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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
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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

Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.

James J. Kozich, +4 more
- 01 Sep 2013 - 
TL;DR: This work presents an improved method for sequencing variable regions within the 16S rRNA gene using Illumina's MiSeq platform, which is currently capable of producing paired 250-nucleotide reads and demonstrates that it can provide data that are at least as good as that generated by the 454 platform while providing considerably higher sequencing coverage for a fraction of the cost.
Journal ArticleDOI

A metagenome-wide association study of gut microbiota in type 2 diabetes

Junjie Qin, +56 more
- 04 Oct 2012 - 
TL;DR: MGWAS analysis showed that patients with type 2 diabetes were characterized by a moderate degree of gut microbial dysbiosis, a decrease in the abundance of some universal butyrate-producing bacteria and an increase in various opportunistic pathogens, as well as an enrichment of other microbial functions conferring sulphate reduction and oxidative stress resistance.
Journal ArticleDOI

Diversity, stability and resilience of the human gut microbiota

Catherine A. Lozupone, +5 more
- 13 Sep 2012 - 
TL;DR: Viewing the microbiota from an ecological perspective could provide insight into how to promote health by targeting this microbial community in clinical treatments.
Journal ArticleDOI

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

Patrick M. Smith, +7 more
- 02 Aug 2013 - 
TL;DR: This study determined that short-chain fatty acids, gut microbiota–derived bacterial fermentation products, regulate the size and function of the colonic Treg pool and protect against colitis in a Ffar2-dependent manner in mice, revealing that a class of abundant microbial metabolites underlies adaptive immune microbiota coadaptation and promotes colonic homeostasis and health.
Journal ArticleDOI

Kraken: ultrafast metagenomic sequence classification using exact alignments

Derrick E. Wood, +3 more
- 03 Mar 2014 - 
TL;DR: Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences that achieves classification accuracy comparable to the fastest BLAST program.
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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