Abundance profiling of specific gene groups using precomputed gut metagenomes yields novel biological hypotheses

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

A degenerate PCR-based strategy as a means of identifying homologues of aminoglycoside and β-lactam resistance genes in the gut microbiota

(2014) Fiona Fouhy et al.   BMC MICROBIOLOGY

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

Classification and quantification of bacteriophage taxa in human gut metagenomes

(2014) Alison S Waller et al.   ISME Journal

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Functional metagenomics for the investigation of antibiotic resistance

(2014) Peter Mullany   Virulence

A systematic comparison of the MetaCyc and KEGG pathway databases

(2013) Tomer Altman et al.   BMC BIOINFORMATICS

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Gut Microbiota Regulates Bile Acid Metabolism by Reducing the Levels of Tauro-beta-muricholic Acid, a Naturally Occurring FXR Antagonist

(2013) Sama I. Sayin et al.   Cell Metabolism

Genetic Diversity of Bile Salt Hydrolases Among Human Intestinal Bifidobacteria

(2013) Piotr Jarocki et al.   CURRENT MICROBIOLOGY

Country-specific antibiotic use practices impact the human gut resistome

(2013) K. Forslund et al.   GENOME RESEARCH

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

The gut microbiota — masters of host development and physiology

(2013) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

Second European evidence-based consensus on the diagnosis and management of ulcerative colitis Part 2: Current management

(2012) Axel Dignass et al.   Journal of Crohns & Colitis

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

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The influence of diet on the gut microbiota

(2012) Karen P. Scott et al.   PHARMACOLOGICAL RESEARCH

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

RAPSearch: a fast protein similarity search tool for short reads

(2011) Yuzhen Ye et al.   BMC BIOINFORMATICS

Food Animals and Antimicrobials: Impacts on Human Health

(2011) B. M. Marshall et al.   CLINICAL MICROBIOLOGY REVIEWS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Butyrate and other short-chain fatty acids as modulators of immunity: what relevance for health?

(2010) Kees Meijer et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

(2010) L. Tasse et al.   GENOME RESEARCH

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

A metagenomic  -glucuronidase uncovers a core adaptive function of the human intestinal microbiome

(2010) K. Gloux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Metagenomic Screening for Bleomycin Resistance Genes

(2008) T. Mori et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Factors influencing antibiotic prescribing in China: An exploratory analysis

(2008) Lucy Reynolds et al.   HEALTH POLICY

ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH

MetaSim—A Sequencing Simulator for Genomics and Metagenomics

(2008) Daniel C. Richter et al.   PLoS One