New insights from uncultivated genomes of the global human gut microbiome

Nature, Journal Year: 2019, Volume and Issue: 568(7753), P. 505 - 510

Published: March 13, 2019

The genome sequences of many species the human gut microbiome remain unknown, largely owing to challenges in cultivating microorganisms under laboratory conditions. Here we address this problem by reconstructing 60,664 draft prokaryotic genomes from 3,810 faecal metagenomes, geographically and phenotypically diverse humans. These provide reference points for 2,058 newly identified species-level operational taxonomic units (OTUs), which represents a 50% increase over previously known phylogenetic diversity sequenced bacteria. On average, OTUs comprise 33% richness 28% abundance per individual, are enriched humans rural populations. A meta-analysis clinical gut-microbiome studies pinpointed numerous disease associations OTUs, have potential improve predictive models. Finally, our analysis revealed that uncultured undergone reduction has resulted loss certain biosynthetic pathways, may offer clues improving cultivation strategies future. Draft metagenomes populations enrich understanding identifying two thousand new taxa associations.

Language: Английский

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Prevotella diversity, niches and interactions with the human host

Nature Reviews Microbiology, Journal Year: 2021, Volume and Issue: 19(9), P. 585 - 599

Published: May 28, 2021

Language: Английский

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The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Cell Host & Microbe, Journal Year: 2019, Volume and Issue: 26(5), P. 666 - 679.e7

Published: Oct. 10, 2019

Prevotella copri is a common human gut microbe that has been both positively and negatively associated with host health. In cross-continent meta-analysis exploiting >6,500 metagenomes, we obtained >1,000 genomes explored the genetic population structure of P. copri. encompasses four distinct clades (>10% inter-clade divergence) propose constitute complex, all were confirmed by isolate sequencing. These are nearly ubiquitous co-present in non-Westernized populations. Genomic analysis showed substantial functional diversity complex notable differences carbohydrate metabolism, suggesting multi-generational dietary modifications may be driving reduced prevalence Westernized Analysis ancient metagenomes highlighted patterns presence consistent modern populations clade delineation time pre-dating migratory waves out Africa. findings reveal exhibits high underrepresented Western-lifestyle

Language: Английский

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A comparative study of the gut microbiota in immune-mediated inflammatory diseases—does a common dysbiosis exist?

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Dec. 1, 2018

Immune-mediated inflammatory disease (IMID) represents a substantial health concern. It is widely recognized that IMID patients are at higher risk for developing secondary inflammation-related conditions. While an ambiguous etiology common to all IMIDs, in recent years, considerable knowledge has emerged regarding the plausible role of gut microbiome IMIDs. This study used 16S rRNA gene amplicon sequencing compare microbiota with Crohn's (CD; N = 20), ulcerative colitis (UC; 19), multiple sclerosis (MS; and rheumatoid arthritis (RA; 21) versus healthy controls (HC; 23). Biological replicates were collected from participants within 2-month interval. aimed identify (or unique) taxonomic biomarkers IMIDs using both differential abundance testing machine learning approach.Significant microbial community differences between cohorts observed (pseudo F 4.56; p 0.01). Richness diversity significantly different (pFDR < 0.001) lowest CD while highest HC. Abundances Actinomyces, Eggerthella, Clostridium III, Faecalicoccus, Streptococcus relative HC, whereas lower abundances Gemmiger, Lachnospira, Sporobacter 0.001). Several taxa found be differentially abundant HC including Intestinibacter CD, Bifidobacterium UC, unclassified Erysipelotrichaceae MS Coprococcus Dialister MS, Roseburia RA. A approach classify was (AUC 0.93 AUC 0.95 OTU genus features, respectively) followed by RA, UC. Gemmiger Faecalicoccus identified as important features classification subjects In general, consistent feature importance.This several patterns We also These may serve detection diagnosis suggest there component etiology.

Language: Английский

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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals

Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)

Published: Sept. 11, 2020

Abstract Gut mucosal microbes evolved closest to the host, developing specialized local communities. There is, however, insufficient knowledge of these communities as most studies have employed sequencing technologies investigate faecal microbiota only. This work used shotgun metagenomics biopsies explore microbial communities’ compositions terminal ileum and large intestine in 5 healthy individuals. Functional annotations genome-scale metabolic modelling selected species were then identify functional enrichments. While provided a good approximation average gut microbiome composition, allowed detecting subtle variations Given their significant enrichment microbiota, we highlight roles Bacteroides describe antimicrobial resistance biogeography along intestine. We also detail which species, at locations, are involved with tryptophan/indole pathway, whose malfunctioning has been linked pathologies including inflammatory bowel disease. Our study thus provides invaluable resources for investigating mechanisms connecting host pathophysiology.

Language: Английский

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Smoking and microbiome in oral, airway, gut and some systemic diseases

Journal of Translational Medicine, Journal Year: 2019, Volume and Issue: 17(1)

Published: July 15, 2019

The human microbiome harbors a diverse array of microbes which establishes mutually beneficial relation with the host in healthy conditions, however, dynamic homeostasis is influenced by both and environmental factors. Smoking contributes to modifications oral, lung gut microbiome, leading various diseases, such as periodontitis, asthma, chronic obstructive pulmonary disease, Crohn's ulcerative colitis cancers. However, exact causal relationship between smoking alteration remains be further explored.

Language: Английский

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Partners in Leaky Gut Syndrome: Intestinal Dysbiosis and Autoimmunity

Frontiers in Immunology, Journal Year: 2021, Volume and Issue: 12

Published: April 22, 2021

The intestinal surface is constitutively exposed to diverse antigens, such as food food-borne pathogens, and commensal microbes. Intestinal epithelial cells have developed unique barrier functions that prevent the translocation of potentially hostile antigens into body. Disruption increases permeability, resulting in leaky gut syndrome (LGS). Clinical reports suggested LGS contributes autoimmune diseases type 1 diabetes, multiple sclerosis, rheumatoid arthritis, celiac disease. Furthermore, microbiota plays a critical role regulating host immunity; abnormalities microbial community, known dysbiosis, are observed patients with diseases. However, pathological links among LGS, not been fully elucidated. This review discusses current understanding how pathogenesis by modifying barrier.

Language: Английский

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Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment

Frontiers in Microbiology, Journal Year: 2021, Volume and Issue: 12

Published: Feb. 19, 2021

The number of microbiome-related studies has notably increased the availability data on human microbiome composition and function. These provide essential material to deeply explore host-microbiome associations their relation development progression various complex diseases. Improved data-analytical tools are needed exploit all information from these biological datasets, taking into account peculiarities data, i.e., compositional, heterogeneous sparse nature datasets. possibility predicting host-phenotypes based taxonomy-informed feature selection establish an association between predict disease states is beneficial for personalized medicine. In this regard, machine learning (ML) provides new insights models that can be used outputs, such as classification prediction in microbiology, infer host phenotypes diseases use microbial communities stratify patients by characterization state-specific signatures. Here we review state-of-the-art ML methods respective software applied studies, performed part COST Action ML4Microbiome activities. This scoping focuses application related clinical diagnostics, prognostics, therapeutics. Although presented here more bacterial community, many algorithms could general, regardless type. literature covering broad topic aligned with methodology. manual identification sources been complemented with: (1) automated publication search through digital libraries three major publishers using natural language processing (NLP) Toolkit, (2) relevant repositories GitHub ranking research papers relying rank approach.

Language: Английский

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Ankylosing spondylitis: an autoimmune or autoinflammatory disease?

Nature Reviews Rheumatology, Journal Year: 2021, Volume and Issue: 17(7), P. 387 - 404

Published: June 10, 2021

Language: Английский

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A metagenomic study of the gut microbiome in Behcet’s disease

Microbiome, Journal Year: 2018, Volume and Issue: 6(1)

Published: Aug. 4, 2018

Behcet's disease (BD) is a recalcitrant, multisystemic inflammatory that can lead to irreversible blindness. Microbial agents have been considered contribute the pathogenesis of this disease, but underlying mechanisms remain unclear. In study, we investigated association gut microbiome composition with BD as well its possible roles in development disease. Fecal and saliva samples were collected from 32 active patients 74 healthy controls. DNA extracted fecal was subjected metagenomic analysis, whereas 16S rRNA gene sequencing analysis. The results used compare biological function between Lastly, transplantation pooled into B10RIII mice undergoing experimental autoimmune uveitis (EAU) performed determine causal relationship BD. shown be enriched Bilophila spp., sulfate-reducing bacteria (SRB) several opportunistic pathogens (e.g., Parabacteroides spp. Paraprevotella spp.) along lower level butyrate-producing (BPB) Clostridium methanogens (Methanoculleus Methanomethylophilus spp.). Analysis microbial functions revealed capsular polysaccharide transport system, oxidation-reduction process, type III, IV secretion systems also increased patients. Network analysis showed BD-enriched SRB positively correlated each other, they negatively associated BPB methanogens. Animal experiments microbiota feces significantly exacerbated EAU activity production cytokines including IL-17 IFN-γ. Our findings considerable changes, which corroborated by mouse study transplants. A model explaining proposed.

Language: Английский

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