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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

Ecological Approaches to Oral Biofilms: Control without Killing

Phil D. Marsh, +2 more
- 01 Jan 2015 - 
TL;DR: Modelling studies support the concept that either reducing the frequency of acid challenge and/or the terminal pH, or by merely slowing bacterial growth, results in maintaining a community of beneficial bacteria under conditions that might otherwise lead to disease (control without killing).
Journal ArticleDOI

Engineered Regulatory Systems Modulate Gene Expression of Human Commensals in the Gut.

Bentley Lim, +3 more
- 20 Apr 2017 - 
TL;DR: A panel of tunable expression platforms for the prominent genus Bacteroides in which gene expression is controlled by a synthetic inducer is developed, which is used to measure the dynamic relationship between commensal sialidase activity and liberation of mucosal sialic acid, a receptor and nutrient for pathogens.
Journal ArticleDOI

COCACOLA: binning metagenomic contigs using sequence COmposition, read CoverAge, CO-alignment and paired-end read LinkAge

Yang Young Lu, +4 more
- 02 Jun 2016 - 
TL;DR: COCACOLA as discussed by the authors is a general framework automatically bin contigs into OTUs based on sequence composition and coverage across multiple samples, which is demonstrated in both simulated and real datasets in comparison with state-of-the-art binning approaches such as CONCOCT, GroopM, MaxBin and MetaBAT.
Journal ArticleDOI

Gut microbial molecules in behavioural and neurodegenerative conditions.

Brittany D. Needham, +2 more
- 16 Oct 2020 - 
TL;DR: Bacterial metabolites with known or suspected neuromodulatory activity are described, mechanisms of signalling pathways from the gut microbiota to the brain are defined and direct effects that gut bacterial molecules are likely exerting on specific brain cells are discussed.
Journal ArticleDOI

NetCoMi: network construction and comparison for microbiome data in R

Stefanie Peschel, +4 more
- 20 Jul 2021 - 
TL;DR: NetCoMi (Network Construction and comparison for Microbiome data), an R package that integrates existing methods for each analysis step in a single reproducible computational workflow, is introduced, enabling insights into whether single taxa, groups of taxa or the overall network structure change between groups.
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 core gut microbiome in obese and lean twins

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