Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

(2020) Sidhartha R. Sinha et al.   Cell Host & Microbe

Assessment of Inter-Laboratory Variation in the Characterization and Analysis of the Mucosal Microbiota in Crohn’s Disease and Ulcerative Colitis

(2020) Jake C. Szamosi et al.   Frontiers in Microbiology

Fruit consumption is associated with alterations in microbial composition and lower rates of pouchitis

(2019) L Godny et al.   Journal of Crohns & Colitis

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Metagenomic analysis of bile salt biotransformation in the human gut microbiome

(2019) Promi Das et al.   BMC GENOMICS

Predominantly Antibiotic-resistant Intestinal Microbiome Persists in Patients With Pouchitis Who Respond to Antibiotic Therapy

(2019) Vadim Dubinsky et al.   GASTROENTEROLOGY

Adherence to the Mediterranean diet is associated with decreased fecal calprotectin in patients with ulcerative colitis after pouch surgery

(2019) L. Godny et al.   EUROPEAN JOURNAL OF NUTRITION

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Prevalence of Yersinia Species in the Ileum of Crohn's Disease Patients and Controls

(2018) Guillaume Le Baut et al.   Frontiers in Cellular and Infection Microbiology

Pathogenic functions of host microbiota

(2018) Silke Rath et al.   Microbiome

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Microbiota profile in new-onset pediatric Crohn’s disease: data from a non-Western population

(2018) Mohammad I. El Mouzan et al.   Gut Pathogens

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Roles for Intestinal Bacteria, Viruses, and Fungi in Pathogenesis of Inflammatory Bowel Diseases and Therapeutic Approaches

(2017) R. Balfour Sartor et al.   GASTROENTEROLOGY

Guiding longitudinal sampling in IBD cohorts

(2017) Yoshiki Vázquez-Baeza et al.   GUT

Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis

(2017) Emilio J Laserna-Mendieta et al.   Journal of Crohns & Colitis

Environmental triggers in IBD: a review of progress and evidence

(2017) Ashwin N. Ananthakrishnan et al.   Nature Reviews Gastroenterology & Hepatology

A role for bacterial urease in gut dysbiosis and Crohn’s disease

(2017) Josephine Ni et al.   Science Translational Medicine

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Colonic Butyrate-Producing Communities in Humans: an Overview Using Omics Data

(2017) Marius Vital et al.   mSystems

Review article: the pathogenesis of pouchitis

(2016) K. M. Schieffer et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Formation of propionate and butyrate by the human colonic microbiota

(2016) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Host-mediated sugar oxidation promotes post-antibiotic pathogen expansion

(2016) Franziska Faber et al.   NATURE

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut

(2016) Audrey Rivière et al.   Frontiers in Microbiology

MicroRNAs Expression in the Ileal Pouch of Patients with Ulcerative Colitis Is Robustly Up-Regulated and Correlates with Disease Phenotypes

(2016) Shay Ben-Shachar et al.   PLoS One

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Pouch Inflammation Is Associated With a Decrease in Specific Bacterial Taxa

(2015) Leah Reshef et al.   GASTROENTEROLOGY

Serology of Patients with Ulcerative Colitis After Pouch Surgery Is More Comparable with that of Patients with Crohnʼs Disease

(2015) Idan Goren et al.   INFLAMMATORY BOWEL DISEASES

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

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

Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals

(2014) Jacob Tveiten Bjerrum et al.   Metabolomics

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Revealing the Bacterial Butyrate Synthesis Pathways by Analyzing (Meta)genomic Data

(2014) M. Vital et al.   mBio

The dynamics of gut-associated microbial communities during inflammation

(2013) Sebastian E Winter et al.   EMBO REPORTS

A decrease of the butyrate-producing speciesRoseburia hominisandFaecalibacterium prausnitziidefines dysbiosis in patients with ulcerative colitis

(2013) Kathleen Machiels et al.   GUT

Gene Expression Profiles of Ileal Inflammatory Bowel Disease Correlate with Disease Phenotype and Advance Understanding of Its Immunopathogenesis

(2013) Shay Ben-Shachar et al.   INFLAMMATORY BOWEL DISEASES

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Commensal Akkermansia muciniphila Exacerbates Gut Inflammation in Salmonella Typhimurium-Infected Gnotobiotic Mice

(2013) Bhanu Priya Ganesh et al.   PLoS One

Utilisation of Mucin Glycans by the Human Gut Symbiont Ruminococcus gnavus Is Strain-Dependent

(2013) Emmanuelle H. Crost et al.   PLoS One

Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases

(2012) Henri Duboc et al.   GUT

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

New IBD genetics: common pathways with other diseases

(2011) C. W. Lees et al.   GUT

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

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

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Comprehensive pouch clinic concept for follow-up of patients after ileal pouch anal anastomosis: Report of 3 yearsʼ experience in a tertiary referral center

(2008) Hagit Tulchinsky et al.   INFLAMMATORY BOWEL DISEASES

Glutathione: Overview of its protective roles, measurement, and biosynthesis

(2008) Henry Jay Forman et al.   MOLECULAR ASPECTS OF MEDICINE

A multifaceted role for polyamines in bacterial pathogens

(2008) Pratik Shah et al.   MOLECULAR MICROBIOLOGY

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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