Inflammation-associated enterotypes, host genotype, cage and inter-individual effects drive gut microbiota variation in common laboratory mice

Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma

(2012) Shannon L Russell et al.   EMBO REPORTS

Fecal calprotectin is a surrogate marker for endoscopic lesions in inflammatory bowel disease

(2012) Geert DʼHaens et al.   INFLAMMATORY BOWEL DISEASES

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

(2012) Junjie Qin et al.   NATURE

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Analysis of the Gut Microbiota in the Old Order Amish and Its Relation to the Metabolic Syndrome

(2012) Margaret L. Zupancic et al.   PLoS One

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice

(2011) Richard Kellermayer et al.   FASEB JOURNAL

Bile Acid Is a Host Factor That Regulates the Composition of the Cecal Microbiota in Rats

(2011) K.B.M. Saiful Islam et al.   GASTROENTEROLOGY

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

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

Altered gut microbiota composition in immune-impairedNod2−/−mice

(2011) Stanislas Mondot et al.   GUT

Microbiota Downregulates Dendritic Cell Expression of miR-10a, Which Targets IL-12/IL-23p40

(2011) X. Xue et al.   JOURNAL OF IMMUNOLOGY

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Subspecific origin and haplotype diversity in the laboratory mouse

(2011) Hyuna Yang et al.   NATURE GENETICS

The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes

(2011) Mark W. J. van Passel et al.   PLoS One

Prebiotic Effects of Wheat Arabinoxylan Related to the Increase in Bifidobacteria, Roseburia and Bacteroides/Prevotella in Diet-Induced Obese Mice

(2011) Audrey M. Neyrinck et al.   PLoS One

Gut Microbiome Metagenomics Analysis Suggests a Functional Model for the Development of Autoimmunity for Type 1 Diabetes

(2011) Christopher T. Brown et al.   PLoS One

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Caspase deficiency alters the murine gut microbiome

(2011) B M Brinkman et al.   Cell Death & Disease

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

High temporal and inter-individual variation detected in the human ileal microbiota

(2010) Carien C. G. M. Booijink et al.   ENVIRONMENTAL MICROBIOLOGY

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Gut-Residing Segmented Filamentous Bacteria Drive Autoimmune Arthritis via T Helper 17 Cells

(2010) Hsin-Jung Wu et al.   IMMUNITY

Regulation of the Polymeric Immunoglobulin Receptor in Intestinal Epithelial Cells byEnterobacteriaceae: Implications for Mucosal Homeostasis

(2010) Maria E. C. Bruno et al.   IMMUNOLOGICAL INVESTIGATIONS

Strain-Specific Polymorphisms in Paneth Cell α-Defensins of C57BL/6 Mice and Evidence of Vestigial Myeloid α-Defensin Pseudogenes

(2010) Michael T. Shanahan et al.   INFECTION AND IMMUNITY

Microbial ecology of the murine gut associated with the development of dextran sodium sulfate-induced colitis

(2010) Nabeetha A. Nagalingam et al.   INFLAMMATORY BOWEL DISEASES

Numerical ecology validates a biogeographical distribution and gender-based effect on mucosa-associated bacteria along the human colon

(2010) Daniel Aguirre de Cárcer et al.   ISME Journal

Creating and characterizing communities of human gut microbes in gnotobiotic mice

(2010) Jeremiah J Faith et al.   ISME Journal

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients

(2010) A. Rehman et al.   JOURNAL OF MEDICAL MICROBIOLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Site and Strain-Specific Variation in Gut Microbiota Profiles and Metabolism in Experimental Mice

(2010) Melissa K. Friswell et al.   PLoS One

Regional Mucosa-Associated Microbiota Determine Physiological Expression of TLR2 and TLR4 in Murine Colon

(2010) Yunwei Wang et al.   PLoS One

Epithelial crosstalk at the microbiota-mucosal interface

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

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

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Like Will to Like: Abundances of Closely Related Species Can Predict Susceptibility to Intestinal Colonization by Pathogenic and Commensal Bacteria

(2010) Bärbel Stecher et al.   PLoS Pathogens

Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice

(2009) Chenhong Zhang et al.   ISME Journal

Role of Gut Commensal Microflora in the Development of Experimental Autoimmune Encephalomyelitis

(2009) J. Ochoa-Reparaz et al.   JOURNAL OF IMMUNOLOGY

Enteric defensins are essential regulators of intestinal microbial ecology

(2009) Nita H Salzman et al.   NATURE IMMUNOLOGY

Human gut microbiota in obesity and after gastric bypass

(2009) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

NKT Cell-Dependent Amelioration of a Mouse Model of Multiple Sclerosis by Altering Gut Flora

(2008) Hiroaki Yokote et al.   AMERICAN JOURNAL OF PATHOLOGY

Metagenomic Approaches for Defining the Pathogenesis of Inflammatory Bowel Diseases

(2008) Daniel A. Peterson et al.   Cell Host & Microbe

Increased Gastrointestinal Permeability and Gut Inflammation in Children with Functional Abdominal Pain and Irritable Bowel Syndrome

(2008) Robert J. Shulman et al.   JOURNAL OF PEDIATRICS

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

(2008) Li Wen et al.   NATURE

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

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

Predominant Role of Host Genetics in Controlling the Composition of Gut Microbiota

(2008) Zaruhi A. Khachatryan et al.   PLoS One

Species Variation in the Fecal Metabolome Gives Insight into Differential Gastrointestinal Function

(2007) Jasmina Saric et al.   JOURNAL OF PROTEOME RESEARCH