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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

MicroRNAs and complex diseases: from experimental results to computational models.

Xing Chen, +3 more
- 20 May 2021 - 
TL;DR: Twenty state-of-the-art computational models of predicting miRNA-disease associations from different perspectives are reviewed, including five feasible and important research schemas, and future directions for further development of computational models are summarized.
Journal ArticleDOI

Minimum entropy decomposition: unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences.

A. Murat Eren, +5 more
- 17 Mar 2015 - 
TL;DR: Minimum Entropy Decomposition (MED) provides a computationally efficient means to partition marker gene datasets into ‘MED nodes’, which represent homogeneous operational taxonomic units and enables sensitive discrimination of closely related organisms in marker gene amplicon datasets without relying on extensive computational heuristics and user supervision.
Journal ArticleDOI

Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity

Amandine Everard, +9 more
- 03 Apr 2014 - 
TL;DR: Deep metagenomic sequencing analysis revealed that HFD and prebiotic treatment significantly affected the gut microbiome at different taxonomic levels and identified novel putative taxa and metabolic functions that may contribute to the development of or protection against the metabolic alterations observed during HFD feeding and HFD-Pre feeding.
Journal ArticleDOI

Sequence assembly demystified

Niranjan Nagarajan, +1 more
- 01 Mar 2013 - 
TL;DR: The theoretical foundations that underlie modern assembly are surveyed and the options and practical trade-offs that need to be considered are highlighted, focusing on how individual features address the needs of specific applications.
Journal ArticleDOI

A guide to enterotypes across the human body: meta-analysis of microbial community structures in human microbiome datasets.

Omry Koren, +8 more
- 10 Jan 2013 - 
TL;DR: This work tested how the following factors influenced the detection of enterotypes: clustering methodology, distance metrics, OTU-picking approaches, sequencing depth, data type (whole genome shotgun (WGS) vs.16S rRNA gene sequence data), and 16S r RNA region.
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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