Carrageenan Gum and Adherent Invasive Escherichia coli in a Piglet Model of Inflammatory Bowel Disease: Impact on Intestinal Mucosa-associated Microbiota

Genome-based Definition of an Inflammatory Bowel Disease-associated Adherent-Invasive Escherichia coli Pathovar

(2016) Michael Desilets et al.   INFLAMMATORY BOWEL DISEASES

High Molecular Weight Barley β-Glucan Alters Gut Microbiota Toward Reduced Cardiovascular Disease Risk

(2016) Yanan Wang et al.   Frontiers in Microbiology

Immune Responses to Intestinal Microbes in Inflammatory Bowel Diseases

(2015) Jonathan J. Hansen   CURRENT ALLERGY AND ASTHMA REPORTS

Recent Advances in Characterizing the Gastrointestinal Microbiome in Crohnʼs Disease

(2015) Emily K. Wright et al.   INFLAMMATORY BOWEL DISEASES

An extended single-index multiplexed 16S rRNA sequencing for microbial community analysis on MiSeq illumina platforms

(2015) Hooman Derakhshani et al.   JOURNAL OF BASIC MICROBIOLOGY

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

Role of the gut microbiota in inflammatory bowel disease pathogenesis: What have we learnt in the past 10 years?

(2014) Georgina L Hold   WORLD JOURNAL OF GASTROENTEROLOGY

Association betweenFaecalibacterium prausnitziiReduction and Inflammatory Bowel Disease: A Meta-Analysis and Systematic Review of the Literature

(2014) Yuan Cao et al.   Gastroenterology Research and Practice

Understanding Host-Adherent-InvasiveEscherichia coliInteraction in Crohn’s Disease: Opening Up New Therapeutic Strategies

(2014) Allison Agus et al.   Biomed Research International

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

An intestinal arsonist: pathobiont ignites IBD and flees the scene

(2013) Stefan Jellbauer et al.   GUT

AIEC pathobiont instigates chronic colitis in susceptible hosts by altering microbiota composition

(2013) Benoit Chassaing et al.   GUT

Faecalibacterium prausnitzii upregulates regulatory T cells and anti-inflammatory cytokines in treating TNBS-induced colitis

(2013) Xinyun Qiu et al.   Journal of Crohns & Colitis

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Use of pigs as a potential model for research into dietary modulation of the human gut microbiota

(2013) Sonja N. Heinritz et al.   NUTRITION RESEARCH REVIEWS

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

The Microbiome in Infectious Disease and Inflammation

(2012) Kenya Honda et al.   Annual Review of Immunology

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Longitudinal Analyses of Gut Mucosal Microbiotas in Ulcerative Colitis in Relation to Patient Age and Disease Severity and Duration

(2012) Alemu Fite et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The gut microbiota in IBD

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

IBD—what role do Proteobacteria play?

(2012) Indrani Mukhopadhya et al.   Nature Reviews Gastroenterology & Hepatology

Pyrosequencing Reveals the Influence of Organic and Conventional Farming Systems on Bacterial Communities

(2012) Ru Li et al.   PLoS One

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Interactions Between the Host Innate Immune System and Microbes in Inflammatory Bowel Disease

(2011) Clara Abraham et al.   GASTROENTEROLOGY

Comparison of the fecal microbiota profiles between ulcerative colitis and Crohn’s disease using terminal restriction fragment length polymorphism analysis

(2011) Akira Andoh et al.   JOURNAL OF GASTROENTEROLOGY

Intestinal homeostasis and its breakdown in inflammatory bowel disease

(2011) Kevin J. Maloy et al.   NATURE

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

The role of bacteria and pattern-recognition receptors in Crohn's disease

(2011) Si Ming Man et al.   Nature Reviews Gastroenterology & Hepatology

Potential beneficial effects of butyrate in intestinal and extraintestinal diseases

(2011) Roberto Berni Canani   WORLD JOURNAL OF GASTROENTEROLOGY

Identifying biologically relevant differences between metagenomic communities

(2010) Donovan H. Parks et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

The Role of Bacteria in the Pathogenesis of Inflammatory Bowel Disease

(2010) Melissa Friswell et al.   Gut and Liver

Characterization of Escherichia coli isolated from gut biopsies of newly diagnosed patients with inflammatory bowel disease

(2010) Shadi Sepehri et al.   INFLAMMATORY BOWEL DISEASES

Complete Genome Sequence of Adherent Invasive Escherichia coli UM146 Isolated from Ileal Crohn's Disease Biopsy Tissue

(2010) D. O. Krause et al.   JOURNAL OF BACTERIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Complete Genome Sequence of Crohn's Disease-Associated Adherent-Invasive E. coli Strain LF82

(2010) Sylvie Miquel et al.   PLoS One

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

(2010) M. Vijay-Kumar et al.   SCIENCE

Rumen Microbiome Composition Determined Using Two Nutritional Models of Subacute Ruminal Acidosis

(2009) E. Khafipour et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

PyNAST: a flexible tool for aligning sequences to a template alignment

(2009) J. G. Caporaso et al.   BIOINFORMATICS

Phylogenetic analysis of inflammatory bowel disease associated Escherichia coli and the fimH virulence determinant

(2009) Shadi Sepehri et al.   INFLAMMATORY BOWEL DISEASES

Low counts of Faecalibacterium prausnitzii in colitis microbiota

(2009) H. Sokol et al.   INFLAMMATORY BOWEL DISEASES

Molecular-phylogenetic characterization of microbial communities imbalances in the small intestine of dogs with inflammatory bowel disease

(2008) Panagiotis G. Xenoulis et al.   FEMS MICROBIOLOGY ECOLOGY

Microbial Influences in Inflammatory Bowel Diseases

(2008) R. Balfour Sartor   GASTROENTEROLOGY

Analysis of bacterial bowel communities of IBD patients: What has it revealed?

(2008) Harry Sokol et al.   INFLAMMATORY BOWEL DISEASES

Imbalance in intestinal microflora constitution could be involved in the pathogenesis of inflammatory bowel disease

(2007) Hiromasa Takaishi et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY