Differential Susceptibility to T Cell-Induced Colitis in Mice: Role of the Intestinal Microbiota

Fucosylation Deficiency in Mice Leads to Colitis and Adenocarcinoma

(2017) Yiwei Wang et al.   GASTROENTEROLOGY

The gut microbiota and inflammatory bowel diseases

(2017) Jun Miyoshi et al.   Translational Research

Fecal Microbiota and Metabolome in a Mouse Model of Spontaneous Chronic Colitis

(2016) Ainsley M. Robinson et al.   INFLAMMATORY BOWEL DISEASES

Dysbiosis in intestinal inflammation: Cause or consequence

(2016) Ludovica F. Buttó et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Mechanisms of inflammation-driven bacterial dysbiosis in the gut

(2016) M Y Zeng et al.   Mucosal Immunology

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Comparative genomics and physiology of the butyrate-producing bacteriumIntestinimonas butyriciproducens

(2016) Thi Phuong Nam Bui et al.   Environmental Microbiology Reports

The Mouse Intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota

(2016) Ilias Lagkouvardos et al.   Nature Microbiology

Adjuvant use of antibiotics with corticosteroids in inflammatory bowel disease exacerbations requiring hospitalisation: a retrospective cohort study and meta-analysis

(2015) V. Gupta et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Intestinal Blautia Is Associated with Reduced Death from Graft-versus-Host Disease

(2015) Robert R. Jenq et al.   BIOLOGY OF BLOOD AND MARROW TRANSPLANTATION

An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases

(2015) Marta Wlodarska et al.   Cell Host & Microbe

Experimental colitis models: Insights into the pathogenesis of inflammatory bowel disease and translational issues

(2015) Vassilis Valatas et al.   EUROPEAN JOURNAL OF PHARMACOLOGY

Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis

(2015) Noortje G. Rossen et al.   GASTROENTEROLOGY

Dysbiotic gut microbiota causes transmissible Crohn's disease-like ileitis independent of failure in antimicrobial defence

(2015) Monika Schaubeck et al.   GUT

Manipulating the Gut Microbiota: Methods and Challenges: Figure 1

(2015) Aaron C. Ericsson et al.   ILAR JOURNAL

Engineering the gut microbiota to treat hyperammonemia

(2015) Ting-Chin David Shen et al.   JOURNAL OF CLINICAL INVESTIGATION

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Mechanisms of Microbe–Host Interaction in Crohn’s Disease: Dysbiosis vs. Pathobiont Selection

(2015) Ludovica F. Buttó et al.   Frontiers in Immunology

Ablation of Tumor Necrosis Factor Is Associated with Decreased Inflammation and Alterations of the Microbiota in a Mouse Model of Inflammatory Bowel Disease

(2015) Yava L. Jones-Hall et al.   PLoS One

Effects of Vendor and Genetic Background on the Composition of the Fecal Microbiota of Inbred Mice

(2015) Aaron C. Ericsson et al.   PLoS One

The Gut Microbiota of Wild Mice

(2015) Laura Weldon et al.   PLoS One

Faecal microbiota transplantation

(2014) M. Nieuwdorp   BRITISH JOURNAL OF SURGERY

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

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

Host adaptive immunity alters gut microbiota

(2014) Husen Zhang et al.   ISME Journal

Gut microbiome composition and function in experimental colitis during active disease and treatment-induced remission

(2014) Michelle G Rooks et al.   ISME Journal

pH of Drinking Water Influences the Composition of Gut Microbiome and Type 1 Diabetes Incidence

(2013) M. H. Sofi et al.   DIABETES

Beyond Gene Discovery in Inflammatory Bowel Disease: The Emerging Role of Epigenetics

(2013) Nicholas T. Ventham et al.   GASTROENTEROLOGY

Therapeutic Evaluation of Ex Vivo-Generated Versus Natural Regulatory T-cells in a Mouse Model of Chronic Gut Inflammation

(2013) Fridrik Karlsson et al.   INFLAMMATORY BOWEL DISEASES

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Intestinal Microbiota Composition of Interleukin-10 Deficient C57BL/6J Mice and Susceptibility to Helicobacter hepaticus-Induced Colitis

(2013) Ines Yang et al.   PLoS One

Extracellular Vesicles Derived from Gut Microbiota, Especially Akkermansia muciniphila, Protect the Progression of Dextran Sulfate Sodium-Induced Colitis

(2013) Chil-sung Kang et al.   PLoS One

Sex Differences in the Gut Microbiome Drive Hormone-Dependent Regulation of Autoimmunity

(2013) J. G. M. Markle et al.   SCIENCE

Microbiotas from UC patients display altered metabolism and reduced ability of LAB to colonize mucus

(2013) Louise Kristine Vigsnaes et al.   Scientific Reports

Transient Inability to Manage Proteobacteria Promotes Chronic Gut Inflammation in TLR5-Deficient Mice

(2012) Frederic A. Carvalho et al.   Cell Host & Microbe

Host-dependent control of early regulatory and effector T-cell differentiation underlies the genetic susceptibility of RAG2-deficient mouse strains to transfer colitis

(2012) V Valatas et al.   Mucosal Immunology

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

The gut microbiota in IBD

(2012) Chaysavanh Manichanh et al.   Nature Reviews Gastroenterology & Hepatology

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Commensal Bacteroides Species Induce Colitis in Host-Genotype-Specific Fashion in a Mouse Model of Inflammatory Bowel Disease

(2011) Seth M. Bloom et al.   Cell Host & Microbe

The Commensal Microbiota and Enteropathogens in the Pathogenesis of Inflammatory Bowel Diseases

(2011) Benoit Chassaing et al.   GASTROENTEROLOGY

The influence of the microbiota on type-1 diabetes: on the threshold of a leap forward in our understanding

(2011) Diane Mathis et al.   IMMUNOLOGICAL REVIEWS

Pharmacological intervention studies using mouse models of the inflammatory bowel diseases

(2011) Iurii Koboziev et al.   INFLAMMATORY BOWEL DISEASES

Naturally transmitted segmented filamentous bacteria segregate with diabetes protection in nonobese diabetic mice

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

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

Helicobacter hepaticus infection in mice: models for understanding lower bowel inflammation and cancer

(2010) J G Fox et al.   Mucosal Immunology

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Regulatory Lymphocytes and Intestinal Inflammation

(2009) Ana Izcue et al.   Annual Review of Immunology

Associations between species and groups of sites: indices and statistical inference

(2009) Miquel De Cáceres et al.   ECOLOGY

T cell transfer model of chronic colitis: concepts, considerations, and tricks of the trade

(2008) Dmitry V. Ostanin et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases

(2008) C. N Bernstein et al.   GUT

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE