Gut microbiota and IBD: causation or correlation?

Understanding and Preventing the Global Increase of Inflammatory Bowel Disease

(2017) Gilaad G. Kaplan et al.   GASTROENTEROLOGY

Diet as a Trigger or Therapy for Inflammatory Bowel Diseases

(2017) James D. Lewis et al.   GASTROENTEROLOGY

Host-Microbiota Interactions Shape Local and Systemic Inflammatory Diseases

(2017) John B. Grigg et al.   JOURNAL OF IMMUNOLOGY

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial

(2017) Sudarshan Paramsothy et al.   LANCET

A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice

(2017) Tyson R. Chiaro et al.   Science Translational Medicine

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Immunological Consequences of Intestinal Fungal Dysbiosis

(2016) Matthew L. Wheeler et al.   Cell Host & Microbe

T Regulatory Cell Biology in Health and Disease

(2016) Fayhan J. Alroqi et al.   CURRENT ALLERGY AND ASTHMA REPORTS

Fungal microbiota dysbiosis in IBD

(2016) Harry Sokol et al.   GUT

T-bet as a key regulator of mucosal immunity

(2016) Rami Mohamed et al.   IMMUNOLOGY

O-001 A Multicenter, Double-Blind, Placebo-Controlled Phase3 Study of Ustekinumab, a Human IL-12/23P40 mAB, in Moderate-Service Crohnʼs Disease Refractory to Anti-TFNα

(2016) William Sandborn et al.   INFLAMMATORY BOWEL DISEASES

Mucosa-Associated Ileal Microbiota in New-Onset Pediatric Crohnʼs Disease

(2016) Amit Assa et al.   INFLAMMATORY BOWEL DISEASES

Exclusive enteral nutrition in active pediatric Crohn disease: Effects on intestinal microbiota and immune regulation

(2016) Tobias Schwerd et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Oxygen metabolism and barrier regulation in the intestinal mucosa

(2016) Louise E. Glover et al.   JOURNAL OF CLINICAL INVESTIGATION

Innate lymphoid cells: models of plasticity for immune homeostasis and rapid responsiveness in protection

(2016) F F Almeida et al.   Mucosal Immunology

Association of host genome with intestinal microbial composition in a large healthy cohort

(2016) Williams Turpin et al.   NATURE GENETICS

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands

(2016) Bruno Lamas et al.   NATURE MEDICINE

Innate Immunity and Asthma Risk in Amish and Hutterite Farm Children

(2016) Michelle M. Stein et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Association of Mycobacterium avium subsp. paratuberculosis with Inflammatory Bowel Disease

(2016) Verlaine J. Timms et al.   PLoS One

Virulence factors enhance Citrobacter rodentium expansion through aerobic respiration

(2016) C. A. Lopez et al.   SCIENCE

Gut Microbiota Diversity and Human Diseases: Should We Reintroduce Key Predators in Our Ecosystem?

(2016) Alexis Mosca et al.   Frontiers in Microbiology

Innate Sensing of the Gut Microbiota: Modulation of Inflammatory and Autoimmune Diseases

(2016) Aline Ignacio et al.   Frontiers in Immunology

Prevalence of Inflammatory Bowel Disease Among Adults Aged ≥18 Years — United States, 2015

(2016) James M. Dahlhamer et al.   MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT

Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation

(2015) Kaija-Leena Kolho et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

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

(2015) Jason M. Norman et al.   CELL

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

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

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

Geographical patterns of the standing and active human gut microbiome in health and IBD

(2015) Ateequr Rehman et al.   GUT

Gut Fungal Microbiota

(2015) Mathias L. Richard et al.   INFLAMMATORY BOWEL DISEASES

Fecal Microbial Transplant Effect on Clinical Outcomes and Fecal Microbiome in Active Crohnʼs Disease

(2015) David L. Suskind et al.   INFLAMMATORY BOWEL DISEASES

Fungal Dysbiosis in Mucosa-associated Microbiota of Crohn’s Disease Patients

(2015) Giuseppina Liguori et al.   Journal of Crohns & Colitis

Fecal Microbial Transplant Via Nasogastric Tube for Active Pediatric Ulcerative Colitis

(2015) David L. Suskind et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Step-up fecal microbiota transplantation strategy: a pilot study for steroid-dependent ulcerative colitis

(2015) Bota Cui et al.   Journal of Translational Medicine

The fungal microbiota of de-novo paediatric inflammatory bowel disease

(2015) I. Mukhopadhya et al.   MICROBES AND INFECTION

Mongersen, an Oral SMAD7 Antisense Oligonucleotide, and Crohn’s Disease

(2015) Giovanni Monteleone et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Treg/Th17 Axis: A Dynamic Balance Regulated by the Gut Microbiome

(2015) Sara Omenetti et al.   Frontiers in Immunology

Immunoglobulin A Coating Identifies Colitogenic Bacteria in Inflammatory Bowel Disease

(2014) Noah W. Palm et al.   CELL

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

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

Correlation Between Intraluminal Oxygen Gradient and Radial Partitioning of Intestinal Microbiota

(2014) Lindsey Albenberg et al.   GASTROENTEROLOGY

Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease

(2014) Lindsey G. Albenberg et al.   GASTROENTEROLOGY

Comprehensive Intestinal T Helper Cell Profiling Reveals Specific Accumulation of IFN-γ+IL-17+Coproducing CD4+ T Cells in Active Inflammatory Bowel Disease

(2014) Anna-Maria Globig et al.   INFLAMMATORY BOWEL DISEASES

Decline in Presumptively Protective Gut Bacterial Species and Metabolites Are Paradoxically Associated with Disease Improvement in Pediatric Crohn’s Disease During Enteral Nutrition

(2014) Konstantinos Gerasimidis et al.   INFLAMMATORY BOWEL DISEASES

Association Between IgA Deficiency & Other Autoimmune Conditions: A Population-Based Matched Cohort Study

(2014) Jonas F. Ludvigsson et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Pro-inflammatory human Th17 cells selectively express P-glycoprotein and are refractory to glucocorticoids

(2014) Radha Ramesh et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Fecal microbiota transplantation through mid-gut for refractory Crohn's disease: Safety, feasibility, and efficacy trial results

(2014) Bota Cui et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Mycobacterium aviumsubspeciesparatuberculosisin the etiology of Crohn’s disease, cause or epiphenomenon?

(2014) Elisa Liverani   WORLD JOURNAL OF GASTROENTEROLOGY

Temporal Bacterial Community Dynamics Vary Among Ulcerative Colitis Patients After Fecal Microbiota Transplantation

(2013) Sieglinde Angelberger et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

The dynamics of gut-associated microbial communities during inflammation

(2013) Sebastian E Winter et al.   EMBO REPORTS

An update on the use and investigation of probiotics in health and disease

(2013) Mary Ellen Sanders et al.   GUT

Bacteriophages in Gut Samples From Pediatric Crohn’s Disease Patients

(2013) Josef Wagner et al.   INFLAMMATORY BOWEL DISEASES

Safety, Tolerability, and Clinical Response After Fecal Transplantation in Children and Young Adults With Ulcerative Colitis

(2013) Sachin Kunde et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2013) P. M. Smith et al.   SCIENCE

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

(2013) Falk Hildebrand et al.   GENOME BIOLOGY

Microbiota of De-Novo Pediatric IBD: Increased Faecalibacterium Prausnitzii and Reduced Bacterial Diversity in Crohn's But Not in Ulcerative Colitis

(2012) Richard Hansen et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Dysbiosis modulates capacity for bile acid modification in the gut microbiomes of patients with inflammatory bowel disease: a mechanism and marker of disease?: Figure 1

(2012) Lesley A Ogilvie et al.   GUT

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

(2012) Henri Duboc et al.   GUT

Commensal Bacteria Calibrate the Activation Threshold of Innate Antiviral Immunity

(2012) Michael C. Abt et al.   IMMUNITY

Immunohistochemical search for viral and bacterial antigens in Crohn's disease

(2012) William S. Magin et al.   Journal of Crohns & Colitis

Microbiota Separation and C-reactive Protein Elevation in Treatment-naïve Pediatric Granulomatous Crohn Disease

(2012) Richard Kellermayer et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Colonic epithelial response to injury requires Myd88 signaling in myeloid cells

(2012) N P Malvin et al.   Mucosal Immunology

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

The gut microbiota in IBD

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

Effect of exclusive enteral nutrition on gut microflora function in children with Crohn's disease

(2012) Bo Tjellström et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

(2012) T. Olszak et al.   SCIENCE

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

Meta-analysis of broad-spectrum antibiotic therapy in patients with active inflammatory bowel disease

(2012) SHENG-LAN WANG et al.   Experimental and Therapeutic Medicine

MyD88 signalling in colonic mononuclear phagocytes drives colitis in IL-10-deficient mice

(2012) Namiko Hoshi et al.   Nature Communications

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Antibiotic Therapy in Inflammatory Bowel Disease: A Systematic Review and Meta-Analysis

(2011) Khurram J Khan et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease

(2011) Alan W Walker et al.   BMC MICROBIOLOGY

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection

(2011) Ethan Gough et al.   CLINICAL INFECTIOUS DISEASES

Pathobionts of the gastrointestinal microbiota and inflammatory disease

(2011) Janet Chow et al.   CURRENT OPINION IN IMMUNOLOGY

Antibiotic Combination Therapy for Steroid Withdrawal in Steroid-Dependent Ulcerative Colitis

(2011) Shuichi Terao et al.   DIGESTION

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

Increasing Incidence and Prevalence of the Inflammatory Bowel Diseases With Time, Based on Systematic Review

(2011) Natalie A. Molodecky et al.   GASTROENTEROLOGY

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

(2011) S. Minot et al.   GENOME RESEARCH

Farnesoid X receptor activation inhibits inflammation and preserves the intestinal barrier in inflammatory bowel disease

(2011) R. M. Gadaleta et al.   GUT

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

(2011) M. Joossens et al.   GUT

Fusobacterium nucleatum Infection of Colonic Cells Stimulates MUC2 Mucin and Tumor Necrosis Factor Alpha

(2011) Poonam Dharmani et al.   INFECTION AND IMMUNITY

Mycobacterium avium subspecies paratuberculosis in children with early-onset crohnʼs disease

(2011) Josef Wagner et al.   INFLAMMATORY BOWEL DISEASES

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease

(2011) Manuel A Rivas et al.   NATURE GENETICS

Association Between the Use of Antibiotics in the First Year of Life and Pediatric Inflammatory Bowel Disease

(2010) Souradet Y Shaw et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Newly Developed Antibiotic Combination Therapy for Ulcerative Colitis: A Double-Blind Placebo-Controlled Multicenter Trial

(2010) Toshifumi Ohkusa et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Virus-Plus-Susceptibility Gene Interaction Determines Crohn's Disease Gene Atg16L1 Phenotypes in Intestine

(2010) Ken Cadwell et al.   CELL

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

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

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

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

The NLRP3 Inflammasome Protects against Loss of Epithelial Integrity and Mortality during Experimental Colitis

(2010) Md. Hasan Zaki et al.   IMMUNITY

Control of Intestinal Homeostasis, Colitis, and Colitis-Associated Colorectal Cancer by the Inflammatory Caspases

(2010) Jeremy Dupaul-Chicoine et al.   IMMUNITY

An innately dangerous balancing act: intestinal homeostasis, inflammation, and colitis-associated cancer: Figure 1.

(2010) Mark Asquith et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The NLRP3 inflammasome functions as a negative regulator of tumorigenesis during colitis-associated cancer

(2010) Irving C. Allen et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Efficacy of antibiotic combination therapy in patients with active ulcerative colitis, including refractory or steroid-dependent cases

(2010) Toshiki Uehara et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Guidelines for the Management of Inflammatory Bowel Disease in Children in the United Kingdom

(2010) Bhupinder K Sandhu et al.   JOURNAL OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

Modulation of Shigella virulence in response to available oxygen in vivo

(2010) Benoit Marteyn et al.   NATURE

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

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

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Regulation of Colonic Epithelial Repair in Mice by Toll-Like Receptors and Hyaluronic Acid

(2009) Ling Zheng et al.   GASTROENTEROLOGY

Colitis-Associated Variant of TLR2 Causes Impaired Mucosal Repair Because of TFF3 Deficiency

(2009) Daniel K. Podolsky et al.   GASTROENTEROLOGY

Enteric defensins are essential regulators of intestinal microbial ecology

(2009) Nita H Salzman et al.   NATURE IMMUNOLOGY

Nod1 and Nod2 direct autophagy by recruiting ATG16L1 to the plasma membrane at the site of bacterial entry

(2009) Leonardo H Travassos et al.   NATURE IMMUNOLOGY

NOD2 stimulation induces autophagy in dendritic cells influencing bacterial handling and antigen presentation

(2009) Rachel Cooney et al.   NATURE MEDICINE

Intestinal Epithelial-Derived TAK1 Signaling Is Essential for Cytoprotection against Chemical-Induced Colitis

(2009) Jae-Young Kim et al.   PLoS One

Sustained modulation of intestinal bacteria by exclusive enteral nutrition used to treat children with Crohn’s disease

(2008) S. T. LEACH et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Smad7 Controls Resistance of Colitogenic T Cells to Regulatory T Cell-Mediated Suppression

(2008) Massimo C. Fantini et al.   GASTROENTEROLOGY

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells

(2008) Ken Cadwell et al.   NATURE

The aryl hydrocarbon receptor links TH17-cell-mediated autoimmunity to environmental toxins

(2008) Marc Veldhoen et al.   NATURE

Control of Treg and TH17 cell differentiation by the aryl hydrocarbon receptor

(2008) Francisco J. Quintana et al.   NATURE

A microbial symbiosis factor prevents intestinal inflammatory disease

(2008) Sarkis K. Mazmanian et al.   NATURE

Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility

(2008) Andre Franke et al.   NATURE GENETICS

Common variants in the NLRP3 region contribute to Crohn's disease susceptibility

(2008) Alexandra-Chloé Villani et al.   NATURE GENETICS

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

(2008) Jeffrey C Barrett et al.   NATURE GENETICS

Therapeutic correction of bacterial dysbiosis discovered by molecular techniques

(2008) R. B. Sartor   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Fungi and inflammatory bowel diseases: Alterations of composition and diversity

(2008) Stephan J. Ott et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

MyD88 signalling plays a critical role in host defence by controlling pathogen burden and promoting epithelial cell homeostasis during Citrobacter rodentium-induced colitis

(2007) D. L. Gibson et al.   CELLULAR MICROBIOLOGY

Active Crohnʼs disease and ulcerative colitis can be specifically diagnosed and monitored based on the biostructure of the fecal flora

(2007) Alexander Swidsinski et al.   INFLAMMATORY BOWEL DISEASES