Inflammatory Bowel Diseases (IBD) and the Microbiome—Searching the Crime Scene for Clues

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

(2020) Jens Walter et al.   CELL

Dysbiosis-Induced Secondary Bile Acid Deficiency Promotes Intestinal Inflammation

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

Imprinting of the immune system by the microbiota early in life

(2020) Ziad Al Nabhani et al.   Mucosal Immunology

Label or Concept – What Is a Pathobiont?

(2020) Lara Jochum et al.   TRENDS IN MICROBIOLOGY

AGA Technical Review on the Role of Probiotics in the Management of Gastrointestinal Disorders

(2020) Geoffrey A. Preidis et al.   GASTROENTEROLOGY

Bile acids drive the newborn’s gut microbiota maturation

(2020) N. van Best et al.   Nature Communications

IBD and Bile Acid Absorption: Focus on Pre-clinical and Clinical Observations

(2020) Leo R. Fitzpatrick et al.   Frontiers in Physiology

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

Malassezia Is Associated with Crohn’s Disease and Exacerbates Colitis in Mouse Models

(2019) Jose J. Limon et al.   Cell Host & Microbe

Implications of the Westernized Diet in the Onset and Progression of IBD

(2019) Fernando Rizzello et al.   Nutrients

Intestinal Microbiota in Early Life and Its Implications on Childhood Health

(2019) Lu Zhuang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Bacteroides fragilis polysaccharide A induces IL-10 secreting B and T cells that prevent viral encephalitis

(2019) Chandran Ramakrishna et al.   Nature Communications

Inflammatory Bowel Disease Presentation and Diagnosis

(2019) Sean Flynn et al.   SURGICAL CLINICS OF NORTH AMERICA

Alteration of Gut Microbiota in Inflammatory Bowel Disease (IBD): Cause or Consequence? IBD Treatment Targeting the Gut Microbiome

(2019) Israr Khan et al.   Pathogens

Immunomodulating Activity and Therapeutic Effects of Short Chain Fatty Acids and Tryptophan Post-biotics in Inflammatory Bowel Disease

(2019) Edda Russo et al.   Frontiers in Immunology

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration

(2018) Bjoern O. Schroeder et al.   Cell Host & Microbe

Faecalibacterium prausnitzii Produces Butyrate to Maintain Th17/Treg Balance and to Ameliorate Colorectal Colitis by Inhibiting Histone Deacetylase 1

(2018) Lixing Zhou et al.   INFLAMMATORY BOWEL DISEASES

Comparison of the microbial community structure between inflamed and non-inflamed sites in patients with ulcerative colitis

(2018) Atsushi Hirano et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Role of priority effects in the early-life assembly of the gut microbiota

(2018) Daniel Sprockett et al.   Nature Reviews Gastroenterology & Hepatology

Murine colitis reveals a disease-associated bacteriophage community

(2018) Breck A. Duerkop et al.   Nature Microbiology

Bacteroides thetaiotaomicron Ameliorates Colon Inflammation in Preclinical Models of Crohn’s Disease

(2018) Margaret Delday et al.   INFLAMMATORY BOWEL DISEASES

Specific Bacteria and Metabolites Associated with Response to Fecal Microbiota Transplantation in Patients with Ulcerative Colitis

(2018) Sudarshan Paramsothy et al.   GASTROENTEROLOGY

Escherichia coli “Marionette” strains with 12 highly optimized small-molecule sensors

(2018) Adam J. Meyer et al.   Nature Chemical Biology

The Human Microbiome and Child Growth – First 1000 Days and Beyond

(2018) Ruairi C. Robertson et al.   TRENDS IN MICROBIOLOGY

Understanding and Preventing the Global Increase of Inflammatory Bowel Disease

(2017) Gilaad G. Kaplan et al.   GASTROENTEROLOGY

Compositional Changes in the Gut Mucus Microbiota Precede the Onset of Colitis-Induced Inflammation

(2017) Maria Glymenaki et al.   INFLAMMATORY BOWEL DISEASES

Trace derivatives of kynurenine potently activate the aryl hydrocarbon receptor (AHR)

(2017) Seung-Hyeon Seok et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Faecal Microbiota Transplantation for Inflammatory Bowel Disease: A Systematic Review and Meta-analysis

(2017) Sudarshan Paramsothy et al.   Journal of Crohns & Colitis

Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease

(2017) Kyohei Nishino et al.   JOURNAL OF GASTROENTEROLOGY

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

(2017) Sudarshan Paramsothy et al.   LANCET

The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota

(2017) Christian Milani et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Gut microbiota and IBD: causation or correlation?

(2017) Josephine Ni et al.   Nature Reviews Gastroenterology & Hepatology

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B 12 Production by Intestinal Symbionts

(2017) Clara Belzer et al.   mBio

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring

(2017) Jun Miyoshi et al.   Cell Reports

Safe-by-Design: from Safety to Responsibility

(2017) Ibo van de Poel et al.   NanoEthics

Patterns of Early-Life Gut Microbial Colonization during Human Immune Development: An Ecological Perspective

(2017) Isabelle Laforest-Lapointe et al.   Frontiers in Immunology

Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics

(2017) Sonny T. M. Lee et al.   Microbiome

The human gastrointestinal tract and oral microbiota in inflammatory bowel disease: a state of the science review

(2016) Rosario Lucas López et al.   APMIS

Butyrate inhibits interleukin-17 and generates Tregs to ameliorate colorectal colitis in rats

(2016) Mingming Zhang et al.   BMC GASTROENTEROLOGY

Intestinal Crosstalk between Bile Acids and Microbiota and Its Impact on Host Metabolism

(2016) Annika Wahlström et al.   Cell Metabolism

Physiological Role of Gut Microbiota for Maintaining Human Health

(2016) Akira Andoh   DIGESTION

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease

(2016) Floris Imhann et al.   GUT

Molecular classification of Crohn's disease reveals two clinically relevant subtypes

(2016) Matthew Weiser et al.   GUT

Fungal microbiota dysbiosis in IBD

(2016) Harry Sokol et al.   GUT

Diet, gut microbes, and the pathogenesis of inflammatory bowel diseases

(2016) Kyle T. Dolan et al.   MOLECULAR NUTRITION & FOOD RESEARCH

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

(2016) Bruno Lamas et al.   NATURE MEDICINE

Healthy human gut phageome

(2016) Pilar Manrique et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotics, birth mode, and diet shape microbiome maturation during early life

(2016) Nicholas A. Bokulich et al.   Science Translational Medicine

Bile Acid Modifications at the Microbe-Host Interface: Potential for Nutraceutical and Pharmaceutical Interventions in Host Health

(2016) Susan A. Joyce et al.   Annual Review of Food Science and Technology

Patient-Specific Bacteroides Genome Variants in Pouchitis

(2016) Joseph H. Vineis et al.   mBio

Revised Estimates for the Number of Human and Bacteria Cells in the Body

(2016) Ron Sender et al.   PLOS BIOLOGY

Impact of maternal intrapartum antibiotics, method of birth and breastfeeding on gut microbiota during the first year of life: a prospective cohort study

(2015) MB Azad et al.   BJOG-AN INTERNATIONAL JOURNAL OF OBSTETRICS AND GYNAECOLOGY

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

(2015) Jason M. Norman et al.   CELL

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

Interactions between Gut Microbiota, Host Genetics and Diet Modulate the Predisposition to Obesity and Metabolic Syndrome

(2015) Siegfried Ussar et al.   Cell Metabolism

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

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

Gut Fungal Microbiota

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

Inherited CARD9 deficiency in otherwise healthy children and adults with Candida species–induced meningoencephalitis, colitis, or both

(2015) Fanny Lanternier et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Mucosal Barrier Depletion and Loss of Bacterial Diversity are Primary Abnormalities in Paediatric Ulcerative Colitis

(2015) Misagh Alipour et al.   Journal of Crohns & Colitis

The microbiota in inflammatory bowel disease

(2015) Donal Sheehan et al.   JOURNAL OF GASTROENTEROLOGY

Ecology of bacteria in the human gastrointestinal tract—identification of keystone and foundation taxa

(2015) Pål Trosvik et al.   Microbiome

Tu1988 Impact of the Commensal Bacterium Faecalibacterium prausnitzii in a Non Active Inflammation Murine Model

(2015) Rebeca Martin et al.   GASTROENTEROLOGY

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

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

CARD9 mediates Dectin-1–induced ERK activation by linking Ras-GRF1 to H-Ras for antifungal immunity

(2014) Xin-Ming Jia et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Microfluidic organs-on-chips

(2014) Sangeeta N Bhatia et al.   NATURE BIOTECHNOLOGY

The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic

(2014) Colin Hill et al.   Nature Reviews Gastroenterology & Hepatology

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Cesarean delivery and risk of inflammatory bowel disease: a systematic review and meta-analysis

(2014) Yi Li et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Complex host genetics influence the microbiome in inflammatory bowel disease

(2014) Dan Knights et al.   Genome Medicine

Colonisation byFaecalibacterium prausnitziiand maintenance of clinical remission in patients with ulcerative colitis

(2013) E. Varela et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Gut microbiota of healthy Canadian infants: profiles by mode of delivery and infant diet at 4 months

(2013) M. B. Azad et al.   CANADIAN MEDICAL ASSOCIATION JOURNAL

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

Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis

(2013) Lionel Rigottier-Gois   ISME Journal

Development of a Stress-Inducible Controlled Expression (SICE) system in Lactococcus lactis for the production and delivery of therapeutic molecules at mucosal surfaces

(2013) Bouasria Benbouziane et al.   JOURNAL OF BIOTECHNOLOGY

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

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

(2013) Koji Atarashi et al.   NATURE

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

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

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) P. M. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Host-Derived Nitrate Boosts Growth of E. coli in the Inflamed Gut

(2013) S. E. Winter et al.   SCIENCE

Transient inflammatory-like state and microbial dysbiosis are pivotal in establishment of mucosal homeostasis during colonisation of germ-free mice

(2013) S. El Aidy et al.   Beneficial Microbes

Oxidative stress and redox signaling mechanisms of inflammatory bowel disease: updated experimental and clinical evidence

(2012) Hong Zhu et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10 −/− mice

(2012) Suzanne Devkota et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

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

(2012) Luke Jostins et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

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

Postbiotics: what else?

(2012) K. Tsilingiri et al.   Beneficial Microbes

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment

(2011) Joan Vermeiren et al.   FEMS MICROBIOLOGY ECOLOGY

Aryl Hydrocarbon Receptor-Induced Signals Up-regulate IL-22 Production and Inhibit Inflammation in the Gastrointestinal Tract

(2011) Ivan Monteleone et al.   GASTROENTEROLOGY

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

(2011) Benoit Chassaing et al.   GASTROENTEROLOGY

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

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

(2011) Stanislas Mondot et al.   GUT

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

(2011) R. M. Gadaleta et al.   GUT

Innate immune signaling in defense against intestinal microbes

(2011) Melissa A. Kinnebrew et al.   IMMUNOLOGICAL REVIEWS

Cesarean section and offspringʼs risk of inflammatory bowel disease: A national cohort study

(2011) Peter Bager et al.   INFLAMMATORY BOWEL DISEASES

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

(2011) Carl A Anderson et al.   NATURE GENETICS

Clinical trial: the microbiological and immunological effects of synbiotic consumption - a randomized double-blind placebo-controlled study in active Crohn’s disease

(2010) H. Steed et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

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

Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal Flora

(2010) Martin J. Grehan et al.   JOURNAL OF CLINICAL GASTROENTEROLOGY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease

(2010) Yukihide Momozawa et al.   NATURE GENETICS

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

(2010) Andre Franke et al.   NATURE GENETICS

The two mucus layers of colon are organized by the MUC2 mucin, whereas the outer layer is a legislator of host-microbial interactions

(2010) M. E. V. Johansson 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

Inflammatory Bowel Disease and Mutations Affecting the Interleukin-10 Receptor

(2009) Erik-Oliver Glocker et al.   NEW ENGLAND JOURNAL OF MEDICINE

Nod2 is required for the regulation of commensal microbiota in the intestine

(2009) T. Petnicki-Ocwieja et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis

(2008) Pauline D Scanlan et al.   BMC MICROBIOLOGY

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

Dysbiosis in inflammatory bowel disease: a role for bacteriophages?

(2008) P Lepage et al.   GUT

Thickness and continuity of the adherent colonic mucus barrier in active and quiescent ulcerative colitis and Crohn’s disease

(2008) V. Strugala et al.   INTERNATIONAL JOURNAL OF CLINICAL PRACTICE

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

(2008) Ken Cadwell et al.   NATURE

Regulation of surface architecture by symbiotic bacteria mediates host colonization

(2008) C. H. Liu et al.   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

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE

Characterization of epithelial IL-8 response to inflammatory bowel disease mucosal E. coli and its inhibition by mesalamine

(2007) Sreedhar Subramanian et al.   INFLAMMATORY BOWEL DISEASES