Genomic approaches to studying the human microbiota

A framework for human microbiome research

(2012)   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Artificial Polyploidy Improves Bacterial Single Cell Genome Recovery

(2012) Armand E. K. Dichosa et al.   PLoS One

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Evaluation of 16S rDNA-Based Community Profiling for Human Microbiome Research

(2012)   PLoS One

Sequence Analysis of the Human Virome in Febrile and Afebrile Children

(2012) Kristine M. Wylie et al.   PLoS One

Optimizing Read Mapping to Reference Genomes to Determine Composition and Species Prevalence in Microbial Communities

(2012) John Martin et al.   PLoS One

Hypervariable loci in the human gut virome

(2012) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

DECIPHER, a Search-Based Approach to Chimera Identification for 16S rRNA Sequences

(2011) Erik S. Wright et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

The Human Microbiome Project in 2011 and Beyond

(2011) Lita M. Proctor   Cell Host & Microbe

Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection

(2011) Ethan Gough et al.   CLINICAL INFECTIOUS DISEASES

Regulation of innate and adaptive immunity by the commensal microbiota

(2011) Irene Jarchum et al.   CURRENT OPINION IN IMMUNOLOGY

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

The human metagenome: our other genome?

(2011) T. Bruls et al.   HUMAN MOLECULAR GENETICS

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection

(2011) Lawrence J. Brandt et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Efficient de novo assembly of single-cell bacterial genomes from short-read data sets

(2011) Hamidreza Chitsaz et al.   NATURE BIOTECHNOLOGY

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

(2011) Samuel V. Angiuoli et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Regulation of inflammatory responses by the commensal microbiota: Figure 1

(2011) Benjamin J Marsland   THORAX

Microbial Eukaryotes in the Human Microbiome: Ecology, Evolution, and Future Directions

(2011) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Siderophores from Neighboring Organisms Promote the Growth of Uncultured Bacteria

(2010) Anthony D'Onofrio et al.   CHEMISTRY & BIOLOGY

The intestinal microbiome: A separate organ inside the body with the metabolic potential to influence the bioactivity of botanicals

(2010) Sam Possemiers et al.   FITOTERAPIA

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

PhyloChip microarray analysis reveals altered gastrointestinal microbial communities in a rat model of colonic hypersensitivity

(2010) T. A. Nelson et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Comparison of two next-generation sequencing technologies for resolving highly complex microbiota composition using tandem variable 16S rRNA gene regions

(2010) Marcus J. Claesson et al.   NUCLEIC ACIDS RESEARCH

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

Deep Sequencing of the Vaginal Microbiota of Women with HIV

(2010) Ruben Hummelen et al.   PLoS One

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

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

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Deciphering the role of phage in the cystic fibrosis airway

(2010) Dana Willner et al.   Virulence

A Primer on Metagenomics

(2010) John C. Wooley et al.   PLoS Computational Biology

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

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Prolonged Impact of Antibiotics on Intestinal Microbial Ecology and Susceptibility to Enteric Salmonella Infection

(2009) A. Croswell et al.   INFECTION AND IMMUNITY

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

(2009) Vladimir Lazarevic et al.   JOURNAL OF MICROBIOLOGICAL METHODS

The core gut microbiome, energy balance and obesity

(2009) Peter J. Turnbaugh et al.   JOURNAL OF PHYSIOLOGY-LONDON

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

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

(2008) P Lepage et al.   GUT

Antibiotic-Induced Perturbations of the Intestinal Microbiota Alter Host Susceptibility to Enteric Infection

(2008) I. Sekirov et al.   INFECTION AND IMMUNITY

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

(2008) Harry J. Flint et al.   NATURE REVIEWS MICROBIOLOGY

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Viral diversity and dynamics in an infant gut

(2008) Mya Breitbart et al.   RESEARCH IN MICROBIOLOGY

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

(2008) Stacy R. Finkbeiner et al.   PLoS Pathogens