4.7 Review

Experimental and analytical tools for studying the human microbiome

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Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

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A human gut microbial gene catalogue established by metagenomic sequencing

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Jens Reeder et al.

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Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

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QIIME allows analysis of high-throughput community sequencing data

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KEGG for representation and analysis of molecular networks involving diseases and drugs

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FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments

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Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

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ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

Erik Kristiansson et al.

BIOINFORMATICS (2009)

Review Biochemistry & Molecular Biology

Redefining Chronic Viral Infection

Herbert W. Virgin et al.

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The NIH Human Microbiome Project

Jane Peterson et al.

GENOME RESEARCH (2009)

Article Biochemical Research Methods

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing

Vladimir Lazarevic et al.

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A core gut microbiome in obese and lean twins

Peter J. Turnbaugh et al.

NATURE (2009)

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The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

J. R. Cole et al.

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Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

T. Andrew Clayton et al.

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Bacteriophages Encode Factors Required for Protection in a Symbiotic Mutualism

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Bacterial Community Variation in Human Body Habitats Across Space and Time

Elizabeth K. Costello et al.

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Peter J. Turnbaugh et al.

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Microbial influences in inflammatory bowel diseases

R. Balfour Sartor

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A diversity profile of the human skin microbiota

Elizabeth A. Grice et al.

GENOME RESEARCH (2008)

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The rational exploration of microbial diversity

Christopher Quince et al.

ISME JOURNAL (2008)

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Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

Zongzhi Liu et al.

NUCLEIC ACIDS RESEARCH (2008)

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The influence of sex, handedness, and washing on the diversity of hand surface bacteria

Noah Fierer et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Microbiology

Viral diversity and dynamics in an infant gut

Mya Breitbart et al.

RESEARCH IN MICROBIOLOGY (2008)

Article Gastroenterology & Hepatology

Fungi and inflammatory bowel diseases: Alterations of composition and diversity

Stephan J. Ott et al.

SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY (2008)

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IMG/M: a data management and analysis system for metagenomes

Victor M. Markowitz et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

The Pfam protein families database

Robert D. Finn et al.

NUCLEIC ACIDS RESEARCH (2008)

Article Biochemistry & Molecular Biology

SILVA:: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Elmar Pruesse et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

The Human Microbiome Project

Peter J. Turnbaugh et al.

NATURE (2007)

Article Biochemistry & Molecular Biology

Short pyrosequencing reads suffice for accurate microbial community analysis

Zongzhi Liu et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biotechnology & Applied Microbiology

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

Qiong Wang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Biochemistry & Molecular Biology

Development of the human infant intestinal microbiota

Chana Palmer et al.

PLOS BIOLOGY (2007)

Article Ecology

Metaproteomics: A new approach for studying functional microbial ecology

Pierre-Alain Maron et al.

MICROBIAL ECOLOGY (2007)

Article Multidisciplinary Sciences

Quantitative phylogenetic assessment of microbial communities in diverse environments

C. von Mering et al.

SCIENCE (2007)

Article Multidisciplinary Sciences

Molecular analysis of human forearm superficial skin bacterial biota

Zhan Gao et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Biotechnology & Applied Microbiology

Accuracy and quality of massively parallel DNA pyrosequencing

Susan M. Huse et al.

GENOME BIOLOGY (2007)

Article Microbiology

Molecular analysis of fungal microbiota in samples from healthy human skin and psoriatic lesions

Luciana C. Paulino et al.

JOURNAL OF CLINICAL MICROBIOLOGY (2006)

Article Multidisciplinary Sciences

A Sanger/pyrosequencing hybrid approach tor the generation of high-quality draft assemblies of marine microbial genomes

Susanne M. D. Goldberg et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biotechnology & Applied Microbiology

Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB

T. Z. DeSantis et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2006)

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NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes

T. Z. DeSantis et al.

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UniFrac: a new phylogenetic method for comparing microbial communities

C Lozupone et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2005)

Article Multidisciplinary Sciences

Obesity alters gut microbial ecology

RE Ley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Review Biochemical Research Methods

Bioinformatics for whole-genome shotgun sequencing of microbial communities

K Chen et al.

PLOS COMPUTATIONAL BIOLOGY (2005)

Article Multidisciplinary Sciences

Comparative metagenomics of microbial communities

SG Tringe et al.

SCIENCE (2005)

Article Biochemical Research Methods

DNA microarray analysis of predominant human intestinal bacteria in fecal samples

RF Wang et al.

MOLECULAR AND CELLULAR PROBES (2004)

Review Microbiology

The uncultured microbial majority

MS Rappe et al.

ANNUAL REVIEW OF MICROBIOLOGY (2003)

Article Biochemical Research Methods

A comparison of five methods for extraction of bacterial DNA from human faecal samples

AL McOrist et al.

JOURNAL OF MICROBIOLOGICAL METHODS (2002)