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Open AccessJournal ArticleDOI

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

Sequence-Based Discovery of Bradyrhizobium enterica in Cord Colitis Syndrome

Ami B. Bhatt, +29 more
- 07 Aug 2013 - 
TL;DR: In this article, the authors performed shotgun DNA sequencing on four archived, paraffin-embedded endoscopic colon-biopsy specimens obtained from two patients with cord colitis.
Journal ArticleDOI

The athletic gut microbiota.

Alex E. Mohr, +23 more
- 12 May 2020 - 
TL;DR: Current knowledge of the athletic gut microbiota and the factors that shape it are summarized to promote a more “health-associated” gut microbiota, including a higher abundance of health-promoting bacterial species, increased microbial diversity, functional metabolic capacity, and microbial-associated metabolites.
Posted ContentDOI

Metacoder: An R Package for Visualization and Manipulation of Community Taxonomic Diversity Data

Zachary Foster, +2 more
- 07 Dec 2016 - 
TL;DR: The metacoder package, an R package for easily parsing, manipulating, and graphing publication-ready plots of hierarchical data, was designed for data from metabarcoding research and can be applied to any data that has a hierarchical component such as gene ontology or geographic location data.
Journal ArticleDOI

Geographical patterns of the standing and active human gut microbiome in health and IBD

Ateequr Rehman, +11 more
- 01 Feb 2016 - 
TL;DR: Analysis of mucosal biopsies reveals important interactions of patients’ geographical origin and disease in the interpretation of disease-associated changes in microbial communities and highlights the added value of analysing communities on both the 16S rRNA gene (DNA) and transcript (RNA) level.
Journal ArticleDOI

Gut microbiome composition is associated with temperament during early childhood.

Lisa M. Christian, +5 more
- 01 Mar 2015 - 
TL;DR: Differences in gut microbiome composition, including alpha diversity, beta diversity, and abundances of specific bacterial species, were observed in association with temperament in toddlers.
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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A human gut microbial gene catalogue established by metagenomic sequencing

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QIIME allows analysis of high-throughput community sequencing data.

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A core gut microbiome in obese and lean twins

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Diet rapidly and reproducibly alters the human gut microbiome

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