally assumed to live in natural environments, although they may also be found in foods such as cheese and seafood. These salt-loving bacteria have been occasionally characterized in cheese, and studies on their ecological and technological functions are still scarce. We therefore selected 13 traditional cheeses to systematically characterize these microorganisms in their rinds via cultural, genomic and metagenomic methods. Using different salt-based media, we identified 35 strains with unique 16S rRNA and rpoB gene sequences, whose whole genome was sequenced. Twenty are Gram-positive species including notably Brevibacterium aurantiacum (6) and Staphylococcus equorum (3), which are also frequently added as starters. ANI and pan-genomic analyses confirm the high genetic diversity of B. aurantiacum and reveal the presence of two subspecies in S. equorum, as well as the genetic proximity of several cheese strains to bovine isolates. Additionally, we isolated 15 Gram-negative strains, potentially defining ten new species of halophilic/halotolerant cheese bacteria, in particular for the genera Halomonas and Psychrobacter. The use of all the genomes sequenced in this study as a reference to complement those existing in the databases allowed us to study the representativeness of 66 species of halophilic/halotolerant bacteria in 74 cheese rind metagenomes. While Gram-positive strains may flourish in the different types of technologies, Gram-negative species are particularly abundant in cheeses with high moisture, such as washed-rind cheeses. Finally, analyses of co-occurrences reveal assemblies, including the frequent coexistence of several species of the same genus, forming moderately complex ecosystems with functional redundancies that probably ensure stable cheese development.},
}

Animals
Bacteria/genetics
Brevibacterium
Cattle
*Cheese/analysis
Metagenome
Metagenomics
*Microbiota
RNA, Ribosomal, 16S/genetics
Staphylococcus

@article {pmid34103703,
year = {2021},
author = {Wang, W and Wei, X and Wu, L and Shang, X and Cheng, F and Li, B and Zhou, X and Zhang, J},
title = {The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach.},
journal = {The Journal of antibiotics},
volume = {74},
number = {8},
pages = {508-518},
pmid = {34103703},
issn = {1881-1469},
mesh = {Animal Feed ; Animals ; Cattle/*microbiology ; Dairy Products ; Drug Resistance, Bacterial/*genetics ; Feces/microbiology ; Humans ; Integrons/genetics ; Interspersed Repetitive Sequences/genetics ; Meat ; Metagenomics/*methods ; Microbiota/*genetics ; Soil Microbiology ; Species Specificity ; },
abstract = {Drug resistance has been partly driven by the overuse of antimicrobials in agricultural animal feed. Better understanding of antibiotic resistance in bovine gut is needed to assess its potential effects based on metagenomic approach and analysis. In this study, we collected 40 fecal samples to explore drug resistance derived from antibiotic use in the bacterial community by an analysis of the diversities and differences of antibiotic-resistant genes (ARGs) in the gut microbiota from yak, beef, and dairy cattle. Overall, 1688 genes were annotated, including 734 ARG subtypes. The ARGs were related to tetracyclines, quinolones, β-lactam, and aminoglycosides, in accordance with the antibiotics widely used in the clinic for humans or animals. The emergence, prevalence, and differences in resistance genes in the intestines of yaks, beef, and dairy cattle may be caused by the selective pressure of different feeding patterns, where yaks were raised without antibiotics for growth promotion. In addition, the abundance of ARGs in yak was lower than in beef and dairy cattle, whereas the abundance of integron, a kind of mobile genetic elements (MGEs) was higher in yaks than those in beef and dairy cattle. Furthermore, the results of this study could provide the basis for a comprehensive profile of various ARGs among yak, beef, and dairy cattle in future.},
}

Animal Feed
Animals
Cattle/*microbiology
Dairy Products
Drug Resistance, Bacterial/*genetics
Feces/microbiology
Humans
Integrons/genetics
Interspersed Repetitive Sequences/genetics
Meat
Metagenomics/*methods
Microbiota/*genetics
Soil Microbiology
Species Specificity

@article {pmid33973321,
year = {2021},
author = {Lugli, GA and Alessandri, G and Milani, C and Viappiani, A and Fontana, F and Tarracchini, C and Mancabelli, L and Argentini, C and Ruiz, L and Margolles, A and van Sinderen, D and Turroni, F and Ventura, M},
title = {Genetic insights into the dark matter of the mammalian gut microbiota through targeted genome reconstruction.},
journal = {Environmental microbiology},
volume = {23},
number = {6},
pages = {3294-3305},
pmid = {33973321},
issn = {1462-2920},
mesh = {Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Genome, Bacterial/genetics ; Metagenome ; Metagenomics ; },
abstract = {Whole metagenomic shotgun (WMS) sequencing has dramatically enhanced our ability to study microbial genomics. The possibility to unveil the genetic makeup of bacteria that cannot be easily isolated has significantly expanded our microbiological horizon. Here, we report an approach aimed at uncovering novel bacterial species by the use of targeted WMS sequencing. Employing in silico data retrieved from metabolic modelling to formulate a chemically defined medium (CDM), we were able to isolate and subsequently sequence the genomes of six putative novel species of bacteria from the gut of non-human primates.},
}

Animals
Bacteria/genetics
*Gastrointestinal Microbiome/genetics
Genome, Bacterial/genetics
Metagenome
Metagenomics

@article {pmid33638901,
year = {2021},
author = {Shah, AS and Wakelin, SA and Moot, DJ and Blond, C and Laugraud, A and Ridgway, HJ},
title = {Trifolium repens and T. subterraneum modify their nodule microbiome in response to soil pH.},
journal = {Journal of applied microbiology},
volume = {131},
number = {4},
pages = {1858-1869},
doi = {10.1111/jam.15050},
pmid = {33638901},
issn = {1365-2672},
support = {C10X1308//Ministry of Business, Innovation and Employment/ ; },
mesh = {Hydrogen-Ion Concentration ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Rhizobium ; Root Nodules, Plant ; Soil ; Symbiosis ; *Trifolium ; },
abstract = {AIMS: The influence of soil edaphic factors on recruitment and composition of bacteria in the legume nodule is unknown. Typically, low (acidic) pH soils have a negative effect on the plant-rhizobia symbiosis and thereby reduce clover growth. However, the specific relationship between soil pH and the ecology of rhizobia is unknown, in either their free-living or nodule-inhabiting states. We used New Zealand pasture systems with soils of different pH, and white (WC) and subterranean (SC) clovers, to examine the relationship between soil pH and the diversity of bacteria that inhabit the nodules.

METHODS AND RESULTS: Amplicon sequencing (16S rRNA) assessed the bacterial community in 5299 nodules recovered from both legume species grown in 47 soils of different edaphic (including pH) properties. Fewer nodules were formed on both clovers at low soil pH. As expected, rhizobia comprised ∼ 92% of the total reads in both clovers, however 28 non-rhizobia genera were also present. Soil pH influenced the community structure of bacteria within the nodule, and this was more evident in non-Rhizobium taxa than Rhizobium. Host strongly influenced the diversity of bacteria in the nodules. The alpha diversity of nodule microbiome in SC nodules was higher than in WC nodules and SC nodules also harbored a higher relative abundance of non-Rhizobium bacteria than WC. Beta diversity of Rhizobium and non-Rhizobium bacteria was influenced more by clover species rather than edaphic factors.

CONCLUSIONS: The results indicate that these clover species modified their nodule biomes in response to pH-stress.

The non-Rhizobium bacteria may have some functional significance (such as improved clover persistence in low pH soils) in legume nodules.},
}

Hydrogen-Ion Concentration
*Microbiota
Phylogeny
RNA, Ribosomal, 16S/genetics
*Rhizobium
Root Nodules, Plant
Soil
Symbiosis
*Trifolium

@article {pmid33615652,
year = {2021},
author = {Mancabelli, L and Tarracchini, C and Milani, C and Lugli, GA and Fontana, F and Turroni, F and van Sinderen, D and Ventura, M},
title = {Vaginotypes of the human vaginal microbiome.},
journal = {Environmental microbiology},
volume = {23},
number = {3},
pages = {1780-1792},
doi = {10.1111/1462-2920.15441},
pmid = {33615652},
issn = {1462-2920},
mesh = {Female ; Humans ; Lactobacillus/genetics ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Vagina ; },
abstract = {The human vaginal environment harbours a community of bacteria that plays an important role in maintaining vaginal health and in protecting this environment from various urogenital infections. This bacterial population, also known as vaginal microbiota, has been demonstrated to be dominated by members of the Lactobacillus genus. Several studies employing 16S rRNA gene-based amplicon sequencing have classified the vaginal microbiota into five distinct community state types (CSTs) or vaginotypes. To deepen our understanding of the vaginal microbiota we performed an in-depth meta-analysis of 1312 publicly available datasets concerning healthy vaginal microbiome information obtained by metagenomics sequencing. The analysis confirmed the predominance of taxa belonging to the Lactobacillus genus, followed by members of the genera Gardnerella, Vibrio and Atopobium. Moreover, the statistical robustness offered by this meta-analysis allowed us to disentangle the species-level composition of dominant and accessory taxa constituting each vaginotype and to revisit and refine the previously proposed CST classification. In addition, a functional characterization of the metagenomic datasets revealed particular genetic features associated with each assigned vaginotype.},
}

Female
Humans
Lactobacillus/genetics
Metagenomics
*Microbiota/genetics
RNA, Ribosomal, 16S/genetics
Vagina

@article {pmid32431114,
year = {2021},
author = {Dash, NR and Al Bataineh, MT},
title = {Metagenomic Analysis of the Gut Microbiome Reveals Enrichment of Menaquinones (Vitamin K2) Pathway in Diabetes Mellitus.},
journal = {Diabetes & metabolism journal},
volume = {45},
number = {1},
pages = {77-85},
pmid = {32431114},
issn = {2233-6087},
mesh = {*Diabetes Mellitus, Type 2/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; Vitamin K 2 ; },
abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is a chronic metabolic disease with a high prevalence worldwide, especially among overweight and obese populations. T2DM is multifactorial with several genetic and acquired risk factors that lead to insulin resistance. Mounting evidence indicates that alteration of gut microbiome composition contribute to insulin resistance and inflammation. However, the precise link between T2DM and gut microbiome role and composition remains unknown.

METHODS: We evaluated the metabolic capabilities of the gut microbiome of twelve T2DM and six healthy individuals through shotgun metagenomics using MiSeq platform.

RESULTS: We identified no significant differences in the overall taxonomic composition between healthy and T2DM subjects when controlling for differences in diet. However, results showed that T2DM enriched in metabolic pathways involved in menaquinone (vitamin K2) superpathway biosynthesis (PWY-5838) as compared to healthy individuals. Covariance analysis between the bacterial genera and metabolic pathways displaying difference in abundance (analysis of variance P<0.05) in T2DM as compared to healthy subjects revealed that genera belonging Firmicutes, Actinobacteria, and Bacteroidetes phyla contribute significantly to vitamin K2 biosynthesis. Further, the microbiome corresponding to T2DM with high glycosylated hemoglobin (HbA1c) (>6.5%) exhibit high abundance of genes involved in lysine biosynthesis and low abundance of genes involved in creatinine degradation as compared to T2DM with lower HbA1c (<6.5%).

CONCLUSION: The identified differences in metabolic capabilities provide important information that may eventually lead to the development of novel biomarkers and more effective management strategies to treat T2DM.},
}

*Diabetes Mellitus, Type 2/genetics
*Gastrointestinal Microbiome/genetics
Humans
Metagenome
Metagenomics
Vitamin K 2

@article {pmid34508085,
year = {2021},
author = {Bramble, MS and Vashist, N and Ko, A and Priya, S and Musasa, C and Mathieu, A and Spencer, A and Lupamba Kasendue, M and Mamona Dilufwasayo, P and Karume, K and Nsibu, J and Manya, H and Uy, MNA and Colwell, B and Boivin, M and Mayambu, JPB and Okitundu, D and Droit, A and Mumba Ngoyi, D and Blekhman, R and Tshala-Katumbay, D and Vilain, E},
title = {The gut microbiome in konzo.},
journal = {Nature communications},
volume = {12},
number = {1},
pages = {5371},
pmid = {34508085},
issn = {2041-1723},
support = {D43 TW009343/TW/FIC NIH HHS/United States ; R01 ES019841/ES/NIEHS NIH HHS/United States ; },
mesh = {Child ; Democratic Republic of the Congo/epidemiology ; Disease Susceptibility/*microbiology ; Feces/microbiology ; *Feeding Behavior ; Female ; Gastrointestinal Microbiome/*physiology ; Humans ; Manihot/*adverse effects/chemistry ; Metagenomics ; Motor Neuron Disease/epidemiology/*microbiology ; Nitriles/adverse effects ; },
abstract = {Konzo, a distinct upper motor neuron disease associated with a cyanogenic diet and chronic malnutrition, predominately affects children and women of childbearing age in sub-Saharan Africa. While the exact biological mechanisms that cause this disease have largely remained elusive, host-genetics and environmental components such as the gut microbiome have been implicated. Using a large study population of 180 individuals from the Democratic Republic of the Congo, where konzo is most frequent, we investigate how the structure of the gut microbiome varied across geographical contexts, as well as provide the first insight into the gut flora of children affected with this debilitating disease using shotgun metagenomic sequencing. Our findings indicate that the gut microbiome structure is highly variable depending on region of sampling, but most interestingly, we identify unique enrichments of bacterial species and functional pathways that potentially modulate the susceptibility of konzo in prone regions of the Congo.},
}

Child
Democratic Republic of the Congo/epidemiology
Disease Susceptibility/*microbiology
Feces/microbiology
*Feeding Behavior
Female
Gastrointestinal Microbiome/*physiology
Humans
Manihot/*adverse effects/chemistry
Metagenomics
Motor Neuron Disease/epidemiology/*microbiology
Nitriles/adverse effects

@article {pmid34047368,
year = {2021},
author = {Leonardi, A and Modugno, RL and Cavarzeran, F and Rosani, U},
title = {Metagenomic analysis of the conjunctival bacterial and fungal microbiome in vernal keratoconjunctivitis.},
journal = {Allergy},
volume = {76},
number = {10},
pages = {3215-3217},
doi = {10.1111/all.14963},
pmid = {34047368},
issn = {1398-9995},
mesh = {Bacteria/genetics ; *Conjunctivitis, Allergic ; Humans ; Metagenome ; Metagenomics ; *Mycobiome ; RNA, Ribosomal, 16S ; },
}

Bacteria/genetics
*Conjunctivitis, Allergic
Humans
Metagenome
Metagenomics
*Mycobiome
RNA, Ribosomal, 16S

@article {pmid33764980,
year = {2021},
author = {Ahmad, T and Gupta, G and Sharma, A and Kaur, B and El-Sheikh, MA and Alyemeni, MN},
title = {Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0248116},
pmid = {33764980},
issn = {1932-6203},
mesh = {Altitude ; Bacteria/classification/*genetics/isolation & purification ; Genome, Bacterial ; India ; Lakes/*microbiology ; *Metagenome ; Metagenomics ; Microbiota ; },
abstract = {Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).},
}

Altitude
Bacteria/classification/*genetics/isolation & purification
Genome, Bacterial
India
Lakes/*microbiology
*Metagenome
Metagenomics
Microbiota

@article {pmid33668457,
year = {2021},
author = {do Nascimento, WM and Machiavelli, A and Ferreira, LGE and Cruz Silveira, L and de Azevedo, SSD and Bello, G and Smith, DP and Mezzari, MP and Petrosino, JF and Delgado Duarte, RT and Zárate-Bladés, CR and Pinto, AR},
title = {Gut Microbiome Profiles and Associated Metabolic Pathways in HIV-Infected Treatment-Naïve Patients.},
journal = {Cells},
volume = {10},
number = {2},
pages = {},
pmid = {33668457},
issn = {2073-4409},
mesh = {Adult ; Bacteria/classification ; Discriminant Analysis ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome ; HIV Infections/epidemiology/*metabolism/*microbiology/transmission ; HIV-1/physiology ; Humans ; *Metabolic Networks and Pathways ; Middle Aged ; },
abstract = {The normal composition of the intestinal microbiota is a key factor for maintaining healthy homeostasis, and accordingly, dysbiosis is well known to be present in HIV-1 patients. This article investigates the gut microbiota profile of antiretroviral therapy-naive HIV-1 patients and healthy donors living in Latin America in a cohort of 13 HIV positive patients (six elite controllers, EC, and seven non-controllers, NC) and nine healthy donors (HD). Microbiota compositions in stool samples were determined by sequencing the V3-V4 region of the bacterial 16S rRNA, and functional prediction was inferred using PICRUSt. Several taxa were enriched in EC compared to NC or HD groups, including Acidaminococcus, Clostridium methylpentosum, Barnesiella, Eubacterium coprostanoligenes, and Lachnospiraceae UCG-004. In addition, our data indicate that the route of infection is an important factor associated with changes in gut microbiome composition, and we extend these results by identifying several metabolic pathways associated with each route of infection. Importantly, we observed several bacterial taxa that might be associated with different viral subtypes, such as Succinivibrio, which were more abundant in patients infected by HIV subtype B, and Streptococcus enrichment in patients infected by subtype C. In conclusion, our data brings a significant contribution to the understanding of dysbiosis-associated changes in HIV infection and describes, for the first time, differences in microbiota composition according to HIV subtypes. These results warrant further confirmation in a larger cohort of patients.},
}

Adult
Bacteria/classification
Discriminant Analysis
Feces/microbiology
Female
*Gastrointestinal Microbiome
HIV Infections/epidemiology/*metabolism/*microbiology/transmission
HIV-1/physiology
Humans
*Metabolic Networks and Pathways
Middle Aged

@article {pmid33485839,
year = {2021},
author = {Khalyfa, A and Ericsson, A and Qiao, Z and Almendros, I and Farré, R and Gozal, D},
title = {Circulating exosomes and gut microbiome induced insulin resistance in mice exposed to intermittent hypoxia: Effects of physical activity.},
journal = {EBioMedicine},
volume = {64},
number = {},
pages = {103208},
pmid = {33485839},
issn = {2352-3964},
support = {R01 HL130984/HL/NHLBI NIH HHS/United States ; R56 HL140548/HL/NHLBI NIH HHS/United States ; },
mesh = {Animals ; Biomarkers/*blood ; Body Weight ; Cell Line ; Disease Models, Animal ; Exosomes/*metabolism ; *Gastrointestinal Microbiome ; Hypoxia/*metabolism ; Insulin/metabolism ; *Insulin Resistance ; Metabolome ; Metagenome ; Metagenomics/methods ; Mice ; *Physical Conditioning, Animal ; Sleep Apnea, Obstructive ; },
abstract = {BACKGROUND: Gut microbiota (GM) contribute to obesity and insulin resistance (IR). Obstructive sleep apnea (OSA), characterized by intermittent hypoxia (IH), promotes IR and alters GM. Since circulating exosomes are implicated in IR, we examined the effects of IH and physical activity (PA) in mice on GM, colonic epithelium permeability, systemic IR, and plasma exosome cargo, and exosome effects on visceral white adipose tissues (vWAT) IR.

METHODS: C57BL/6 mice were exposed to IH or room air (RA) for 6 weeks with and without PA (n = 12/group), and GM and systemic IR changes were assessed, as well as the effects of plasma exosomes on naïve adipocyte insulin sensitivity. Fecal microbiota transfers (FMT) were performed in naïve mice (n = 5/group), followed by fecal 16S rRNA sequencing, and systemic IR and exosome-induced effects on adipocyte insulin sensitivity were evaluated.

FINDINGS: Principal coordinate analysis (PCoA) ordinates revealed B-diversity among IH and FMT recipients that accounted for 64% principal component 1 (PC1) and 12.5% (PC2) of total variance. Dominant microbiota families and genera in IH-exposed and FMT-treated were preserved, and IH-exposed GM and IH-FMT induced increased gut permeability. Plasma exosomes from IH-exposed and IH-FMT mice decreased pAKT/AKT responses to exogenous insulin in adipocytes vs. IH+PA or RA FMT-treated mice (p = 0.001).

INTERPRETATION: IH exposures mimicking OSA induce changes in GM, increase gut permeability, and alter plasma exosome cargo, the latter inducing adipocyte dysfunction (increased IR). Furthermore, these alterations improved with PA. Thus, IH leads to perturbations of a singular GM-circulating exosome pathway that disrupts adipocyte homeostasis resulting in metabolic dysfunction, as reflected by IR.

FUNDING: This study was supported by grants from the National Institutes of Health grants HL130984 and HL140548 and University of Missouri Tier 2 grant. The study has not received any funding or grants from pharmaceutical or other industrial corporations.},
}

Animals
Biomarkers/*blood
Body Weight
Cell Line
Disease Models, Animal
Exosomes/*metabolism
*Gastrointestinal Microbiome
Hypoxia/*metabolism
Insulin/metabolism
*Insulin Resistance
Metabolome
Metagenome
Metagenomics/methods
Mice
*Physical Conditioning, Animal
Sleep Apnea, Obstructive

@article {pmid33339953,
year = {2020},
author = {Kwun, JS and Kang, SH and Lee, HJ and Park, HK and Lee, WJ and Yoon, CH and Suh, JW and Cho, YS and Youn, TJ and Chae, IH},
title = {Comparison of thrombus, gut, and oral microbiomes in Korean patients with ST-elevation myocardial infarction: a case-control study.},
journal = {Experimental & molecular medicine},
volume = {52},
number = {12},
pages = {2069-2079},
pmid = {33339953},
issn = {2092-6413},
support = {2019R1C1C1006611//National Research Foundation of Korea (NRF)/ ; },
mesh = {Aged ; Case-Control Studies ; Disease Susceptibility ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics/methods ; Metagenome ; Metagenomics ; *Microbiota ; Middle Aged ; Mouth/*microbiology ; Public Health Surveillance ; ST Elevation Myocardial Infarction/diagnosis/*epidemiology/*etiology ; Thrombosis/*complications/*epidemiology ; },
abstract = {ST-segment elevation myocardial infarction (STEMI) is characterized by thrombotic coronary artery occlusions caused by atherosclerotic plaque rupture. The gut microbiome potentially contributes to the pathogenesis of coronary artery diseases. This study investigated the microbial diversity and composition of coronary thrombi in STEMI patients and the composition of the thrombus microbiome relative to that of the oral and gut microbiomes. A case-control study was performed with 22 STEMI patients and 20 age- and sex-matched healthy controls. Coronary thrombi were acquired from STEMI patients via manual thrombus aspiration during primary coronary intervention. Oral swab and stool samples were collected from both groups, and 16S rRNA sequencing and metagenomic microbiome analyses were performed. Microbial DNA was detected in 4 of 22 coronary thrombi. Proteobacteria (p) and Bacteroidetes (p) were the most abundant phyla. The oral and gut microbiomes significantly differed between patients and healthy controls. The patient group presented microbial dysbiosis, as follows: a higher relative abundance of Proteobacteria (p) and Enterobacteriaceae (f) in the gut microbiome and a lower abundance of Firmicutes (p) and Haemophilus (g) in the oral microbiome. Furthermore, 4 significantly abundant genera were observed in the coronary thrombus in the patients: Escherichia, 1.25%; Parabacteroides, 0.25%; Christensenella, 0.0%; and Bacteroides, 7.48%. The present results indicate that the relative abundance of the gut and oral microbiomes was correlated with that of the thrombus microbiome.},
}

Aged
Case-Control Studies
Disease Susceptibility
Dysbiosis
Female
*Gastrointestinal Microbiome
Humans
Male
Metabolomics/methods
Metagenome
Metagenomics
*Microbiota
Middle Aged
Mouth/*microbiology
Public Health Surveillance
ST Elevation Myocardial Infarction/diagnosis/*epidemiology/*etiology
Thrombosis/*complications/*epidemiology

@article {pmid33262480,
year = {2020},
author = {Wang, Y and Yao, W and Li, B and Qian, S and Wei, B and Gong, S and Wang, J and Liu, M and Wei, M},
title = {Nuciferine modulates the gut microbiota and prevents obesity in high-fat diet-fed rats.},
journal = {Experimental & molecular medicine},
volume = {52},
number = {12},
pages = {1959-1975},
pmid = {33262480},
issn = {2092-6413},
support = {81703373//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Aporphines/chemistry/*pharmacology ; Diet, High-Fat/*adverse effects ; Dose-Response Relationship, Drug ; Dysbiosis/drug therapy ; Fatty Acids/metabolism ; Gastrointestinal Microbiome/*drug effects ; Lipid Metabolism ; Metabolome ; Metabolomics/methods ; Metagenome ; Metagenomics/methods ; Obesity/*etiology/*metabolism/prevention & control ; Protective Agents/chemistry/*pharmacology ; Rats ; },
abstract = {Gut microbiota dysbiosis has a significant role in the pathogenesis of metabolic diseases, including obesity. Nuciferine (NUC) is a main bioactive component in the lotus leaf that has been used as food in China since ancient times. Here, we examined whether the anti-obesity effects of NUC are related to modulations in the gut microbiota. Using an obese rat model fed a HFD for 8 weeks, we show that NUC supplementation of HFD rats prevents weight gain, reduces fat accumulation, and ameliorates lipid metabolic disorders. Furthermore, 16S rRNA gene sequencing of the fecal microbiota suggested that NUC changed the diversity and composition of the gut microbiota in HFD-fed rats. In particular, NUC decreased the ratio of the phyla Firmicutes/Bacteroidetes, the relative abundance of the LPS-producing genus Desulfovibrio and bacteria involved in lipid metabolism, whereas it increased the relative abundance of SCFA-producing bacteria in HFD-fed rats. Predicted functional analysis of microbial communities showed that NUC modified genes involved in LPS biosynthesis and lipid metabolism. In addition, serum metabolomics analysis revealed that NUC effectively improved HFD-induced disorders of endogenous metabolism, especially lipid metabolism. Notably, NUC promoted SCFA production and enhanced intestinal integrity, leading to lower blood endotoxemia to reduce inflammation in HFD-fed rats. Together, the anti-obesity effects of NUC may be related to modulations in the composition and potential function of gut microbiota, improvement in intestinal barrier integrity and prevention of chronic low-grade inflammation. This research may provide support for the application of NUC in the prevention and treatment of obesity.},
}

Animals
Aporphines/chemistry/*pharmacology
Diet, High-Fat/*adverse effects
Dose-Response Relationship, Drug
Dysbiosis/drug therapy
Fatty Acids/metabolism
Gastrointestinal Microbiome/*drug effects
Lipid Metabolism
Metabolome
Metabolomics/methods
Metagenome
Metagenomics/methods
Obesity/*etiology/*metabolism/prevention & control
Protective Agents/chemistry/*pharmacology
Rats

@article {pmid33784327,
year = {2021},
author = {Buetti-Dinh, A and Ruinelli, M and Czerski, D and Scapozza, C and Martignier, A and Roman, S and Caminada, A and Tonolla, M},
title = {Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0248877},
pmid = {33784327},
issn = {1932-6203},
mesh = {Bacteria/classification/genetics ; Biodiversity ; Color ; *Ecosystem ; Extracellular Polymeric Substance Matrix/metabolism ; Genes, Bacterial ; Geologic Sediments/*chemistry ; *Metagenomics ; Metals/*analysis ; Nitrogen Fixation ; Phylogeny ; Rivers/*chemistry ; Switzerland ; Water/chemistry ; },
abstract = {The Swiss Alpine environments are poorly described from a microbiological perspective. Near the Greina plateau in the Camadra valley in Ticino (southern Swiss Alps), a green-turquoise-coloured water spring streams off the mountain cliffs. Geochemical profiling revealed naturally elevated concentrations of heavy metals such as copper, lithium, zinc and cadmium, which are highly unusual for the geomorphology of the region. Of particular interest, was the presence of a thick biofilm, that was revealed by microscopic analysis to be mainly composed of Cyanobacteria. A metagenome was further assembled to detail the genes found in this environment. A multitude of genes for resistance/tolerance to high heavy metal concentrations were indeed found, such as, various transport systems, and genes involved in the synthesis of extracellular polymeric substances (EPS). EPS have been evoked as a central component in photosynthetic environments rich in heavy metals, for their ability to drive the sequestration of toxic, positively-charged metal ions under high regimes of cyanobacteria-driven photosynthesis. The results of this study provide a geochemical and microbiological description of this unusual environment in the southern Swiss Alps, the role of cyanobacterial photosynthesis in metal resistance, and the potential role of such microbial community in bioremediation of metal-contaminated environments.},
}

Bacteria/classification/genetics
Biodiversity
Color
*Ecosystem
Extracellular Polymeric Substance Matrix/metabolism
Genes, Bacterial
Geologic Sediments/*chemistry
*Metagenomics
Metals/*analysis
Nitrogen Fixation
Phylogeny
Rivers/*chemistry
Switzerland
Water/chemistry

@article {pmid33730081,
year = {2021},
author = {Szilágyi, Á and Bodor, A and Tolvai, N and Kovács, KL and Bodai, L and Wirth, R and Bagi, Z and Szepesi, Á and Markó, V and Kakuk, B and Bounedjoum, N and Rákhely, G},
title = {A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0248654},
pmid = {33730081},
issn = {1932-6203},
mesh = {Anaerobiosis ; *Biofuels ; Bioreactors/*microbiology ; *Crop Production ; Fermentation ; Lycopersicon esculentum/*chemistry/microbiology ; Metagenomics ; Methane/*biosynthesis ; Microbiota/genetics ; Zea mays/chemistry/microbiology ; },
abstract = {Annually, agricultural activity produces an enormous amount of plant biomass by-product. Many studies have reported the biomethane potential of agro-industrial wastes, but only a few studies have investigated applying the substrates in both batch and continuous mode. Tomato is one of the most popular vegetables globally; its processing releases a substantial amount of by-product, such as stems and leaves. This study examined the BMP of tomato plant (Solanum lycopersicum Mill. L. cv. Alfred) waste. A comparative test revealed that the BMPs of corn stover, tomato waste,and their combination were approximately the same, around 280 mL methane/g Volatile Solid. In contrast, the relative biogas production decreased in the presence of tomato waste in a continuous mesophilic anaerobic digestion system; the daily biogas productions were 860 ± 80, 290 ± 50, and 570 ± 70 mL biogas/gVolatile Solid/day in the case of corn stover, tomato waste, and their mixture, respectively. The methane content of biogas was around 46-48%. The fermentation parameters of the continuous AD experiments were optimal in all cases; thus, TW might have an inhibitory effect on the microbial community. Tomato plant materials contain e.g. flavonoids, glycoalkaloids (such as tomatine and tomatidine), etc. known as antimicrobial and antifungal agents. The negative effect of tomatine on the biogas yield was confirmed in batch fermentation experiments. Metagenomic analysis revealed that the tomato plant waste caused significant rearrangements in the microbial communities in the continuously operated reactors. The results demonstrated that tomato waste could be a good mono-substrate in batch fermentations or a co-substrate with corn stover in a proper ratio in continuous anaerobic fermentations for biogas production. These results also point to the importance of running long-term continuous fermentations to test the suitability of a novel biomass substrate for industrial biogas production.},
}

Anaerobiosis
*Biofuels
Bioreactors/*microbiology
*Crop Production
Fermentation
Lycopersicon esculentum/*chemistry/microbiology
Metagenomics
Methane/*biosynthesis
Microbiota/genetics
Zea mays/chemistry/microbiology

@article {pmid33397406,
year = {2021},
author = {Zhang, R and Walker, AR and Datta, S},
title = {Unraveling city-specific signature and identifying sample origin locations for the data from CAMDA MetaSUB challenge.},
journal = {Biology direct},
volume = {16},
number = {1},
pages = {1},
pmid = {33397406},
issn = {1745-6150},
support = {1UL1TR000064/TR/NCATS NIH HHS/United States ; },
mesh = {Cities ; Humans ; *Machine Learning ; *Metagenome ; Metagenomics ; *Microbiota ; },
abstract = {BACKGROUND: Composition of microbial communities can be location-specific, and the different abundance of taxon within location could help us to unravel city-specific signature and predict the sample origin locations accurately. In this study, the whole genome shotgun (WGS) metagenomics data from samples across 16 cities around the world and samples from another 8 cities were provided as the main and mystery datasets respectively as the part of the CAMDA 2019 MetaSUB "Forensic Challenge". The feature selecting, normalization, three methods of machine learning, PCoA (Principal Coordinates Analysis) and ANCOM (Analysis of composition of microbiomes) were conducted for both the main and mystery datasets.

RESULTS: Features selecting, combined with the machines learning methods, revealed that the combination of the common features was effective for predicting the origin of the samples. The average error rates of 11.93 and 30.37% of three machine learning methods were obtained for main and mystery datasets respectively. Using the samples from main dataset to predict the labels of samples from mystery dataset, nearly 89.98% of the test samples could be correctly labeled as "mystery" samples. PCoA showed that nearly 60% of the total variability of the data could be explained by the first two PCoA axes. Although many cities overlapped, the separation of some cities was found in PCoA. The results of ANCOM, combined with importance score from the Random Forest, indicated that the common "family", "order" of the main-dataset and the common "order" of the mystery dataset provided the most efficient information for prediction respectively.

CONCLUSIONS: The results of the classification suggested that the composition of the microbiomes was distinctive across the cities, which could be used to identify the sample origins. This was also supported by the results from ANCOM and importance score from the RF. In addition, the accuracy of the prediction could be improved by more samples and better sequencing depth.},
}

Cities
Humans
*Machine Learning
*Metagenome
Metagenomics
*Microbiota

@article {pmid33316292,
year = {2021},
author = {Romanis, CS and Pearson, LA and Neilan, BA},
title = {Cyanobacterial blooms in wastewater treatment facilities: Significance and emerging monitoring strategies.},
journal = {Journal of microbiological methods},
volume = {180},
number = {},
pages = {106123},
doi = {10.1016/j.mimet.2020.106123},
pmid = {33316292},
issn = {1872-8359},
mesh = {Bacterial Toxins ; Bacteriological Techniques/methods ; Cyanobacteria/genetics/*growth & development ; Environmental Monitoring ; Fresh Water/microbiology ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Microbiota ; Proteomics/methods ; Sensitivity and Specificity ; Waste Water/*microbiology ; Water Purification/*methods ; },
abstract = {Municipal wastewater treatment facilities (WWTFs) are prone to the proliferation of cyanobacterial species which thrive in stable, nutrient-rich environments. Dense cyanobacterial blooms frequently disrupt treatment processes and the supply of recycled water due to their production of extracellular polymeric substances, which hinder microfiltration, and toxins, which pose a health risk to end-users. A variety of methods are employed by water utilities for the identification and monitoring of cyanobacteria and their toxins in WWTFs, including microscopy, flow cytometry, ELISA, chemoanalytical methods, and more recently, molecular methods. Here we review the literature on the occurrence and significance of cyanobacterial blooms in WWTFs and discuss the pros and cons of the various strategies for monitoring these potentially hazardous events. Particular focus is directed towards next-generation metagenomic sequencing technologies for the development of site-specific cyanobacterial bloom management strategies. Long-term multi-omic observations will enable the identification of indicator species and the development of site-specific bloom dynamics models for the mitigation and management of cyanobacterial blooms in WWTFs. While emerging metagenomic tools could potentially provide deep insight into the diversity and flux of problematic cyanobacterial species in these systems, they should be considered a complement to, rather than a replacement of, quantitative chemoanalytical approaches.},
}

Bacterial Toxins
Bacteriological Techniques/methods
Cyanobacteria/genetics/*growth & development
Environmental Monitoring
Fresh Water/microbiology
High-Throughput Nucleotide Sequencing
Metagenomics
Microbiota
Proteomics/methods
Sensitivity and Specificity
Waste Water/*microbiology
Water Purification/*methods

@article {pmid32433514,
year = {2021},
author = {Iljazovic, A and Roy, U and Gálvez, EJC and Lesker, TR and Zhao, B and Gronow, A and Amend, L and Will, SE and Hofmann, JD and Pils, MC and Schmidt-Hohagen, K and Neumann-Schaal, M and Strowig, T},
title = {Perturbation of the gut microbiome by Prevotella spp. enhances host susceptibility to mucosal inflammation.},
journal = {Mucosal immunology},
volume = {14},
number = {1},
pages = {113-124},
pmid = {32433514},
issn = {1935-3456},
mesh = {Adaptive Immunity ; Animals ; Bacteroidaceae Infections/*immunology/*microbiology ; Cytokines/metabolism ; Disease Models, Animal ; Disease Susceptibility ; Gastrointestinal Microbiome/*immunology ; Host-Pathogen Interactions/*immunology ; Inflammation Mediators/metabolism ; Intestinal Mucosa/*immunology/metabolism/*microbiology/pathology ; Metagenome ; Metagenomics/methods ; Mice ; Mice, Knockout ; Mucositis/etiology/metabolism/pathology ; Prevotella/*immunology ; },
abstract = {Diverse microbial signatures within the intestinal microbiota have been associated with intestinal and systemic inflammatory diseases, but whether these candidate microbes actively modulate host phenotypes or passively expand within the altered microbial ecosystem is frequently not known. Here we demonstrate that colonization of mice with a member of the genus Prevotella, which has been previously associated to colitis in mice, exacerbates intestinal inflammation. Our analysis revealed that Prevotella intestinalis alters composition and function of the ecosystem resulting in a reduction of short-chain fatty acids, specifically acetate, and consequently a decrease in intestinal IL-18 levels during steady state. Supplementation of IL-18 to Prevotella-colonized mice was sufficient to reduce intestinal inflammation. Hence, we conclude that intestinal Prevotella colonization results in metabolic changes in the microbiota, which reduce IL-18 production and consequently exacerbate intestinal inflammation, and potential systemic autoimmunity.},
}

Adaptive Immunity
Animals
Bacteroidaceae Infections/*immunology/*microbiology
Cytokines/metabolism
Disease Models, Animal
Disease Susceptibility
Gastrointestinal Microbiome/*immunology
Host-Pathogen Interactions/*immunology
Inflammation Mediators/metabolism
Intestinal Mucosa/*immunology/metabolism/*microbiology/pathology
Metagenome
Metagenomics/methods
Mice
Mice, Knockout
Mucositis/etiology/metabolism/pathology
Prevotella/*immunology

@article {pmid33662003,
year = {2021},
author = {El Alam, MB and Sims, TT and Kouzy, R and Biegert, GWG and Jaoude, JABI and Karpinets, TV and Yoshida-Court, K and Wu, X and Delgado-Medrano, AY and Mezzari, MP and Ajami, NJ and Solley, T and Ahmed-Kaddar, M and Lin, LL and Ramondetta, L and Jazaeri, A and Jhingran, A and Eifel, PJ and Schmeler, KM and Wargo, J and Klopp, AH and Colbert, LE},
title = {A prospective study of the adaptive changes in the gut microbiome during standard-of-care chemoradiotherapy for gynecologic cancers.},
journal = {PloS one},
volume = {16},
number = {3},
pages = {e0247905},
pmid = {33662003},
issn = {1932-6203},
support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; },
mesh = {Adult ; Antineoplastic Agents/adverse effects/therapeutic use ; Bacteria/drug effects/isolation & purification/radiation effects ; Chemoradiotherapy/adverse effects ; Female ; Gastrointestinal Microbiome/*drug effects/*radiation effects ; Genital Neoplasms, Female/*drug therapy/*radiotherapy ; Humans ; Middle Aged ; Prospective Studies ; },
abstract = {BACKGROUND: A diverse and abundant gut microbiome can improve cancer patients' treatment response; however, the effect of pelvic chemoradiotherapy (CRT) on gut diversity and composition is unclear. The purpose of this prospective study was to identify changes in the diversity and composition of the gut microbiome during and after pelvic CRT.

MATERIALS AND METHODS: Rectal swabs from 58 women with cervical, vaginal, or vulvar cancer from two institutions were prospectively analyzed before CRT (baseline), during CRT (weeks 1, 3, and 5), and at first follow-up (week 12) using 16Sv4 rRNA gene sequencing of the V4 hypervariable region of the bacterial 16S rRNA marker gene. 42 of these patients received antibiotics during the study period. Observed operational taxonomic units (OTUs; representative of richness) and Shannon, Simpson, Inverse Simpson, and Fisher diversity indices were used to characterize alpha (within-sample) diversity. Changes over time were assessed using a paired t-test, repeated measures ANOVA, and linear mixed modeling. Compositional changes in specific bacteria over time were evaluated using linear discriminant analysis effect size.

RESULTS: Gut microbiome richness and diversity levels continually decreased throughout CRT (mean Shannon diversity index, 2.52 vs. 2.91; all P <0.01), but were at or near baseline levels in 60% of patients by week 12. Patients with higher gut diversity at baseline had the steepest decline in gut microbiome diversity. Gut microbiome composition was significantly altered during CRT, with increases in Proteobacteria and decreases in Clostridiales, but adapted after CRT, with increases in Bacteroides species.

CONCLUSION: After CRT, the diversity of the gut microbiomes in this population tended to return to baseline levels by the 12 week follow-up period, but structure and composition remained significantly altered. These changes should be considered when designing studies to analyze the gut microbiome in patients who receive pelvic CRT for gynecologic cancers.},
}

Adult
Antineoplastic Agents/adverse effects/therapeutic use
Bacteria/drug effects/isolation & purification/radiation effects
Chemoradiotherapy/adverse effects
Female
Gastrointestinal Microbiome/*drug effects/*radiation effects
Genital Neoplasms, Female/*drug therapy/*radiotherapy
Humans
Middle Aged
Prospective Studies

@article {pmid33207267,
year = {2021},
author = {Beraud-Martínez, LK and Gómez-Gil, B and Franco-Nava, MÁ and Almazán-Rueda, P and Betancourt-Lozano, M},
title = {A metagenomic assessment of microbial communities in anaerobic bioreactors and sediments: Taxonomic and functional relationships.},
journal = {Anaerobe},
volume = {68},
number = {},
pages = {102296},
doi = {10.1016/j.anaerobe.2020.102296},
pmid = {33207267},
issn = {1095-8274},
mesh = {Anaerobiosis ; Bacteria/*classification/genetics/*isolation & purification ; Bioreactors/*microbiology ; Geologic Sediments/*microbiology ; Manure/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Oxygen/metabolism ; Sewage/microbiology ; },
abstract = {The present study used metagenomic sequencing, metagenome assembly and physical-chemical analysis to describe taxonomically and functionally 3 anaerobic bioreactors treating manure (LI), brewery (BR) and cornmeal (CO) wastes, and an anaerobic estuarine sediment (ES). Proteobacteria, Firmicutes, Euryarchaeota and Bacteroidetes were the most abundant Phyla in all metagenomes. A bacteria/archaea ratio of 3.4 was found in the industrial full-scale anaerobic bioreactors BR and CO, while ratios greater than 10 were found for LI and ES. Canonical correspondence analysis showed that environmental variables such as chemical oxygen demand, lipid content, and ammonium nitrogen influenced the ordination of taxonomic groups. Mesotoga prima was linked to high-temperature conditions, particularly in the BR bioreactor, along with the presence of heat shock proteins genes. Likewise, the hydrogenotrophic methanogen, Methanoregula formicica, was associated with high ammonium concentration in LI bioreactor. The interactions of microbes with specific methanogenic pathways were identified using Clusters of Orthologous Groups (COG) functions, while metagenome-assembled genomes (MAGs) further confirmed relationships between taxa and functions. Our results provide valuable information to understand microbial processes in anaerobic environments.},
}

Anaerobiosis
Bacteria/*classification/genetics/*isolation & purification
Bioreactors/*microbiology
Geologic Sediments/*microbiology
Manure/microbiology
Metagenome
Metagenomics
*Microbiota
Oxygen/metabolism
Sewage/microbiology

@article {pmid32758682,
year = {2021},
author = {Andersen, TO and Kunath, BJ and Hagen, LH and Arntzen, MØ and Pope, PB},
title = {Rumen metaproteomics: Closer to linking rumen microbial function to animal productivity traits.},
journal = {Methods (San Diego, Calif.)},
volume = {186},
number = {},
pages = {42-51},
doi = {10.1016/j.ymeth.2020.07.011},
pmid = {32758682},
issn = {1095-9130},
mesh = {Animal Husbandry/*methods ; Animals ; Gastrointestinal Microbiome/*physiology ; Host Microbial Interactions/physiology ; Livestock/microbiology/physiology ; Metagenome ; Metagenomics/*methods ; Proteomics/*methods ; Quantitative Trait Loci/physiology ; Rumen/*microbiology ; Ruminants/microbiology/physiology ; },
abstract = {The rumen microbiome constitutes a dense and complex mixture of anaerobic bacteria, archaea, protozoa, virus and fungi. Collectively, rumen microbial populations interact closely in order to degrade and ferment complex plant material into nutrients for host metabolism, a process which also produces other by-products, such as methane gas. Our understanding of the rumen microbiome and its functions are of both scientific and industrial interest, as the metabolic functions are connected to animal health and nutrition, but at the same time contribute significantly to global greenhouse gas emissions. While many of the major microbial members of the rumen microbiome are acknowledged, advances in modern culture-independent meta-omic techniques, such as metaproteomics, enable deep exploration into active microbial populations involved in essential rumen metabolic functions. Meaningful and accurate metaproteomic analyses are highly dependent on representative samples, precise protein extraction and fractionation, as well as a comprehensive and high-quality protein sequence database that enables precise protein identification and quantification. This review focuses on the application of rumen metaproteomics, and its potential towards understanding the complex rumen microbiome and its metabolic functions. We present and discuss current methods in sample handling, protein extraction and data analysis for rumen metaproteomics, and finally emphasize the potential of (meta)genome-integrated metaproteomics for accurate reconstruction of active microbial populations in the rumen.},
}

Animal Husbandry/*methods
Animals
Gastrointestinal Microbiome/*physiology
Host Microbial Interactions/physiology
Livestock/microbiology/physiology
Metagenome
Metagenomics/*methods
Proteomics/*methods
Quantitative Trait Loci/physiology
Rumen/*microbiology
Ruminants/microbiology/physiology

@article {pmid32615270,
year = {2021},
author = {Guilloux, CA and Lamoureux, C and Beauruelle, C and Héry-Arnaud, G},
title = {Porphyromonas: A neglected potential key genus in human microbiomes.},
journal = {Anaerobe},
volume = {68},
number = {},
pages = {102230},
doi = {10.1016/j.anaerobe.2020.102230},
pmid = {32615270},
issn = {1095-8274},
mesh = {Bacteroidaceae Infections/*microbiology ; Humans ; *Microbiota ; Phylogeny ; Porphyromonas/classification/genetics/growth & development/*isolation & purification ; },
abstract = {Anaerobes form a large part of microbial communities, and have begun to be specifically studied in both healthy and pathologic contexts. Porphyromonas is one of the top ten anaerobic taxa in the microbiome (anaerobiome) in healthy subjects. However, to date, most studies focused on the deleterious role of P. gingivalis, the most widely described species. Interestingly, targeted metagenomics reveals Porphyromonas other than gingivalis (POTG), highlighting other species such as P. catoniae or P. pasteri as potential biomarkers in disease progression or pathogen colonization susceptibility. From the sparse data, it appears that the Porphyromonas genus may also be a relevant target of investigation in several pulmonary diseases. Moreover, deciphering cutaneous, gastric and oral microbiomes hint that Porphyromonas may be a genus of interest in non-pulmonary diseases. This review aims to summarize the major data on POTG and to report their impact on the various human microbiomes in different clinical states.},
}

Bacteroidaceae Infections/*microbiology
Humans
*Microbiota
Phylogeny
Porphyromonas/classification/genetics/growth & development/*isolation & purification

@article {pmid34622635,
year = {2021},
author = {Xu, Z and Chen, X and Wei, Y and Zhang, Q and Ji, X},
title = {[Metagenomic analysis of the diversity of microbes in the Napahai plateau wetland and their carbon and nitrogen metabolisms].},
journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology},
volume = {37},
number = {9},
pages = {3276-3292},
doi = {10.13345/j.cjb.200658},
pmid = {34622635},
issn = {1872-2075},
abstract = {Due to the special geographical location and the complex ecosystem types, plateau wetlands play important ecological roles in water supply, greenhouse gas regulation and biodiversity preservation. Napahai plateau wetland is a special wetland type with low latitude and high altitude, and its microbial diversity was rarely studied. The diversity of microbial communities in the Napahai plateau wetland was analyzed using metagenomics method. Among the microbes detected, 184 phyla, 3 262 genera and 24 260 species belong to the bacterial domain, 13 phyla and 32 genera belong to the archaeal domain, and 13 phyla and 47 genera belong to the fungal domain. Significant differences in species diversity between soil and water were observed. Acidobacteria, Proteobacteria and Actinobacteria were dominant phyla in soil, while Proteobacteria and Bacteroides were dominant phyla in water. Since the carbon and nitrogen metabolism genes were abundant, the pathways of carbon fixation and nitrogen metabolism were analyzed. Calvin cycle, reductive tricarboxylic acid cycle and 3-hydroxypropionic acid cycle were the main carbon fixation pathways, while Proteobacteria, Chloroflexi, and Crenarchaeota were the main carbon-fixing bacteria group. As for the nitrogen cycle, nitrogen fixation and dissimilatory nitrate reduction were dominant in water, while nitrification and denitrification were dominant in soil. Proteobacteria, Nitrospirae, Verrucomicrobia, Actinobacteria, Thaumarchaeota and Euryarchaeota contributed to the nitrogen cycle. The study on microbial diversity of Napahai plateau wetlands provides new knowledge for the comprehensive management and protection of wetland environment in China.},
}

@article {pmid34519857,
year = {2021},
author = {Zhu, HZ and Jiang, MZ and Zhou, N and Jiang, CY and Liu, SJ},
title = {Submerged macrophytes recruit unique microbial communities and drive functional zonation in an aquatic system.},
journal = {Applied microbiology and biotechnology},
volume = {105},
number = {19},
pages = {7517-7528},
pmid = {34519857},
issn = {1432-0614},
support = {NSFC grant no. 31861133002//National Natural Science Foundation of China/ ; },
mesh = {Beijing ; *Metagenomics ; *Microbiota ; },
abstract = {Aquatic and wetland systems are widely used for landscapes and water regeneration. Microbiomes and submerged macrophytes (hydrophytes) play essential roles in conversions of organic and inorganic compounds in those ecosystems. The systems were extensively investigated for microbial diversities and compositions. However, little is known about how hydrophytes recruited diverse microbiota and affected functional zonation in aquatic systems. To address this issue, epiphytic leaf and root, sediment, and surrounding water samples were collected from the dragon-shape aquatic system in Beijing Olympic Park. Metagenomic DNAs were extracted and subjected to sequencing. Results showed that epiphytic leaf and root microbiomes and metabolic marker genes were remarkably different from that of surrounding environment. Twenty indicator bacterial genera for epiphytic microbiomes were identified and 50 metabolic marker genes were applied to evaluate the function of epiphytic leaf and root, water, and sediment microbiomes. Co-occurrence analysis revealed highly modularized pattern of metabolic marker genes and indicator bacterial genera related to metabolic functions. These results suggested that hydrophytes shaped microbiomes and drove functional zonation in aquatic systems. KEY POINTS: • Microbiomes of hydrophytes and their surrounding environments were investigated. • Twenty indicator bacterial genera highly specific to epiphytic biofilms were identified. • Epiphytes recruited unique microbiomes and drove functional zonation in aquatic systems.},
}

Beijing
*Metagenomics
*Microbiota

@article {pmid34465900,
year = {2021},
author = {Sulaiman, I and Chung, M and Angel, L and Tsay, JJ and Wu, BG and Yeung, ST and Krolikowski, K and Li, Y and Duerr, R and Schluger, R and Thannickal, SA and Koide, A and Rafeq, S and Barnett, C and Postelnicu, R and Wang, C and Banakis, S and Pérez-Pérez, L and Shen, G and Jour, G and Meyn, P and Carpenito, J and Liu, X and Ji, K and Collazo, D and Labarbiera, A and Amoroso, N and Brosnahan, S and Mukherjee, V and Kaufman, D and Bakker, J and Lubinsky, A and Pradhan, D and Sterman, DH and Weiden, M and Heguy, A and Evans, L and Uyeki, TM and Clemente, JC and de Wit, E and Schmidt, AM and Shopsin, B and Desvignes, L and Wang, C and Li, H and Zhang, B and Forst, CV and Koide, S and Stapleford, KA and Khanna, KM and Ghedin, E and Segal, LN},
title = {Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome.},
journal = {Nature microbiology},
volume = {6},
number = {10},
pages = {1245-1258},
pmid = {34465900},
issn = {2058-5276},
support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK110014/DK/NIDDK NIH HHS/United States ; R01 AI143861/AI/NIAID NIH HHS/United States ; R01 HL125816/HL/NHLBI NIH HHS/United States ; R21 AI158997/AI/NIAID NIH HHS/United States ; R37 CA244775/CA/NCI NIH HHS/United States ; P20 CA252728/CA/NCI NIH HHS/United States ; },
mesh = {Adaptive Immunity ; Adult ; Aged ; Bacteria/classification/genetics/isolation & purification ; Bacterial Load ; Bronchoalveolar Lavage Fluid/immunology/*microbiology/virology ; COVID-19/immunology/microbiology/mortality/*therapy ; Critical Illness ; Female ; Hospitalization ; Humans ; Immunity, Innate ; Male ; Microbiota ; Middle Aged ; Odds Ratio ; Prognosis ; Prospective Studies ; *Respiration, Artificial ; Respiratory System/immunology/microbiology/virology ; SARS-CoV-2/immunology/*pathogenicity ; Viral Load ; },
abstract = {Respiratory failure is associated with increased mortality in COVID-19 patients. There are no validated lower airway biomarkers to predict clinical outcome. We investigated whether bacterial respiratory infections were associated with poor clinical outcome of COVID-19 in a prospective, observational cohort of 589 critically ill adults, all of whom required mechanical ventilation. For a subset of 142 patients who underwent bronchoscopy, we quantified SARS-CoV-2 viral load, analysed the lower respiratory tract microbiome using metagenomics and metatranscriptomics and profiled the host immune response. Acquisition of a hospital-acquired respiratory pathogen was not associated with fatal outcome. Poor clinical outcome was associated with lower airway enrichment with an oral commensal (Mycoplasma salivarium). Increased SARS-CoV-2 abundance, low anti-SARS-CoV-2 antibody response and a distinct host transcriptome profile of the lower airways were most predictive of mortality. Our data provide evidence that secondary respiratory infections do not drive mortality in COVID-19 and clinical management strategies should prioritize reducing viral replication and maximizing host responses to SARS-CoV-2.},
}

Adaptive Immunity
Adult
Aged
Bacteria/classification/genetics/isolation & purification
Bacterial Load
Bronchoalveolar Lavage Fluid/immunology/*microbiology/virology
COVID-19/immunology/microbiology/mortality/*therapy
Critical Illness
Female
Hospitalization
Humans
Immunity, Innate
Male
Microbiota
Middle Aged
Odds Ratio
Prognosis
Prospective Studies
*Respiration, Artificial
Respiratory System/immunology/microbiology/virology
SARS-CoV-2/immunology/*pathogenicity
Viral Load

@article {pmid33782219,
year = {2021},
author = {Jeong, M and Choi, DH and Cheon, WJ and Kim, JG},
title = {Pyrosequencing and Taxonomic Composition of the Fungal Community from Soil of Tricholoma matsutake in Gyeongju.},
journal = {Journal of microbiology and biotechnology},
volume = {31},
number = {5},
pages = {686-695},
doi = {10.4014/jmb.2103.03021},
pmid = {33782219},
issn = {1738-8872},
mesh = {Agaricales/classification/genetics/growth & development/*physiology ; Fungi/classification/genetics/growth & development/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Mycobiome/*genetics ; Pinus/microbiology ; Republic of Korea ; Seasons ; *Soil Microbiology ; },
abstract = {Tricholoma matsutake is an ectomycorrhizal fungus that has a symbiotic relationship with the root of Pinus densiflora. Soil microbial communities greatly affect the growth of T. matsutake, however, few studies have examined the characteristics of these communities. In the present study, we analyzed soil fungal communities from Gyeongju and Yeongdeok using metagenomic pyrosequencing to investigate differences in fungal species diversity, richness, and taxonomic composition between the soil under T. matsutake fruiting bodies (Sample 2) and soil where the fairy ring of T. matsutake was no longer present (Sample 1). The same spot was investigated three times at intervals of four months to observe changes in the community. In the samples from Yeongdeok, the number of valid reads was lower than that at Gyeongju. The operational taxonomic units of most Sample 2 groups were less than those of Sample 1 groups, indicating that fungal diversity was low in the T. matsutakedominant soil. The soil under the T. matsutake fruiting bodies was dominated by more than 51% T. matsutake. From fall to the following spring, the ratio of T. matsutake decreased. Basidiomycota was the dominant phylum in most samples. G-F1-2, G-F2-2, and Y-F1-2 had the genera Tricholoma, Umbelopsis, Oidiodendron, Sagenomella, Cladophialophora, and Phialocephala in common. G-F1-1, G-F2-1, and Y-F1-1 had 10 genera including Umbelopsis and Sagenomella in common. From fall to the following spring, the amount of phyla Basidiomycota and Mucoromycota gradually decreased but that of phylum Ascomycota increased. We suggest that the genus Umbelopsis is positively related to T. matsutake.},
}

Agaricales/classification/genetics/growth & development/*physiology
Fungi/classification/genetics/growth & development/isolation & purification
High-Throughput Nucleotide Sequencing
Metagenomics
Mycobiome/*genetics
Pinus/microbiology
Republic of Korea
Seasons
*Soil Microbiology

@article {pmid34530224,
year = {2021},
author = {Kim, DD and Wan, L and Cao, X and Klisarova, D and Gerdzhikov, D and Zhou, Y and Song, C and Yoon, S},
title = {Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea.},
journal = {Water research},
volume = {204},
number = {},
pages = {117625},
doi = {10.1016/j.watres.2021.117625},
pmid = {34530224},
issn = {1879-2448},
mesh = {Cell Proliferation ; *Dinoflagellida/genetics ; Harmful Algal Bloom ; *Microbiota ; *Vibrio ; },
abstract = {Coastal harmful algal blooms (HABs), commonly termed 'red tides', have severe undesirable consequences to the marine ecosystems and local fishery and tourism industries. Increase in nitrogen and/or phosphorus loading is often regarded as the major culprits of increasing frequency and intensity of the coastal HAB; however, fundamental understanding is lacking as to the causes and mechanism of bloom formation despite decades of intensive investigation. In this study, we interrogated the prokaryotic microbiomes of surface water samples collected at two neighboring segments of East China Sea that contrast greatly in terms of the intensity and frequency of Prorocentrum-dominated HAB. Mantel tests identified significant correlations between the structural and functional composition of the microbiomes and the physicochemical state and the algal biomass density of the surface seawater, implying the possibility that prokaryotic microbiota may play key roles in the coastal HAB. A conspicuous feature of the microbiomes at the sites characterized with high trophic state index and eukaryotic algal cell counts was disproportionate proliferation of Vibrio spp., and their complete domination of the functional genes attributable to the dissimilatory nitrate reduction to ammonia (DNRA) pathway substantially enriched at these sites. The genes attributed to phosphorus uptake function were significantly enriched at these sites, presumably due to the Pi-deficiency induced by algal growth; however, the profiles of the phosphorus mineralization genes lacked consistency, barring any conclusive evidence with regard to contribution of prokaryotic microbiota to phosphorus bioavailability. The results of the co-occurrence network analysis performed with the core prokaryotic microbiome supported that the observed proliferation of Vibrio and HAB may be causally associated. The findings of this study suggest a previously unidentified association between Vibrio proliferation and the Prorocentrum-dominated HAB in the subtropical East China Sea, and opens a discussion regarding a theoretically unlikely, but still possible, involvement of Vibrio-mediated DNRA in Vibrio-Prorocentrum symbiosis. Further experimental substantiation of this supposed symbiotic mechanism may prove crucial in understanding the dynamics of explosive local algal growth in the region during spring algal blooms.},
}

Cell Proliferation
*Dinoflagellida/genetics
Harmful Algal Bloom
*Microbiota
*Vibrio

@article {pmid33791954,
year = {2021},
author = {de Oliveira Santos, L and Guedes, IA and Azevedo, SMFOE and Pacheco, ABF},
title = {Occurrence and diversity of viruses associated with cyanobacterial communities in a Brazilian freshwater reservoir.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {52},
number = {2},
pages = {773-785},
pmid = {33791954},
issn = {1678-4405},
mesh = {Bacteriophages/classification/genetics/*isolation & purification ; *Biodiversity ; Brazil ; Cyanobacteria/classification/genetics/growth & development/*virology ; Fresh Water/microbiology/*virology ; Genome, Viral ; Microcystis/genetics/growth & development/virology ; Phylogeny ; Water Resources ; },
abstract = {As part of the phytoplankton of marine and freshwater environments around the world, cyanobacteria interact with viruses (cyanophages) that affect their abundance and diversity. Investigations focusing on cyanophages co-occurring with freshwater cyanobacteria are scarce, particularly in Brazil. The aim of this study was to assess the diversity of cyanophages associated with a Microcystis-dominated cyanobacterial bloom in a tropical reservoir. Samples were processed as viral fractions of water and cellular fractions, and temporal fluctuations in the abundance of Ma-LMM01-type cyanophages and their Microcystis hosts were determined by qPCR. We applied shotgun metagenomics to obtain a wider characterization of the cyanophage community. During the study period, Microcystis gene copies were quantified in all cellular fractions, and the copy number of the Ma-LMM01 phage gene tended to increase with host abundance. Metagenomic analysis demonstrated that Caudovirales was the major viral order associated with the cyanophage families Myoviridae (34-88%), Podoviridae (3-42%), and Siphoviridae (6-23%). The metagenomic analysis results confirmed the presence of Microcystis cyanophages in both viral and cellular fractions and demonstrated a high relative abundance of picocyanobacteria-related viruses and Prochlorococcus (36-52%) and Synechococcus (37-50%) phages. For other main cyanobacterial genera, no related cyanophages were identified, which was probably due to the scarce representation of cyanophage sequences in databanks. Thus, the studied reservoir hosted a diverse cyanophage community with a remarkable contribution of phages related to picoplanktonic cyanobacteria. These results provide insights that motivate future sequencing efforts to assess cyanophage diversity and recover complete genomes.},
}

Bacteriophages/classification/genetics/*isolation & purification
*Biodiversity
Brazil
Cyanobacteria/classification/genetics/growth & development/*virology
Fresh Water/microbiology/*virology
Genome, Viral
Microcystis/genetics/growth & development/virology
Phylogeny
Water Resources

@article {pmid34444797,
year = {2021},
author = {Barber, C and Mego, M and Sabater, C and Vallejo, F and Bendezu, RA and Masihy, M and Guarner, F and Espín, JC and Margolles, A and Azpiroz, F},
title = {Differential Effects of Western and Mediterranean-Type Diets on Gut Microbiota: A Metagenomics and Metabolomics Approach.},
journal = {Nutrients},
volume = {13},
number = {8},
pages = {},
pmid = {34444797},
issn = {2072-6643},
support = {SAF 2016-76648-R//Ministerio de Economía y Competitividad/ ; PID2019-103914RB-I00//Ministerio de Ciencia e Innovacion/ ; AGL2016-78311-R//Ministerio de Ciencia e Innovación/ ; FJC2019-042125-I//Ministerio de Ciencia e Innovación/ ; },
mesh = {Adolescent ; Adult ; Biodiversity ; Colon ; Cross-Over Studies ; *Diet, Mediterranean ; *Diet, Western ; Feces/microbiology ; Flatulence ; *Gastrointestinal Microbiome ; Humans ; Male ; Metabolomics ; *Metagenomics ; Surveys and Questionnaires ; Young Adult ; },
abstract = {Our aim was to determine the effect of diet on gut microbiota, digestive function and sensations, using an integrated clinical, metagenomics and metabolomics approach. We conducted a cross-over, randomised study on the effects of a Western-type diet versus a fibre-enriched Mediterranean diet. In 20 healthy men, each diet was administered for 2 weeks preceded by a 2-week washout diet. The following outcomes were recorded: (a) number of anal gas evacuations; (b) digestive sensations; (c) volume of gas evacuated after a probe meal; (d) colonic content by magnetic resonance imaging; (e) gut microbiota taxonomy and metabolic functions by shotgun sequencing of faecal samples; (f) urinary metabolites using untargeted metabolomics. As compared to a Western diet, the Mediterranean diet was associated with (i) higher number of anal gas evacuations, (ii) sensation of flatulence and borborygmi, (iii) larger volume of gas after the meal and (iv) larger colonic content. Despite the relatively little difference in microbiota composition between both diets, microbial metabolism differed substantially, as shown by urinary metabolite profiles and the abundance of microbial metabolic pathways. The effects of the diet were less evident in individuals with robust microbiotas (higher beta-diversity). To conclude, healthy individuals tolerate dietary changes with minor microbial modifications at the composition level but with remarkable variation in microbial metabolism.},
}

Adolescent
Adult
Biodiversity
Colon
Cross-Over Studies
*Diet, Mediterranean
*Diet, Western
Feces/microbiology
Flatulence
*Gastrointestinal Microbiome
Humans
Male
Metabolomics
*Metagenomics
Surveys and Questionnaires
Young Adult

@article {pmid33247928,
year = {2021},
author = {Pittet, LF and Bertelli, C and Scherz, V and Rochat, I and Mardegan, C and Brouillet, R and Jaton, K and Mornand, A and Kaiser, L and Posfay-Barbe, K and Asner, SA and Greub, G},
title = {Chlamydia pneumoniae and Mycoplasma pneumoniae in children with cystic fibrosis: impact on bacterial respiratory microbiota diversity.},
journal = {Pathogens and disease},
volume = {79},
number = {1},
pages = {},
pmid = {33247928},
issn = {2049-632X},
mesh = {Biodiversity ; Child ; Child, Preschool ; Chlamydophila Infections/microbiology ; Chlamydophila pneumoniae/genetics/*isolation & purification ; Cystic Fibrosis/*microbiology ; DNA, Bacterial ; Humans ; Metagenomics ; *Microbiota ; Mycoplasma pneumoniae/genetics/*isolation & purification ; Pneumonia, Mycoplasma/microbiology ; Prospective Studies ; RNA, Ribosomal, 16S ; Respiratory System/*microbiology ; Sputum/microbiology ; },
abstract = {OBJECTIVES: The contribution of intracellular and fastidious bacteria in Cystic fibrosis (CF) pulmonary exacerbations, and progressive lung function decline remains unknown. This project aimed to explore their impact on bacterial microbiota diversity over time in CF children.

METHODS: Sixty-one children enrolled in the MUCOVIB multicentre prospective cohort provided 746 samples, mostly nasopharyngeal swabs, throat swabs and sputa which were analysed using culture, specific real-time qPCRs and 16S rRNA amplicon metagenomics.

RESULTS: Chlamydia pneumoniae (n = 3) and Mycoplasma pneumoniae (n = 1) were prospectively documented in 6.6% of CF children. Microbiota alpha-diversity in children with a documented C. pneumoniae was highly variable, similarly to children infected with Staphylococcus aureus or Pseudomonas aeruginosa. The transition from routine follow-up visits to pulmonary exacerbation (n = 17) yielded variable changes in diversity indexes with some extreme loss of diversity.

CONCLUSIONS: The high rate of C. pneumoniae detection supports the need for regular screenings in CF patients. A minor impact of C. pneumoniae on the microbial community structure was documented. Although detected in a single patient, M. pneumoniae should also be considered as a possible aetiology of lung infection in CF subjects.},
}

Biodiversity
Child
Child, Preschool
Chlamydophila Infections/microbiology
Chlamydophila pneumoniae/genetics/*isolation & purification
Cystic Fibrosis/*microbiology
DNA, Bacterial
Humans
Metagenomics
*Microbiota
Mycoplasma pneumoniae/genetics/*isolation & purification
Pneumonia, Mycoplasma/microbiology
Prospective Studies
RNA, Ribosomal, 16S
Respiratory System/*microbiology
Sputum/microbiology

@article {pmid33115723,
year = {2020},
author = {Tidjani Alou, M and Naud, S and Khelaifia, S and Bonnet, M and Lagier, JC and Raoult, D},
title = {State of the Art in the Culture of the Human Microbiota: New Interests and Strategies.},
journal = {Clinical microbiology reviews},
volume = {34},
number = {1},
pages = {},
pmid = {33115723},
issn = {1098-6618},
mesh = {Bacteria/classification/*isolation & purification/metabolism ; Bacteriological Techniques/*methods ; Culture Media/*chemistry ; Flow Cytometry ; Gastrointestinal Microbiome ; Humans ; },
abstract = {The last 5 years have seen a turning point in the study of the gut microbiota with a rebirth of culture-dependent approaches to study the gut microbiota. High-throughput methods have been developed to study bacterial diversity with culture conditions aimed at mimicking the gut environment by using rich media such as YCFA (yeast extract, casein hydrolysate, fatty acids) and Gifu anaerobic medium in an anaerobic workstation, as well as media enriched with rumen and blood and coculture, to mimic the symbiosis of the gut microbiota. Other culture conditions target phenotypic and metabolic features of bacterial species to facilitate their isolation. Preexisting technologies such as next-generation sequencing and flow cytometry have also been utilized to develop innovative methods to isolate previously uncultured bacteria or explore viability in samples of interest. These techniques have been applied to isolate CPR (Candidate Phyla Radiation) among other, more classic approaches. Methanogenic archaeal and fungal cultures present different challenges than bacterial cultures. Efforts to improve the available systems to grow archaea have been successful through coculture systems. For fungi that are more easily isolated from the human microbiota, the challenge resides in the identification of the isolates, which has been approached by applying matrix-assisted laser desorption ionization-time of flight mass spectrometry technology to fungi. Bacteriotherapy represents a nonnegligible avenue in the future of medicine to correct dysbiosis and improve health or response to therapy. Although great strides have been achieved in the last 5 years, efforts in bacterial culture need to be sustained to continue deciphering the dark matter of metagenomics, particularly CPR, and extend these methods to archaea and fungi.},
}

Bacteria/classification/*isolation & purification/metabolism
Bacteriological Techniques/*methods
Culture Media/*chemistry
Flow Cytometry
Gastrointestinal Microbiome
Humans

@article {pmid32520351,
year = {2020},
author = {Reddington, K and Eccles, D and O'Grady, J and Drown, DM and Hansen, LH and Nielsen, TK and Ducluzeau, AL and Leggett, RM and Heavens, D and Peel, N and Snutch, TP and Bayega, A and Oikonomopoulos, S and Ragoussis, I and Barry, T and van der Helm, E and Jolic, D and Richardson, H and Jansen, H and Tyson, JR and Jain, M and Brown, BL},
title = {Metagenomic analysis of planktonic riverine microbial consortia using nanopore sequencing reveals insight into river microbe taxonomy and function.},
journal = {GigaScience},
volume = {9},
number = {6},
pages = {},
pmid = {32520351},
issn = {2047-217X},
support = {BB/M011216/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; TL4 GM118992/GM/NIGMS NIH HHS/United States ; BB/J004669/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CSP17270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/N013956/1/MRC_/Medical Research Council/United Kingdom ; P20 GM103395/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; RL5 GM118990/GM/NIGMS NIH HHS/United States ; 10677//CIHR/Canada ; },
mesh = {Biodiversity ; *Metagenome ; Metagenomics/*methods ; *Microbial Consortia ; *Microbiota ; Nanopore Sequencing ; Plankton/*genetics ; Rivers/microbiology ; Water Microbiology ; },
abstract = {BACKGROUND: Riverine ecosystems are biogeochemical powerhouses driven largely by microbial communities that inhabit water columns and sediments. Because rivers are used extensively for anthropogenic purposes (drinking water, recreation, agriculture, and industry), it is essential to understand how these activities affect the composition of river microbial consortia. Recent studies have shown that river metagenomes vary considerably, suggesting that microbial community data should be included in broad-scale river ecosystem models. But such ecogenomic studies have not been applied on a broad "aquascape" scale, and few if any have applied the newest nanopore technology.

RESULTS: We investigated the metagenomes of 11 rivers across 3 continents using MinION nanopore sequencing, a portable platform that could be useful for future global river monitoring. Up to 10 Gb of data per run were generated with average read lengths of 3.4 kb. Diversity and diagnosis of river function potential was accomplished with 0.5-1.0 ⋅ 106 long reads. Our observations for 7 of the 11 rivers conformed to other river-omic findings, and we exposed previously unrecognized microbial biodiversity in the other 4 rivers.

CONCLUSIONS: Deeper understanding that emerged is that river microbial consortia and the ecological functions they fulfil did not align with geographic location but instead implicated ecological responses of microbes to urban and other anthropogenic effects, and that changes in taxa manifested over a very short geographic space.},
}

Biodiversity
*Metagenome
Metagenomics/*methods
*Microbial Consortia
*Microbiota
Nanopore Sequencing
Plankton/*genetics
Rivers/microbiology
Water Microbiology

@article {pmid32473013,
year = {2020},
author = {Li, J and Zhong, H and Ramayo-Caldas, Y and Terrapon, N and Lombard, V and Potocki-Veronese, G and Estellé, J and Popova, M and Yang, Z and Zhang, H and Li, F and Tang, S and Yang, F and Chen, W and Chen, B and Li, J and Guo, J and Martin, C and Maguin, E and Xu, X and Yang, H and Wang, J and Madsen, L and Kristiansen, K and Henrissat, B and Ehrlich, SD and Morgavi, DP},
title = {A catalog of microbial genes from the bovine rumen unveils a specialized and diverse biomass-degrading environment.},
journal = {GigaScience},
volume = {9},
number = {6},
pages = {},
pmid = {32473013},
issn = {2047-217X},
support = {322820/ERC_/European Research Council/International ; },
mesh = {Animals ; Biomass ; Cattle ; Diet ; Digestion ; Drug Resistance, Microbial ; Gastrointestinal Microbiome/*genetics ; Humans ; *Metagenome ; *Metagenomics/methods ; Mice ; Microbiota/*genetics ; Rumen/*microbiology ; Swine ; },
abstract = {BACKGROUND: The rumen microbiota provides essential services to its host and, through its role in ruminant production, contributes to human nutrition and food security. A thorough knowledge of the genetic potential of rumen microbes will provide opportunities for improving the sustainability of ruminant production systems. The availability of gene reference catalogs from gut microbiomes has advanced the understanding of the role of the microbiota in health and disease in humans and other mammals. In this work, we established a catalog of reference prokaryote genes from the bovine rumen.

RESULTS: Using deep metagenome sequencing we identified 13,825,880 non-redundant prokaryote genes from the bovine rumen. Compared to human, pig, and mouse gut metagenome catalogs, the rumen is larger and richer in functions and microbial species associated with the degradation of plant cell wall material and production of methane. Genes encoding enzymes catalyzing the breakdown of plant polysaccharides showed a particularly high richness that is otherwise impossible to infer from available genomes or shallow metagenomics sequencing. The catalog expands the dataset of carbohydrate-degrading enzymes described in the rumen. Using an independent dataset from a group of 77 cattle fed 4 common dietary regimes, we found that only <0.1% of genes were shared by all animals, which contrast with a large overlap for functions, i.e., 63% for KEGG functions. Different diets induced differences in the relative abundance rather than the presence or absence of genes, which explains the great adaptability of cattle to rapidly adjust to dietary changes.

CONCLUSIONS: These data bring new insights into functions, carbohydrate-degrading enzymes, and microbes of the rumen to complement the available information on microbial genomes. The catalog is a significant biological resource enabling deeper understanding of phenotypes and biological processes and will be expanded as new data are made available.},
}

Animals
Biomass
Cattle
Diet
Digestion
Drug Resistance, Microbial
Gastrointestinal Microbiome/*genetics
Humans
*Metagenome
*Metagenomics/methods
Mice
Microbiota/*genetics
Rumen/*microbiology
Swine

@article {pmid32369165,
year = {2020},
author = {Lim, SK and Kim, D and Moon, DC and Cho, Y and Rho, M},
title = {Antibiotic resistomes discovered in the gut microbiomes of Korean swine and cattle.},
journal = {GigaScience},
volume = {9},
number = {5},
pages = {},
pmid = {32369165},
issn = {2047-217X},
mesh = {Animals ; Anti-Infective Agents/*pharmacology ; Bacteria/drug effects/genetics ; Cattle ; Computational Biology ; *Drug Resistance, Microbial ; Farms ; Gastrointestinal Microbiome/*drug effects ; Metagenome ; Metagenomics/methods ; Microbial Sensitivity Tests ; Republic of Korea ; Swine ; },
abstract = {BACKGROUND: Antibiotics administered to farm animals have led to increasing prevalence of resistance genes in different microbiomes and environments. While antibiotic treatments help cure infectious diseases in farm animals, the possibility of spreading antibiotic resistance genes into the environment and human microbiomes raises significant concerns. Through long-term evolution, antibiotic resistance genes have mutated, thereby complicating the resistance problems.

RESULTS: In this study, we performed deep sequencing of the gut microbiomes of 36 swine and 41 cattle in Korean farms, and metagenomic analysis to understand the diversity and prevalence of antibiotic resistance genes. We found that aminoglycoside, β-lactam, lincosamide, streptogramin, and tetracycline were the prevalent resistance determinants in both swine and cattle. Tetracycline resistance was abundant and prevalent in cattle and swine. Specifically, tetQ, tetW, tetO, tet32, and tet44 were the 5 most abundant and prevalent tetracycline resistance genes. Their prevalence was almost 100% in swine and cattle. While tetQ was similarly abundant in both swine and cattle, tetW was more abundant in swine than in cattle. Aminoglycoside was the second highest abundant resistance determinant in swine, but not in cattle. In particular, ANT(6) and APH(3'') were the dominant resistance gene families in swine. β-lactam was also an abundant resistance determinant in both swine and cattle. Cfx was the major contributing gene family conferring resistance against β-lactams.

CONCLUSIONS: Antibiotic resistome was more pervasive in swine than in cattle. Specifically, prevalent antibiotic resistance genes (prevalence >50%) were found more in swine than in cattle. Genomic investigation of specific resistance genes from the gut microbiomes of swine and cattle in this study should provide opportunities to better understand the exchange of antibiotic resistance genes in farm animals.},
}

Animals
Anti-Infective Agents/*pharmacology
Bacteria/drug effects/genetics
Cattle
Computational Biology
*Drug Resistance, Microbial
Farms
Gastrointestinal Microbiome/*drug effects
Metagenome
Metagenomics/methods
Microbial Sensitivity Tests
Republic of Korea
Swine

@article {pmid34559138,
year = {2021},
author = {Tanaka, T and Matsuno, Y and Torisu, T and Shibata, H and Hirano, A and Umeno, J and Kawasaki, K and Fujioka, S and Fuyuno, Y and Moriyama, T and Esaki, M and Kitazono, T},
title = {Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma.},
journal = {Medicine},
volume = {100},
number = {38},
pages = {e27287},
pmid = {34559138},
issn = {1536-5964},
mesh = {Aged ; Case-Control Studies ; Cross-Sectional Studies ; Female ; Gastric Mucosa/*microbiology ; *Gastrointestinal Microbiome ; Humans ; Lymphoma, B-Cell, Marginal Zone/*microbiology ; Male ; Metagenomics ; Middle Aged ; Stomach Neoplasms/*microbiology ; },
abstract = {ABSTRACT: To investigate the mucosal microbiota in the stomach of patients with Helicobacter pylori-negative mucosa-associated lymphoid tissue (MALT) lymphoma by means of metagenomic analysis.Although some gastric MALT lymphomas are associated with the presence of H. pylori, other gastric MALT lymphomas occur independently of H. pylori infection. The pathogenesis of H. pylori-negative MALT lymphoma remains unclear.Mucosal biopsy specimens were collected from the gastric body from 33 MALT lymphoma patients with gastric lesions, including both H. pylori-infection naïve patients and posteradication patients, as well as 27 control participants without H. pylori infection or cancer. Subsequently, the samples were subjected to 16S rRNA gene sequencing. Quantitative insights into microbial ecology, linear discriminant analysis effect size, and phylogenetic investigation of communities by reconstruction of unobserved states softwares were used to analyze the participants' microbiota.H. pylori-negative MALT lymphoma patients had significantly lower alpha diversity (P = .04), compared with control participants. Significant differences were evident in the microbial composition (P = .04), as determined by comparison of beta diversity between the 2 groups. Taxonomic composition analysis indicated that the genera Burkholderia and Sphingomonas were significantly more abundant in MALT lymphoma patients, while the genera Prevotella and Veillonella were less abundant. Functional microbiota prediction showed that the predicted gene pathways "replication and repair," "translation," and "nucleotide metabolism" were downregulated in MALT lymphoma patients.H. pylori-negative MALT lymphoma patients exhibited altered gastric mucosal microbial compositions, suggesting that altered microbiota might be involved in the pathogenesis of H. pylori-negative MALT lymphoma.},
}

Aged
Case-Control Studies
Cross-Sectional Studies
Female
Gastric Mucosa/*microbiology
*Gastrointestinal Microbiome
Humans
Lymphoma, B-Cell, Marginal Zone/*microbiology
Male
Metagenomics
Middle Aged
Stomach Neoplasms/*microbiology

@article {pmid33880565,
year = {2021},
author = {Golob, JL and Rao, K},
title = {Signal Versus Noise: How to Analyze the Microbiome and Make Progress on Antimicrobial Resistance.},
journal = {The Journal of infectious diseases},
volume = {223},
number = {12 Suppl 2},
pages = {S214-S221},
pmid = {33880565},
issn = {1537-6613},
support = {R01 HS027431/HS/AHRQ HHS/United States ; U01 AI124255/AI/NIAID NIH HHS/United States ; },
mesh = {Animals ; Anti-Bacterial Agents/adverse effects ; Clostridioides difficile/growth & development/pathogenicity ; Clostridium Infections/etiology/microbiology ; Disease Models, Animal ; Drug Resistance, Microbial/drug effects/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics/immunology ; High-Throughput Nucleotide Sequencing ; Host-Pathogen Interactions ; Humans ; },
abstract = {Antimicrobial resistance has become a worldwide medical challenge [1], so impactful that vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have entered the common vernacular. We have attempted to reduce the selective pressure through antimicrobial stewardship, curtail the spread by identifying and isolating carriers and individuals with symptomatic infection, and treat antibiotic-resistant organisms (AROs) by developing novel antimicrobials. Despite these extraordinary measures, the challenge of AROs continues to grow. The gut microbiome, the ecosystem of microbes (ie, the microbiota) and metabolites present upon and within all humans, is an emerging target for both the risk for colonization and defense against infection with AROs. Here, informed from experiences and successes with understanding the role of the microbiome in mediating risk of Clostridioides difficile infection (CDI), we (1) review our understanding of the risk from ARO acquisition; (2) review our current understanding of the gut microbiome's ability to resist colonization with AROs; (3) describe how experimental model systems can test these initial, global insights to arrive at more granular, mechanistic ones; and (4) suggest a path forward to make further progress in the field.},
}

Animals
Anti-Bacterial Agents/adverse effects
Clostridioides difficile/growth & development/pathogenicity
Clostridium Infections/etiology/microbiology
Disease Models, Animal
Drug Resistance, Microbial/drug effects/*genetics
Gastrointestinal Microbiome/drug effects/*genetics/immunology
High-Throughput Nucleotide Sequencing
Host-Pathogen Interactions
Humans

@article {pmid33627510,
year = {2021},
author = {Zhu, J and Ren, H and Zhong, H and Li, X and Zou, Y and Han, M and Li, M and Madsen, L and Kristiansen, K and Xiao, L},
title = {An Expanded Gene Catalog of Mouse Gut Metagenomes.},
journal = {mSphere},
volume = {6},
number = {1},
pages = {},
pmid = {33627510},
issn = {2379-5042},
mesh = {Animals ; Bacteria/classification/*genetics/isolation & purification ; Computational Biology/methods ; Feces/microbiology ; Gastrointestinal Microbiome/*genetics ; *Genome, Bacterial ; Male ; *Metagenome ; Metagenomics ; Mice ; Mice, Inbred C57BL ; Phylogeny ; },
abstract = {High-quality and comprehensive reference gene catalogs are essential for metagenomic research. The rather low diversity of samples used to construct existing catalogs of the mouse gut metagenome limits the numbers of identified genes in existing catalogs. We therefore established an expanded catalog of genes in the mouse gut metagenome (EMGC) containing >5.8 million genes by integrating 88 newly sequenced samples, 86 mouse gut-related bacterial genomes, and 3 existing gene catalogs. EMGC increases the number of nonredundant genes by more than 1 million genes compared to the so-far most extensive catalog. More than 60% of the genes in EMGC were assigned to Bacteria, with 54.20% being assigned to a phylum and 35.33% to a genus, while 30.39% were annotated at the KEGG orthology level. Nine hundred two metagenomic species (MGS) assigned to 122 taxa are identified based on the EMGC. The EMGC-based analysis of samples from groups of mice originating from different animal providers, housing laboratories, and genetic strains substantiated that diet is a major contributor to differences in composition and functional potential of the gut microbiota irrespective of differences in environment and genetic background. We envisage that EMGC will serve as a valuable reference data set for future metagenomic studies in mice.IMPORTANCE We established an expanded gene catalog of the mouse gut metagenome not only to increase the sample size compared to that in existing catalogs but also to provide a more comprehensive reference data set of the mouse gut microbiome for bioinformatic analysis. The expanded gene catalog comprises more than 5.8 million unique genes, as well as a wide range of taxonomic and functional information. Particularly, the analysis of metagenomic species with the expanded gene catalog reveals a great novelty of mouse gut-inhabiting microbial species. We envisage that the expanded gene catalog of the mouse gut metagenome will serve as a valuable bioinformatic resource for future gut metagenomic studies in mice.},
}

Animals
Bacteria/classification/*genetics/isolation & purification
Computational Biology/methods
Feces/microbiology
Gastrointestinal Microbiome/*genetics
*Genome, Bacterial
Male
*Metagenome
Metagenomics
Mice
Mice, Inbred C57BL
Phylogeny

@article {pmid33330938,
year = {2021},
author = {Damhorst, GL and Adelman, MW and Woodworth, MH and Kraft, CS},
title = {Current Capabilities of Gut Microbiome-Based Diagnostics and the Promise of Clinical Application.},
journal = {The Journal of infectious diseases},
volume = {223},
number = {12 Suppl 2},
pages = {S270-S275},
pmid = {33330938},
issn = {1537-6613},
support = {K23 AI144036/AI/NIAID NIH HHS/United States ; UM1 AI104681/AI/NIAID NIH HHS/United States ; },
mesh = {*Clinical Laboratory Techniques ; Computational Biology ; Gastrointestinal Microbiome/*genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; },
abstract = {There is increasing evidence for the importance of the gut microbiome in human health and disease. Traditional and modern technologies - from cell culture to next generation sequencing - have facilitated these advances in knowledge. Each of the tools employed in measuring the microbiome exhibits unique capabilities that may be leveraged for clinical diagnostics. However, much still needs to be done to standardize the language and metrics by which a microbiome is characterized. Here we review the capabilities of gut microbiome-based diagnostics, review selected examples, and discuss the outlook towards clinical application.},
}

*Clinical Laboratory Techniques
Computational Biology
Gastrointestinal Microbiome/*genetics
High-Throughput Nucleotide Sequencing
Humans
Metagenomics

@article {pmid33330904,
year = {2021},
author = {Thänert, R and Keen, EC and Dantas, G and Warner, BB and Tarr, PI},
title = {Necrotizing Enterocolitis and the Microbiome: Current Status and Future Directions.},
journal = {The Journal of infectious diseases},
volume = {223},
number = {12 Suppl 2},
pages = {S257-S263},
pmid = {33330904},
issn = {1537-6613},
support = {P30 DK052574/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; },
mesh = {Dysbiosis/microbiology ; Enterocolitis, Necrotizing/*microbiology/therapy ; Gastrointestinal Microbiome/*physiology ; Host-Pathogen Interactions ; Humans ; Infant, Newborn ; Infant, Premature ; Risk Factors ; },
abstract = {Decades of research have failed to define the pathophysiology of necrotizing enterocolitis (NEC), a devastating pediatric gastrointestinal disorder of preterm infants. However, evidence suggests that host-microbiota interactions, in which microbial dysbiosis is followed by loss of barrier integrity, inflammation, and necrosis, are central to NEC development. Thus, greater knowledge of the preterm infant microbiome could accelerate attempts to diagnose, treat, and prevent NEC. In this article, we summarize clinical characteristics of and risk factors for NEC, the structure of the pre-event NEC microbiome, how this community interfaces with host immunology, and microbiome-based approaches that might prevent or lessen the severity of NEC in this very vulnerable population.},
}

Dysbiosis/microbiology
Enterocolitis, Necrotizing/*microbiology/therapy
Gastrointestinal Microbiome/*physiology
Host-Pathogen Interactions
Humans
Infant, Newborn
Infant, Premature
Risk Factors

@article {pmid33326581,
year = {2021},
author = {Anthony, WE and Burnham, CD and Dantas, G and Kwon, JH},
title = {The Gut Microbiome as a Reservoir for Antimicrobial Resistance.},
journal = {The Journal of infectious diseases},
volume = {223},
number = {12 Suppl 2},
pages = {S209-S213},
pmid = {33326581},
issn = {1537-6613},
support = {K23 AI137321/AI/NIAID NIH HHS/United States ; },
mesh = {Anti-Infective Agents/pharmacology ; Bacterial Infections/immunology/microbiology ; Drug Resistance, Microbial/*genetics ; Gastrointestinal Microbiome/drug effects/*genetics ; Gastrointestinal Tract/immunology/microbiology ; Genes, Microbial/genetics ; Humans ; Metagenomics ; Plasmids/drug effects/genetics ; },
abstract = {This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid-mediated quinolone resistance. Finally, the role of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome is discussed, along with the potential for future microbiome-directed methods to detect and prevent infection.},
}

Anti-Infective Agents/pharmacology
Bacterial Infections/immunology/microbiology
Drug Resistance, Microbial/*genetics
Gastrointestinal Microbiome/drug effects/*genetics
Gastrointestinal Tract/immunology/microbiology
Genes, Microbial/genetics
Humans
Metagenomics
Plasmids/drug effects/genetics

@article {pmid32657325,
year = {2020},
author = {Yang, F and Sun, J and Luo, H and Ren, H and Zhou, H and Lin, Y and Han, M and Chen, B and Liao, H and Brix, S and Li, J and Yang, H and Kristiansen, K and Zhong, H},
title = {Assessment of fecal DNA extraction protocols for metagenomic studies.},
journal = {GigaScience},
volume = {9},
number = {7},
pages = {},
pmid = {32657325},
issn = {2047-217X},
mesh = {Biodiversity ; Biomarkers ; Feces/*microbiology ; *Gastrointestinal Microbiome ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Shotgun metagenomic sequencing has improved our understanding of the human gut microbiota. Various DNA extraction methods have been compared to find protocols that robustly and most accurately reflect the original microbial community structures. However, these recommendations can be further refined by considering the time and cost demands in dealing with samples from very large human cohorts. Additionally, fungal DNA extraction performance has so far been little investigated.

RESULTS: We compared 6 DNA extraction protocols, MagPure Fast Stool DNA KF Kit B, Macherey Nagel™ NucleoSpin™®Soil kit, Zymo Research Quick-DNA™ Fecal/Soil Microbe kit, MOBIO DNeasy PowerSoil kit, the manual non-commercial protocol MetaHIT, and the recently published protocol Q using 1 microbial mock community (MMC) (containing 8 bacterial and 2 fungal strains) and fecal samples. All samples were manually extracted and subjected to shotgun metagenomics sequencing. Extracting DNA revealed high reproducibility within all 6 protocols, but microbial extraction efficiencies varied. The MMC results demonstrated that bead size was a determining factor for fungal and bacterial DNA yields. In human fecal samples, the MagPure bacterial extraction performed as well as the standardized protocol Q but was faster and more cost-effective. Extraction using the PowerSoil protocol resulted in a significantly higher ratio of gram-negative to gram-positive bacteria than other protocols, which might contribute to reported gut microbial differences between healthy adults.

CONCLUSIONS: We emphasize the importance of bead size selection for bacterial and fungal DNA extraction. More importantly, the performance of the novel protocol MP matched that of the recommended standardized protocol Q but consumed less time, was more cost-effective, and is recommended for further large-scale human gut metagenomic studies.},
}

Biodiversity
Biomarkers
Feces/*microbiology
*Gastrointestinal Microbiome
High-Throughput Nucleotide Sequencing
*Metagenome
*Metagenomics/methods
Sequence Analysis, DNA

@article {pmid34351018,
year = {2021},
author = {Paul, LJ and Ericsson, AC and Andrews, FM and Keowen, ML and Morales Yniguez, F and Garza, F and Banse, HE},
title = {Gastric microbiome in horses with and without equine glandular gastric disease.},
journal = {Journal of veterinary internal medicine},
volume = {35},
number = {5},
pages = {2458-2464},
doi = {10.1111/jvim.16241},
pmid = {34351018},
issn = {1939-1676},
support = {//LSU Equine Health Studies Program Charles V. Cusimano Grant/ ; },
mesh = {Animals ; Gastric Mucosa ; *Gastrointestinal Microbiome ; *Horse Diseases ; Horses ; RNA, Ribosomal, 16S/genetics ; *Stomach Diseases/veterinary ; *Stomach Ulcer/veterinary ; },
abstract = {BACKGROUND: The role of the gastric microbiome in development or persistence of equine glandular gastric disease (EGGD) remains to be investigated.

HYPOTHESIS/OBJECTIVES: The objective was to characterize the glandular mucosal and gastric fluid microbiomes of horses with and without EGGD. It was hypothesized that differences in the mucosal microbiome are associated with EGGD.

ANIMALS: Twenty-four horses were enrolled.

METHODS: Gastroscopy was performed and EGGD scores recorded (score 0, n = 6; score 1, n = 8; score ≥2, n = 10). Gastric fluid and pinch biopsies of healthy glandular mucosa and EGGD lesions were collected via gastroscope. 16S rRNA amplicon sequencing of the gastric fluid and glandular mucosal biopsies was performed. Relationships between gastric fluid and mucosal microbial community composition were evaluated among EGGD score groups (EGGD 0-BX, EGGD 1-BX, EGGD ≥2-BX) and among endoscopic appearances: controls from horses without EGGD and normal areas, hyperemic areas, and lesions from horses with EGGD.

RESULTS: Microbial community structure of mucosal biopsies differed among EGGD score groups (Jaccard similarity index; P = .009). Principal coordinate analysis showed separate clusters for EGGD 0-BX and EGGD ≥2-BX.

A modest difference was detected in the community structure of the gastric glandular mucosal microbiome in association with EGGD score.},
}

Animals
Gastric Mucosa
*Gastrointestinal Microbiome
*Horse Diseases
Horses
RNA, Ribosomal, 16S/genetics
*Stomach Diseases/veterinary
*Stomach Ulcer/veterinary

@article {pmid34280721,
year = {2021},
author = {Fan, H and Wu, S and Dong, W and Li, X and Dong, Y and Wang, S and Zhu, YG and Zhuang, X},
title = {Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H218O-based DNA-Stable isotope probing and metagenomics.},
journal = {Journal of hazardous materials},
volume = {420},
number = {},
pages = {126440},
doi = {10.1016/j.jhazmat.2021.126440},
pmid = {34280721},
issn = {1873-3336},
mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents ; DNA ; Genes, Bacterial ; Isotopes ; Manure/analysis ; Metagenomics ; *Microbiota/genetics ; *Soil ; Soil Microbiology ; Tetracycline ; },
abstract = {The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H218O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.},
}

Angiotensin Receptor Antagonists
Angiotensin-Converting Enzyme Inhibitors
Anti-Bacterial Agents
DNA
Genes, Bacterial
Isotopes
Manure/analysis
Metagenomics
*Microbiota/genetics
*Soil
Soil Microbiology
Tetracycline

@article {pmid33961112,
year = {2021},
author = {Lim, SH and Shin, JH and Lee, JW and Lee, Y and Seo, JH},
title = {Differences in the eyelid and buccal microbiome of glaucoma patients receiving long-term administration of prostaglandin analog drops.},
journal = {Graefe's archive for clinical and experimental ophthalmology = Albrecht von Graefes Archiv fur klinische und experimentelle Ophthalmologie},
volume = {259},
number = {10},
pages = {3055-3065},
pmid = {33961112},
issn = {1435-702X},
support = {VHSMC19022//VHS Medical Center Research Grant/ ; },
mesh = {Eyelids ; *Glaucoma/drug therapy ; *Glaucoma, Open-Angle/drug therapy ; Humans ; *Microbiota ; Prostaglandins, Synthetic ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: To investigate the differences in the eyelid and buccal microbiomes between patients receiving long-term prostaglandin analogs for open-angle glaucoma (PG-OAG) and naïve-OAG patients by using metagenomics.

METHODS: Eyelid and buccal samples were collected from 30 PG-OAG and 32 naïve-OAG patients. The taxonomic composition of the microbiome was obtained via 16S rRNA gene sequencing, operational taxonomic unit analysis, and diversity analysis. Differential gene expression analysis (DEG) and Bland-Altman (MA) plots were used to determine taxon differences between the microbiomes of PG-OAG and naïve-OAG patients.

RESULTS: The eyelid microbiome showed marginally significant differences, while the alpha-diversity of the buccal microbiome showed significant differences between PG-OAG and naïve-OAG patients. However, the beta-diversity of both eyelid and buccal microbiomes was higher in PG-OAG patients than in naïve-OAG patients. The MA plot showed cluster differences in the eyelid microbiome. DEG analysis of the eyelid microbiome revealed various taxa differences, including enrichment of Azomonas, Pseudomonas, and Granulicatella in PG-OAG patients over naïve-OAG patients, as well as significant depletion of Delftia and Rothia. In the buccal microbiome in PG-OAG patients, taxa such as Rikenella and Stenotrophomonas were significantly enriched.

CONCLUSION: Our findings suggest that the eyelid microbiome differs between PG-OAG and naïve-OAG patients, raising concerns regarding the eyelid environment in patients receiving these drugs. The overexpressed microbiome in the eyelid area suggests that microbiota may change after the administration of glaucoma medications in OAG.},
}

Eyelids
*Glaucoma/drug therapy
*Glaucoma, Open-Angle/drug therapy
Humans
*Microbiota
Prostaglandins, Synthetic
RNA, Ribosomal, 16S/genetics

@article {pmid33731467,
year = {2021},
author = {Leclerc, M and Harrison, MC and Storck, V and Planas, D and Amyot, M and Walsh, DA},
title = {Microbial Diversity and Mercury Methylation Activity in Periphytic Biofilms at a Run-of-River Hydroelectric Dam and Constructed Wetlands.},
journal = {mSphere},
volume = {6},
number = {2},
pages = {},
pmid = {33731467},
issn = {2379-5042},
mesh = {Bacteria/*classification/*genetics ; Biofilms/*growth & development ; *Genetic Variation ; Lakes/microbiology ; Mercury/*metabolism ; Methylation ; Microbiota/*genetics ; RNA, Ribosomal, 16S/genetics ; Rivers ; Water Pollutants, Chemical/analysis ; *Wetlands ; },
abstract = {Periphytic biofilms have the potential to greatly influence the microbial production of the neurotoxicant monomethylmercury in freshwaters although few studies have simultaneously assessed periphyton mercury methylation and demethylation rates and the microbial communities associated with these transformations. We performed a field study on periphyton from a river affected by run-of-river power plants and artificial wetlands in a boreal landscape (Québec, Canada). In situ incubations were performed on three sites using environmental concentrations of isotopically enriched monomethylmercury (MM198Hg) and inorganic mercury (200Hg) for demethylation and methylation rate measurements. Periphytic microbial communities were investigated through 16S rRNA gene analyses and metagenomic screenings for the hgcA gene, involved in mercury methylation. Positive mercury methylation rates ([5.9 ± 3.4] × 10-3 day-1) were observed only in the wetlands, and demethylation rates averaged 1.78 ± 0.21 day-1 for the three studied sites. The 16S rRNA gene analyses revealed Proteobacteria as the most abundant phylum across all sites (36.3% ± 1.4%), from which families associated with mercury methylation were mostly found in the wetland site. Metagenome screening for HgcA identified 24 different hgcA sequences in the constructed wetland site only, associated with 8 known families, where the iron-reducing Geobacteraceae were the most abundant. This work brings new information on mercury methylation in periphyton from habitats of impacted rivers, associating it mostly with putative iron-reducing bacteria.IMPORTANCE Monomethylmercury (MMHg) is a biomagnifiable neurotoxin of global concern with risks to human health mostly associated with fish consumption. Hydroelectric reservoirs are known to be sources of MMHg many years after their impoundment. Little is known, however, on run-of-river dams flooding smaller terrestrial areas, although their numbers are expected to increase considerably worldwide in decades to come. Production of MMHg is associated mostly with anaerobic processes, but Hg methylation has been shown to occur in periphytic biofilms located in oxic zones of the water column. Therefore, in this study, we investigated in situ production of MMHg by periphytic communities in habitats impacted by the construction of a run-of-river dam by combining transformation rate measurements with genomic approaches targeting hgcAB genes, responsible for mercury methylation. These results provide extended knowledge on mercury methylators in river ecosystems impacted by run-of-river dams in temperate habitats.},
}

Bacteria/*classification/*genetics
Biofilms/*growth & development
*Genetic Variation
Lakes/microbiology
Mercury/*metabolism
Methylation
Microbiota/*genetics
RNA, Ribosomal, 16S/genetics
Rivers
Water Pollutants, Chemical/analysis
*Wetlands

@article {pmid33462312,
year = {2021},
author = {Blifernez-Klassen, O and Klassen, V and Wibberg, D and Cebeci, E and Henke, C and Rückert, C and Chaudhari, S and Rupp, O and Blom, J and Winkler, A and Al-Dilaimi, A and Goesmann, A and Sczyrba, A and Kalinowski, J and Bräutigam, A and Kruse, O},
title = {Phytoplankton consortia as a blueprint for mutually beneficial eukaryote-bacteria ecosystems based on the biocoenosis of Botryococcus consortia.},
journal = {Scientific reports},
volume = {11},
number = {1},
pages = {1726},
pmid = {33462312},
issn = {2045-2322},
mesh = {Bacteria/genetics/*metabolism ; Biodegradation, Environmental ; Chlorophyta/*microbiology ; Ecosystem ; Eukaryota/*physiology ; Metagenome ; Microalgae ; *Microbial Consortia ; Phylogeny ; Phytoplankton/*microbiology ; Symbiosis ; },
abstract = {Bacteria occupy all major ecosystems and maintain an intensive relationship to the eukaryotes, developing together into complex biomes (i.e., phycosphere and rhizosphere). Interactions between eukaryotes and bacteria range from cooperative to competitive, with the associated microorganisms affecting their host`s development, growth and health. Since the advent of non-culture dependent analytical techniques such as metagenome sequencing, consortia have been described at the phylogenetic level but rarely functionally. Multifaceted analysis of the microbial consortium of the ancient phytoplankton Botryococcus as an attractive model food web revealed that its all abundant bacterial members belong to a niche of biotin auxotrophs, essentially depending on the microalga. In addition, hydrocarbonoclastic bacteria without vitamin auxotrophies seem adversely to affect the algal cell morphology. Synthetic rearrangement of a minimal community consisting of an alga, a mutualistic and a parasitic bacteria underpins the model of a eukaryote that maintains its own mutualistic microbial community to control its surrounding biosphere. This model of coexistence, potentially useful for defense against invaders by a eukaryotic host could represent ecologically relevant interactions that cross species boundaries. Metabolic and system reconstruction is an opportunity to unravel the relationships within the consortia and provide a blueprint for the construction of mutually beneficial synthetic ecosystems.},
}

Bacteria/genetics/*metabolism
Biodegradation, Environmental
Chlorophyta/*microbiology
Ecosystem
Eukaryota/*physiology
Metagenome
Microalgae
*Microbial Consortia
Phylogeny
Phytoplankton/*microbiology
Symbiosis

@article {pmid32772817,
year = {2020},
author = {Wallace, MJ and Fishbein, SRS and Dantas, G},
title = {Antimicrobial resistance in enteric bacteria: current state and next-generation solutions.},
journal = {Gut microbes},
volume = {12},
number = {1},
pages = {1799654},
pmid = {32772817},
issn = {1949-0984},
support = {T32 CA113275/CA/NCI NIH HHS/United States ; R01 OH011578/OH/NIOSH CDC HHS/United States ; T32 DK077653/DK/NIDDK NIH HHS/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; T32 HD007409/HD/NICHD NIH HHS/United States ; },
mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/classification/drug effects/genetics/*pathogenicity ; Biological Evolution ; *Drug Resistance, Bacterial/drug effects/genetics ; Dysbiosis/microbiology/prevention & control ; *Gastrointestinal Microbiome/drug effects/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Interspersed Repetitive Sequences/genetics ; Metagenomics ; },
abstract = {Antimicrobial resistance is one of the largest threats to global health and imposes substantial burdens in terms of morbidity, mortality, and economic costs. The gut is a key conduit for the genesis and spread of antimicrobial resistance in enteric bacterial pathogens. Distinct bacterial species that cause enteric disease can exist as invasive enteropathogens that immediately evoke gastrointestinal distress, or pathobionts that can arise from established bacterial commensals to inflict dysbiosis and disease. Furthermore, various environmental reservoirs and stressors facilitate the evolution and transmission of resistance. In this review, we present a comprehensive discussion on circulating resistance profiles and gene mobilization strategies of the most problematic species of enteric bacterial pathogens. Importantly, we present emerging approaches toward surveillance of pathogens and their resistance elements as well as promising treatment strategies that can circumvent common resistance mechanisms.},
}