Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice

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

(2015) Jason M. Norman et al.   CELL

Biogeography of the Intestinal Mucosal and Lumenal Microbiome in the Rhesus Macaque

(2015) Koji Yasuda et al.   Cell Host & Microbe

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

(2015) A Lavelle et al.   GUT

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome

(2015) Benoit Chassaing et al.   NATURE

Microbiota organization—a key to understanding CRC development

(2015) Georgina L. Hold et al.   Nature Reviews Gastroenterology & Hepatology

Gut Microbial Succession Follows Acute Secretory Diarrhea in Humans

(2015) Lawrence A. David et al.   mBio

Linear growth faltering in infants is associated with Acidaminococcus sp. and community-level changes in the gut microbiota

(2015) Ethan K. Gough et al.   Microbiome

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

Role of the Microbiota in Immunity and Inflammation

(2014) Yasmine Belkaid et al.   CELL

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

The composition of the gut microbiota shapes the colon mucus barrier

(2014) H. E. Jakobsson et al.   EMBO REPORTS

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Bacteria, phages and pigs: the effects of in-feed antibiotics on the microbiome at different gut locations

(2014) Torey Looft et al.   ISME Journal

Classification and quantification of bacteriophage taxa in human gut metagenomes

(2014) Alison S Waller et al.   ISME Journal

Altered Oral Viral Ecology in Association with Periodontal Disease

(2014) M. Ly et al.   mBio

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

(2014) M. J. Coyne et al.   mBio

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

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

Viruses and the Microbiota

(2014) Christopher M. Robinson et al.   Annual Review of Virology

Modeling dietary patterns to assess sodium recommendations for nutrient adequacy

(2013) Earl S Ford et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis

(2013) Malin E V Johansson et al.   GUT

Spatial heterogeneity and co-occurrence patterns of human mucosal-associated intestinal microbiota

(2013) Zhigang Zhang et al.   ISME Journal

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

(2013) Sheetal R. Modi et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Gene product 0.4 increases bacteriophage T7 competitiveness by inhibiting host cell division

(2013) R. Kiro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid evolution of the human gut virome

(2013) S. Minot et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

(2013) P. C. Kashyap et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacteriophage adhering to mucus provide a non-host-derived immunity

(2013) J. J. Barr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

(2013) Lesley A. Ogilvie et al.   Nature Communications

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Intestinal Commensal Microbes as Immune Modulators

(2012) Ivaylo I. Ivanov et al.   Cell Host & Microbe

Orthologous Gene Clusters and Taxon Signature Genes for Viruses of Prokaryotes

(2012) D. M. Kristensen et al.   JOURNAL OF BACTERIOLOGY

Familial transmission rather than defective innate immunity shapes the distinct intestinal microbiota of TLR-deficient mice

(2012) Carles Ubeda et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Going viral: next-generation sequencing applied to phage populations in the human gut

(2012) Alejandro Reyes et al.   NATURE REVIEWS MICROBIOLOGY

Fecal Lipocalin 2, a Sensitive and Broadly Dynamic Non-Invasive Biomarker for Intestinal Inflammation

(2012) Benoit Chassaing 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

A Crypt-Specific Core Microbiota Resides in the Mouse Colon

(2012) T. Pedron et al.   mBio

Diversity and Abundance of Single-Stranded DNA Viruses in Human Feces

(2011) Min-Soo Kim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

WebMGA: a customizable web server for fast metagenomic sequence analysis

(2011) Sitao Wu et al.   BMC GENOMICS

Integrative analysis of environmental sequences using MEGAN4

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

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

(2011) S. Minot et al.   GENOME RESEARCH

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

PHAST: A Fast Phage Search Tool

(2011) Y. Zhou et al.   NUCLEIC ACIDS RESEARCH

Microviridae Goes Temperate: Microvirus-Related Proviruses Reside in the Genomes of Bacteroidetes

(2011) Mart Krupovic et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Spatial organization of intestinal microbiota in the mouse ascending colon

(2010) Gerardo M Nava et al.   ISME Journal

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

(2010) D. Willner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Microbiota Mediates Pathogen Clearance from the Gut Lumen after Non-Typhoidal Salmonella Diarrhea

(2010) Kathrin Endt et al.   PLoS Pathogens

The role of pH in determining the species composition of the human colonic microbiota

(2009) Sylvia H. Duncan et al.   ENVIRONMENTAL MICROBIOLOGY

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Changes in Gut Microbiota Control Metabolic Endotoxemia-Induced Inflammation in High-Fat Diet-Induced Obesity and Diabetes in Mice

(2008) P. D. Cani et al.   DIABETES

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

(2008) P Lepage et al.   GUT

ARDB--Antibiotic Resistance Genes Database

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