Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population

Animal Microbiome, Год журнала: 2021, Номер 3(1)

Опубликована: Дек. 20, 2021

The vertebrate gut microbiome (GM) can vary substantially across individuals within the same natural population. Although there is evidence linking GM to health in captive animals, very little known about consequences of variation for host fitness wild. Here, we explore relationship between faecal diversity, body condition, and survival using data from long-term study a discrete population Seychelles warbler (Acrocephalus sechellensis) on Cousin Island. To our knowledge, this first time that differences associated with have been fully characterised species, multiple age groups breeding seasons.

Язык: Английский

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Microbiomes of microscopic marine invertebrates do not reveal signatures of phylosymbiosis

Nature Microbiology, Год журнала: 2022, Номер 7(6), С. 810 - 819

Опубликована: Май 26, 2022

Язык: Английский

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The Gut Microbiome of 54 Mammalian Species

Frontiers in Microbiology, Год журнала: 2022, Номер 13

Опубликована: Июнь 16, 2022

The gut microbiome plays a critical role in many aspects of host life, and the microbial community composition is heavily influenced by prevailing conditions environment. Community has been suggested to have large implications for conservation efforts, health become interest optimizing animal care captivity. In this study, we explore wide range animals context biology. 54 mammalian species was investigated using 16S rRNA gene amplicon sequencing. microbiota clearly reflects diet structure gastrointestinal system, it certain degree more similar between closely related animals. Specific clusters taxa were observed across same species, diet, morphology. retained regardless captivity status hypothesized cover important symbiotic relationships with host, while remaining part artificial living can therefore be used as future tool biologists. For five (giraffes, horses, baboons, elephants, zebras), possible compare wild captive individuals. Differences proportion detected specimens species. We propose that harbours which potentially serve indicators well-being effect

Язык: Английский

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Recovering metagenome-assembled genomes from shotgun metagenomic sequencing data: Methods, applications, challenges, and opportunities

Microbiological Research, Год журнала: 2022, Номер 260, С. 127023 - 127023

Опубликована: Апрель 9, 2022

Язык: Английский

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Even allocation of benefits stabilizes microbial community engaged in metabolic division of labor

Cell Reports, Год журнала: 2022, Номер 40(13), С. 111410 - 111410

Опубликована: Сен. 1, 2022

Microbial communities execute metabolic pathways to drive global nutrient cycles. Within a community, functionally specialized strains can perform different yet complementary steps within linear pathway, phenomenon termed division of labor (MDOL). However, little is known about how such behaviors shape microbial communities. Here, we derive theoretical framework define the assembly community that degrades an organic compound through MDOL. The indicates ensure stability, performing initial should hold growth advantage (m) over "private benefit" (n) strain last step. steady-state frequency then determined by quotient n and m. Our experiments show accurately predicts our synthetic consortia degrade naphthalene results provide insights for designing managing stable systems pathway optimization.

Язык: Английский

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Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes

Nature Communications, Год журнала: 2022, Номер 13(1)

Опубликована: Сен. 6, 2022

Abstract Coronavirus disease 2019 (COVID-19), primarily a respiratory caused by infection with Severe Acute Respiratory Syndrome 2 (SARS-CoV-2), is often accompanied gastrointestinal symptoms. However, little known about the relation between human microbiome and COVID-19, largely due to fact that most previous studies fail provide high taxonomic resolution identify microbes likely interact SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together assembly binning strategies reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal fecal samples in six independent cohorts. We reconstructed total of 11,584 medium-and high-quality microbial MAGs obtained 5403 non-redundant (nrMAGs) strain-level resolution. found there significant reduction strain richness for many species gut patients. The signatures can accurately distinguish cases healthy controls predict progression COVID-19. Moreover, identified set nrMAGs putative causal role clinical manifestations revealed their functional pathways potentially Finally, demonstrated main findings our study be validated three presented results highlight importance incorporating understanding progression.

Язык: Английский

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Microbial Dark Matter: From Discovery to Applications

Genomics Proteomics & Bioinformatics, Год журнала: 2022, Номер 20(5), С. 867 - 881

Опубликована: Апрель 26, 2022

With the rapid increase of microbiome samples and sequencing data, more knowledge about microbial communities has been gained. However, there is still much to learn communities, including billions novel species genes, as well countless spatiotemporal dynamic patterns within which together form dark matter. In this work, we summarized matter in research reviewed current data mining methods, especially artificial intelligence (AI) for different types discovery from We also provided case studies on using AI methods discovery. summary, view not a problem be solved but an opportunity explore, with goal advancing our understanding developing better solutions global concerns human health environment.

Язык: Английский

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Host Genetic Determinants of the Microbiome Across Animals: From Caenorhabditis elegans to Cattle

Annual Review of Animal Biosciences, Год журнала: 2022, Номер 10(1), С. 203 - 226

Опубликована: Фев. 15, 2022

Animals harbor diverse communities of microbes within their gastrointestinal tracts. Phylogenetic relationship, diet, gut morphology, host physiology, and ecology all influence microbiome composition between animal clades. Emerging evidence points to genetics as also playing a role in determining microbial species. Here, we discuss recent advances the study heritability across variety species . Candidate gene discovery-based studies humans, mice, Drosophila, Caenorhabditis elegans, cattle, swine, poultry, baboons reveal trends types that are heritable genes pathways involved shaping microbiome. Heritable tend be phylogenetically restricted. Host genetic variation immune- growth-related drives abundances these bacteria gut. With only small slice metazoan branch tree life explored date, this is an area rife with opportunities shed light into mechanisms governing host–microbe relationships.

Язык: Английский

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Impact of microbial genome completeness on metagenomic functional inference

ISME Communications, Год журнала: 2023, Номер 3(1)

Опубликована: Фев. 16, 2023

Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that completeness has significant impact on recovered signal, spanning all domains metabolic functions. We identify factors affect this relationship between genome and function fullness, provide baseline knowledge to guide efforts correct for overlooked bias metagenomic inference.

Язык: Английский

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Characterizing core microbiota and regulatory functions of the pig gut microbiome

The ISME Journal, Год журнала: 2024, Номер 18(1)

Опубликована: Янв. 1, 2024

Abstract Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of microbial structure function will improve our understanding resources mechanisms underlying host–microbe interactions. Here, we investigated microbiomes seven pig breeds using metagenomics 16S rRNA gene amplicon sequencing. We established an expanded reference catalog comprising 17 020 160 genes identified 4910 metagenome-assembled genomes. also analyzed resistome to provide overview profiles antimicrobial resistance in pigs. By analyzing relative abundances microbes, three core-predominant microbes (Phascolarctobacterium succinatutens, Prevotella copri, Oscillibacter valericigenes) this study. Oral administration increased organ indexes (including heart, spleen, thymus), but decreased gastrointestinal lengths germ-free mice. core enhanced intestinal epithelial barrier altered mucosal morphology, as was evident from increase crypt depths duodenum ileum. Furthermore, affected several metabolic pathways (such “steroid hormone biosynthesis,” “primary bile acid “phenylalanine, tyrosine tryptophan “phenylalanine metabolism”) These findings a panoramic view microbiome insights into functional contributions host.

Язык: Английский

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