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Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower, +253 more
- 14 Jun 2012 - 
- Vol. 486, Iss: 7402, pp 207-214
TLDR
The Human Microbiome Project Consortium reported the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome as discussed by the authors.
Abstract: 
The Human Microbiome Project Consortium reports the first results of their analysis of microbial communities from distinct, clinically relevant body habitats in a human cohort; the insights into the microbial communities of a healthy population lay foundations for future exploration of the epidemiology, ecology and translational applications of the human microbiome.

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Journal ArticleDOI

Pretreatment gut microbiome predicts chemotherapy-related bloodstream infection

Emmanuel Montassier, +9 more
- 28 Apr 2016 - 
TL;DR: It is found that patients who developed subsequent BSI exhibited decreased overall diversity and decreased abundance of taxa including Barnesiellaceae, Coriobacteriaceae, Faecalibacterium, Christensenella, Dehalobacterium and Sutterella.
Journal ArticleDOI

Biogeography of the Oral Microbiome: The Site-Specialist Hypothesis.

Jessica L. Mark Welch, +3 more
- 08 Sep 2019 - 
TL;DR: The literature supports the idea that most oral microbes are site specialists, and a clear understanding of microbiota structure at different sites in the mouth enables mechanistic studies, informs the generation of hypotheses, and strengthens the position of oral microbiology as a model system for microbial ecology in general.
Journal ArticleDOI

Discovery of novel carbohydrate-active enzymes through the rational exploration of the protein sequences space.

William Helbert, +16 more
- 26 Mar 2019 - 
TL;DR: This work recombinantly produced 564 proteins selected from subfamilies without any biochemically characterized representatives, from distant relatives of characterized enzymes and from nonclassified proteins that show little similarity with known CAZymes, to better explore the sequence-to-function relationships of these enzymes.
Journal ArticleDOI

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

Elizabeth A. Rettedal, +2 more
- 28 Aug 2014 - 
TL;DR: It is shown that carefully designed conditions enable cultivation of a representative proportion of human gut bacteria, enabling rapid multiplex phenotypic profiling, and determines the phylogenetic distribution of antibiotic tolerance phenotypes for 16 antibiotics in the human gut microbiota.
Journal ArticleDOI

Microbiology meets big data: The case of gut microbiota-derived trimethylamine

Gwen Falony, +2 more
- 21 Oct 2015 - 
TL;DR: Reviewing pathway abundance in public data sets shows that TMA production potential is associated with symptomatic atherosclerosis and allows identification of currently uncharacterized TMA-producing bacteria, and demonstrates the potential for integrating big data into a functional microbiology workflow.
References
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Journal ArticleDOI

QIIME allows analysis of high-throughput community sequencing data.

J. Gregory Caporaso, +27 more
- 11 Apr 2010 - 
TL;DR: An overview of the analysis pipeline and links to raw data and processed output from the runs with and without denoising are provided.
Journal ArticleDOI

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin, +52 more
- 04 Mar 2010 - 
TL;DR: The Illumina-based metagenomic sequencing, assembly and characterization of 3.3 million non-redundant microbial genes, derived from 576.7 gigabases of sequence, from faecal samples of 124 European individuals are described, indicating that the entire cohort harbours between 1,000 and 1,150 prevalent bacterial species and each individual at least 160 such species.
Journal ArticleDOI

A core gut microbiome in obese and lean twins

Peter J. Turnbaugh, +14 more
- 22 Jan 2009 - 
TL;DR: The faecal microbial communities of adult female monozygotic and dizygotic twin pairs concordant for leanness or obesity, and their mothers are characterized to address how host genotype, environmental exposure and host adiposity influence the gut microbiome.
Journal ArticleDOI

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

Harry Sokol, +19 more
- 28 Oct 2008 - 
TL;DR: The results suggest that counterbalancing dysbiosis using F. prausnitzii as a probiotic is a promising strategy in CD treatment and exhibits anti-inflammatory effects on cellular and TNBS colitis models, partly due to secreted metabolites able to block NF-κB activation and IL-8 production.
Journal ArticleDOI

Vaginal microbiome of reproductive-age women

Jacques Ravel, +14 more
- 15 Mar 2011 - 
TL;DR: The inherent differences within and between women in different ethnic groups strongly argues for a more refined definition of the kinds of bacterial communities normally found in healthy women and the need to appreciate differences between individuals so they can be taken into account in risk assessment and disease diagnosis.
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