Diversity and functional landscapes in the microbiota of animals in the wild

Science, Journal Year: 2021, Volume and Issue: 372(6539)

Published: March 25, 2021

Animals in the wild are able to subsist on pathogen-infected and poisonous food show immunity various diseases. These may be due their microbiota, yet we have a poor understanding of animal microbial diversity function. We used metagenomics analyze gut microbiota more than 180 species wild, covering diverse classes, feeding behaviors, geographies, traits. Using de novo metagenome assembly, constructed functionally annotated database 5000 genomes, comprising 1209 bacterial which 75% unknown. The composition, diversity, functional content exhibit associations with taxonomy, diet, activity, social structure, life span. identify animals as largely untapped resource for discovery therapeutics biotechnology applications.

Language: Английский

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Codiversification of gut microbiota with humans

Science, Journal Year: 2022, Volume and Issue: 377(6612), P. 1328 - 1332

Published: Sept. 15, 2022

The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. question is whether such specificity arises from shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification host microbiota, we analyzed paired metagenomes genomes 1225 individuals Europe, Asia, Africa, including mothers children. Between countries, parallel was evident Moreover, displaying the strongest independently evolved traits characteristic dependency, reduced oxygen temperature sensitivity. These findings all point to importance understanding potential role population-specific microbiome-mediated disease phenotypes.

Language: Английский

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Cryptic diversity of cellulose-degrading gut bacteria in industrialized humans

Science, Journal Year: 2024, Volume and Issue: 383(6688)

Published: March 14, 2024

Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, main component plant fiber. However, evidence cellulose fermentation in human is scarce. We have identified ruminococcal species microbiota populations that assemble functional multienzymatic cellulosome structures capable degrading cell wall polysaccharides. One these species, which strongly associated with humans, likely originated ruminant and was subsequently transferred to gut, potentially during domestication where it underwent diversification diet-related adaptation through acquisition genes from other microbes. Collectively, are abundant widespread among ancient hunter-gatherers, rural but rare industrialized societies thus indicating potential disappearance response westernized lifestyle.

Language: Английский

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Roles of the gut microbiota in the adaptive evolution of mammalian species

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2020, Volume and Issue: 375(1808), P. 20190597 - 20190597

Published: Aug. 9, 2020

Every mammalian species harbours a gut microbiota, and variation in the microbiota within can have profound effects on host phenotypes. In this review, we summarize recent evidence that microbiotas influenced course of adaptation diversification. Associations with have: (i) promoted diversification by enabling dietary transitions onto difficult-to-digest carbon sources toxic food items; (ii) shaped evolution adaptive phenotypic plasticity through amplification signals from external environment postnatal developmental processes; (iii) generated selection for mechanisms, including innate immune to control benefit fitness. The stability specific lineages varies substantially across phylogeny, may alter ultimate evolutionary outcomes relationships different clades. some species, humans, species-specific appear led dependence certain functions. These studies implicate as significant environmental factor selective agent shaping diet, plasticity, gastrointestinal morphology immunity. This article is part theme issue 'The role microbiome evolution'.

Language: Английский

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Species identity dominates over environment in shaping the microbiota of small mammals

Ecology Letters, Journal Year: 2019, Volume and Issue: 22(5), P. 826 - 837

Published: March 13, 2019

The mammalian gut microbiota is considered pivotal to host fitness, yet the determinants of community composition remain poorly understood. Laboratory studies show that environmental factors, particularly diet, are important, while comparative work emphasises genetics. Here, we compare influence genetics and environment on sympatric small mammal species (mice, voles, shrews) across multiple habitats. While sharing a habitat caused some convergence, identity dominated. In all three genera examined, an individual's was more similar conspecifics living elsewhere than heterospecifics at same site. Our results suggest this species-specificity arises in part through host-microbe codiversification. Stomach contents analysis suggested diet also shapes microbiota, but where itself influenced by identity. way, can reconcile importance both genetics, showing strongest predictor composition.

Language: Английский

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Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

Proceedings of the Royal Society B Biological Sciences, Journal Year: 2019, Volume and Issue: 286(1901), P. 20190431 - 20190431

Published: April 24, 2019

Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population behaviours, environments, genetics and geographical distance. However, which factors most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon spanning a natural hybrid zone. Sampling across zone allowed us additionally test whether phylosymbiosis (codiversification between hosts their microbiota) is detectable admixed, closely related primates. We found little evidence of genetic effects: none ancestry, relatedness nor distance were strong predictors gut microbiota. Instead, best explained the baboons' especially soil's geologic history exchangeable sodium. Indeed, soil effects 15 times stronger than those host–population F ST, perhaps because predicts foods present, or terrestrial consume microbes incidentally with food. Our results support an emerging picture variation dominant predictor host-associated microbiomes. first show that such overshadow species identity among members same primate genus.

Language: Английский

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Microbiome evolution during host aging

PLoS Pathogens, Journal Year: 2019, Volume and Issue: 15(7), P. e1007727 - e1007727

Published: July 25, 2019

Host-microbiota interactionsCommensal microbes and their multicellular eukaryotic hosts constitute a highly integrated system-termed the holobiont [1]-which undergoes dynamic changes through time as it integrates responds to signals from environment.Dwelling at interface between host epithelia external environment, commensal actively modulate development, nutrient absorption, disease onset in host.Host metabolism is significantly modulated by microbes, gut microbial composition affects blood metabolite [2].Microbial communities differ among epithelia, reaching highest complexity taxonomic diversity oral cavity gastrointestinal tract [3,4].Environmental factors, such diet, drug use, social shape of epithelia-associated microbiota [5-7], environmental heterogeneity-rather than genetics-can explain much interindividual differences humans [8].The assembly specific host-associated communities, however, also dictated cell activity, molecular components mucus layer, peristaltic contractility [9], epithelial integrity [10].In primates, recent evidence supports that phylogenetic relatedness physiology are overall better predictors diet [11].Together, community, subject conjunction with evolution lifetime individual hosts. Microbiota timeJust varies within tissues [12], consortia do vary tissues.Microbial newborns dramatically shaped depending on whether infant fed maternal milk [13] or formula [14].Drug administration antibiotic use importantly microbiota, leading significant community shifts increased abundance otherwise rare taxa [15].Although largely unstable first years life, they become more stable during adulthood [13,16] undergo dramatic richness upon frailty [17,18].The diseases, cancer, obesity, diabetes, inflammatory bowel (IBD), associated signatures [19,20].Studies laboratory model organisms, flies, fish, mice, have additionally shown aging health life span [17,[21][22][23][24].In e.g., lipopolysaccharide (LPS) can accelerate agedependent inflammation ("inflammaging") [25], mice lacking Toll-Like receptor 4 (TLR4), which LPS receptor, protected age-dependent [26], showing microbial-specific substrate induces aging-specific phenotypes.Inflammaging be further

Language: Английский

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Newly Explored Faecalibacterium Diversity Is Connected to Age, Lifestyle, Geography, and Disease

Current Biology, Journal Year: 2020, Volume and Issue: 30(24), P. 4932 - 4943.e4

Published: Oct. 15, 2020

Faecalibacterium is prevalent in the human gut and a promising microbe for development of next-generation probiotics (NGPs) or biotherapeutics. Analyzing reference genomes almost 3,000 Faecalibacterium-like metagenome-assembled (MAGs) reconstructed from 7,907 203 non-human primate metagenomes, we identified presence 22 different species-level genome bins (SGBs), some further divided strains according to subject geographical origin. Twelve SGBs are globally spread show genomic potential utilization complex polysaccharides, suggesting that higher SGB diversity may be related with increased plant-based foods. Moreover, up 11 species co-occur same subject, lower Western populations, as well intestinal inflammatory states obesity. The newly explored will able support choice suitable NGPs, guided by consideration differences existing their functional potential.

Language: Английский

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Engineering the microbiome for animal health and conservation

Experimental Biology and Medicine, Journal Year: 2019, Volume and Issue: 244(6), P. 494 - 504

Published: Feb. 18, 2019

Considering the clear effects of microbiota on important aspects animal biology and development (including in humans), this topic is timely broadly appealing, as it compels us to consider possibilities altering microbiome (without antibiotics) positively affect health. In review, we highlight three general approaches manipulating that have demonstrated success promise for use We also point out knowledge gaps where further inquiry would most benefit field. Our paper not only provides a short digestible overview current state application, but calls exploration microbial diversity at hand expand our toolkit, while leveraging flexibility systems better understand mechanisms efficacy.

Language: Английский

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Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Genome biology, Journal Year: 2020, Volume and Issue: 21(1)

Published: June 8, 2020

Eubacterium rectale is one of the most prevalent human gut bacteria, but its diversity and population genetics are not well understood because large-scale whole-genome investigations this microbe have been carried out.

Language: Английский

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