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 Healthy Microbiome—What Is the Definition of a Healthy Gut Microbiome?

Gastroenterology, Journal Year: 2020, Volume and Issue: 160(2), P. 483 - 494

Published: Nov. 27, 2020

Language: Английский

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The person-to-person transmission landscape of the gut and oral microbiomes

Nature, Journal Year: 2023, Volume and Issue: 614(7946), P. 125 - 135

Published: Jan. 18, 2023

Abstract The human microbiome is an integral component of the body and a co-determinant several health conditions 1,2 . However, extent to which interpersonal relations shape individual genetic makeup its transmission within across populations remains largely unknown 3,4 Here, capitalizing on more than 9,700 metagenomes computational strain-level profiling, we detected extensive bacterial strain sharing individuals (more 10 million instances) with distinct mother-to-infant, intra-household intra-population patterns. Mother-to-infant gut was considerable stable during infancy (around 50% same strains among shared species (strain-sharing rate)) remained detectable at older ages. By contrast, oral occurred horizontally enhanced by duration cohabitation. There substantial cohabiting individuals, 12% 32% median strain-sharing rates for microbiomes, time since cohabitation affected age or genetics did. Bacterial additionally recapitulated host population structures better species-level profiles Finally, taxa appeared as efficient spreaders modes were associated different predicted phenotypes linked out-of-host survival capabilities. microorganism that describe underscores relevance in studies 5 , especially those non-infectious, microbiome-associated diseases.

Language: Английский

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Trophic Interactions and the Drivers of Microbial Community Assembly

Current Biology, Journal Year: 2020, Volume and Issue: 30(19), P. R1176 - R1188

Published: Oct. 1, 2020

Despite numerous surveys of gene and species content in heterotrophic microbial communities, such as those found animal guts, oceans, or soils, it is still unclear whether there are generalizable biological ecological processes that control their dynamics function. Here, we review experimental theoretical advances to argue networks trophic interactions, which the metabolic excretions one primary resource for another, constitute central drivers community assembly. Trophic interactions emerge from deconstruction complex forms organic matter into a wealth smaller intermediates, some released environment serve nutritional buffet community. The structure emergent network rate at resources supplied many features assembly, including relative contributions competition cooperation emergence alternative states. Viewing assembly through lens also has important implications spatial communities well functional redundancy taxonomic groups. Given ubiquity across environments, they impart common logic can enable development more quantitative predictive ecology.

Language: Английский

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Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases

Nature Medicine, Journal Year: 2022, Volume and Issue: 28(9), P. 1913 - 1923

Published: Sept. 1, 2022

Fecal microbiota transplantation (FMT) is highly effective against recurrent Clostridioides difficile infection and considered a promising treatment for other microbiome-related disorders, but comprehensive understanding of microbial engraftment dynamics lacking, which prevents informed applications this therapeutic approach. Here, we performed an integrated shotgun metagenomic systematic meta-analysis new publicly available stool microbiomes collected from 226 triads donors, pre-FMT recipients post-FMT across eight different disease types. By leveraging improved strain-profiling to infer strain sharing, found that with higher donor were more likely experience clinical success after FMT (P = 0.017) when evaluated studies. Considering all cohorts, increased was noted in individuals receiving multiple routes (for example, both via capsules colonoscopy during the same treatment) as well antibiotic-treated infectious diseases compared antibiotic-naïve patients noncommunicable diseases. Bacteroidetes Actinobacteria species (including Bifidobacteria) displayed than Firmicutes except six under-characterized species. Cross-dataset machine learning predicted presence or absence recipient at 0.77 average AUROC leave-one-dataset-out evaluation, highlighted relevance abundance, prevalence taxonomy presence. exploring microbiome their association variables, our study uncovered species-specific patterns presented models able predict donors might optimize specific characteristics disease-targeted protocols.

Language: Английский

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High-throughput, single-microbe genomics with strain resolution, applied to a human gut microbiome

Science, Journal Year: 2022, Volume and Issue: 376(6597)

Published: June 2, 2022

Characterizing complex microbial communities with single-cell resolution has been a long-standing goal of microbiology. We present Microbe-seq, high-throughput method that yields the genomes individual microbes from communities. encapsulate in droplets microfluidics and liberate their DNA, which we then amplify, tag droplet-specific barcodes, sequence. explore human gut microbiome, sequencing more than 20,000 single-amplified (SAGs) single donor coassembling almost 100 bacterial species, including several multiple subspecies strains. use these to probe interactions, reconstructing horizontal gene transfer (HGT) network observing HGT between 92 species pairs; also identify significant vivo host-phage association crAssphage one strain Bacteroides vulgatus. Microbe-seq contributes culture-free capabilities investigate genomic blueprints single-microbe resolution.

Language: Английский

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Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: May 28, 2021

Abstract Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics demonstrate carbohydrate secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal bacterial iron metabolism functionality is correlated with enrichment. Using time-series RNA-Seq data, homeostasis impacted by stress, loss of a plant phytosiderophore transporter impacts microbial community composition, leading significant increases lineage, Actinobacteria. Finally, show exogenous application disrupts drought-induced enrichment Actinobacteria, as well their improvement host phenotype during stress. Collectively, our findings implicate microbiome’s response may inform efforts improve tolerance increase food security.

Language: Английский

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GUNC: detection of chimerism and contamination in prokaryotic genomes

Genome biology, Journal Year: 2021, Volume and Issue: 22(1)

Published: June 13, 2021

Abstract Genomes are critical units in microbiology, yet ascertaining quality prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), tool that accurately detects and quantifies chimerism based on the lineage homogeneity of individual contigs using genome’s full complement genes. complements existing approaches by targeting previously underdetected types contamination: we conservatively estimate 5.7% genomes GenBank, 5.2% RefSeq, 15–30% pre-filtered “high-quality” metagenome-assembled recent studies undetected chimeras. provides fast robust to substantially improve quality.

Language: Английский

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Staphylococcus epidermidis and its dual lifestyle in skin health and infection

Nature Reviews Microbiology, Journal Year: 2022, Volume and Issue: 21(2), P. 97 - 111

Published: Aug. 30, 2022

Language: Английский

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Bacteria in cancer initiation, promotion and progression

Nature reviews. Cancer, Journal Year: 2023, Volume and Issue: 23(9), P. 600 - 618

Published: July 3, 2023

Language: Английский

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