Gut Microbiota beyond Bacteria—Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD

International Journal of Molecular Sciences, Год журнала: 2020, Номер 21(8), С. 2668 - 2668

Опубликована: Апрель 11, 2020

The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well numerous disease etiologies. Dominated by bacteria, the also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in past two decades, these non-bacterial microorganisms, their functional roles, interaction one another or host immune system have not been widely explored. This review covers recent findings on communities gastrointestinal involvement health disease, particular focus pathophysiology inflammatory bowel disease.

Язык: Английский

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The host-associated archaeome

Nature Reviews Microbiology, Год журнала: 2020, Номер 18(11), С. 622 - 636

Опубликована: Июль 20, 2020

Язык: Английский

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A microbial sea of possibilities: current knowledge and prospects for an improved understanding of the fish microbiome

Reviews in Aquaculture, Год журнала: 2019, Номер 12(2), С. 1101 - 1134

Опубликована: Авг. 13, 2019

Abstract The mucosal surfaces of fish represent an important barrier that supports and regulates a diverse array microbial assemblages contributes to the overall health fitness host. For farmed species, knowledge how these host–microbial systems adapt respond various stressors is pivotal for managing health, nutrition optimizing productivity in aquaculture. While our understanding communities factors shape them now suggest balanced microbiota critical healthy functioning fish, mechanisms behind interactions are still poorly understood. Much existing research has focused on characterizing taxonomic diversity different across body (e.g. skin, gills gastrointestinal tract), response changing nutrition, environmental conditions. However, specific functional contributions (or members) remain elusive, especially or diseased fish. Here, we review current their interplay likely involvement with We also seek address identify gaps explore future prospects improving

Язык: Английский

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Genomic diversity, lifestyles and evolutionary origins of DPANN archaea

FEMS Microbiology Letters, Год журнала: 2019, Номер 366(2)

Опубликована: Янв. 1, 2019

Archaea—a primary domain of life besides Bacteria—have for a long time been regarded as peculiar organisms that play marginal roles in biogeochemical cycles. However, this picture changed with the discovery large diversity archaea non-extreme environments enabled by use cultivation-independent methods. These approaches have allowed reconstruction genomes uncultivated microorganisms and revealed are diverse broadly distributed biosphere seemingly include putative symbiotic organisms, most which belong to tentative archaeal superphylum referred DPANN. This group encompasses at least 10 different lineages includes extremely small cell genome sizes limited metabolic capabilities. Therefore, many members DPANN may be obligately dependent on interactions other even novel parasites. In contribution, we review current knowledge gene repertoires lifestyles discuss their placement tree life, is basis our understanding deep microbial roots role symbiosis evolution Earth.

Язык: Английский

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Challenges in exploring and manipulating the human skin microbiome

Microbiome, Год журнала: 2021, Номер 9(1)

Опубликована: Май 30, 2021

Abstract The skin is the exterior interface of human body with environment. Despite its harsh physical landscape, colonized by diverse commensal microbes. In this review, we discuss recent insights into microbial populations, including their composition and role in health disease modulation intrinsic extrinsic factors, a focus on pathobiological basis aging. We also describe most tools for investigating microbiota microbe-skin relationships perspectives regarding challenges microbiome manipulation.

Язык: Английский

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Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems

Nature Microbiology, Год журнала: 2021, Номер 6(3), С. 354 - 365

Опубликована: Янв. 25, 2021

Abstract Candidate phyla radiation (CPR) bacteria and DPANN archaea are unisolated, small-celled symbionts that often detected in groundwater. The effects of groundwater geochemistry on the abundance, distribution, taxonomic diversity host association CPR has not been studied. Here, we performed genome-resolved metagenomic analysis one agricultural seven pristine microbial communities recovered 746 genomes total. sites, which serve as local sources drinking water, contained up to 31% 4% archaea. We observed little species-level overlap metagenome-assembled (MAGs) across indicating may be differentiated according physicochemical conditions populations. Cryogenic transmission electron microscopy imaging genomic analyses enabled us identify lineages reproducibly attach cells showed growth seems stimulated by attachment host-cell surfaces. Our reveals site-specific coexist with diverse hosts aquifers. Given organisms have identified human microbiomes their presence is correlated diseases such periodontitis, our findings relevant considerations water quality health.

Язык: Английский

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A catalogue of 1,167 genomes from the human gut archaeome

Nature Microbiology, Год журнала: 2021, Номер 7(1), С. 48 - 61

Опубликована: Дек. 30, 2021

The human gut microbiome plays an important role in health, but its archaeal diversity remains largely unexplored. In the present study, we report analysis of 1,167 nonredundant genomes (608 high-quality genomes) recovered from gastrointestinal tract, sampled across 24 countries and rural urban populations. We identified previously undescribed taxa including 3 genera, 15 species 52 strains. Based on distinct genomic features, justify split Methanobrevibacter smithii clade into two separate species, with one represented by 'Candidatus intestini'. Patterns derived 28,581 protein clusters showed significant associations sociodemographic characteristics such as age groups lifestyle. additionally show that archaea are characterized specific functional adaptations to host carry a complex virome. Our work expands our current understanding archaeome provides large genome catalogue for future analyses decipher impact physiology.

Язык: Английский

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Examining the healthy human microbiome concept

Nature Reviews Microbiology, Год журнала: 2024, Номер unknown

Опубликована: Окт. 23, 2024

Язык: Английский

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Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet

Microbiome, Год журнала: 2018, Номер 6(1)

Опубликована: Авг. 24, 2018

The surface of marine animals is covered by abundant and diversified microbial communities, which have major roles for the health their host. While such microbiomes been deeply examined in invertebrates as corals sponges, living on vertebrates received less attention. Specifically, diversity these microbiomes, variability among species, drivers are still mostly unknown, especially fish species coral reefs that contribute to key ecosystem services while they increasingly affected human activities. Here, we investigated knowledge gaps analyzing skin microbiome 138 individuals belonging 44 reef same area. Prokaryotic communities fishes highly diverse, with average more than 600 OTUs per fish, differ from planktonic microbes. Skin varied between individual interspecific differences were slightly coupled phylogenetic affiliation host its ecological traits. These results highlight biodiversity greater previously appreciated, since high macro-organisms supports a community. This suggest beyond loss reefs-associated macroscopic anthropic activities could also lead unexplored host-associated diversity, urgently needs be assessed.

Язык: Английский

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Cross-Domain and Viral Interactions in the Microbiome

Microbiology and Molecular Biology Reviews, Год журнала: 2019, Номер 83(1)

Опубликована: Янв. 8, 2019

The importance of the microbiome to human health is increasingly recognized and has become a major focus recent research. However, much work focused on few aspects, particularly bacterial component microbiome, most frequently in gastrointestinal tract.

Язык: Английский

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