Microbiota and mucosal defense in IBD: an update

Microbial network disturbances in relapsing refractory Crohn’s disease

(2019) Bahtiyar Yilmaz et al.   NATURE MEDICINE

Gut pathobionts underlie intestinal barrier dysfunction and liver T helper 17 cell immune response in primary sclerosing cholangitis

(2019) Nobuhiro Nakamoto et al.   Nature Microbiology

Paneth cell α-defensins HD-5 and HD-6 display differential degradation into active antimicrobial fragments

(2019) D. Ehmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Influence of Crohn’s disease related polymorphisms in innate immune function on ileal microbiome

(2019) Ellen Li et al.   PLoS One

The gut mycobiota: insights into analysis, environmental interactions and role in gastrointestinal diseases

(2019) Mathias L. Richard et al.   Nature Reviews Gastroenterology & Hepatology

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Structural weakening of the colonic mucus barrier is an early event in ulcerative colitis pathogenesis

(2019) Sjoerd van der Post et al.   GUT

Individualized Dynamics in the Gut Microbiota Precede Crohnʼs Disease Flares

(2019) Tzipi Braun et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Environmental Risk Factors for Inflammatory Bowel Diseases: an Umbrella Review of Meta-analyses

(2019) Daniele Piovani et al.   GASTROENTEROLOGY

The potential probiotic Lactobacillus rhamnosus CNCM I-3690 strain protects the intestinal barrier by stimulating both mucus production and cytoprotective response

(2019) Rebeca Martín et al.   Scientific Reports

Contribution of Non-immune Cells to Activation and Modulation of the Intestinal Inflammation

(2019) Renata Curciarello et al.   Frontiers in Immunology

Inflammation-related differences in mucosa-associated microbiota and intestinal barrier function in colonic Crohn's disease

(2018) Josie Libertucci et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Severe Defects in the Macrophage Barrier to Gut Microflora in Inflammatory Bowel Disease and Colon Cancer

(2018) CARLOS A. RUBIO et al.   ANTICANCER RESEARCH

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

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

Bacterial Periplasmic Oxidoreductases Control the Activity of Oxidized Human Antimicrobial β-Defensin 1

(2018) J. Wendler et al.   INFECTION AND IMMUNITY

IBD risk loci are enriched in multigenic regulatory modules encompassing putative causative genes

(2018) Yukihide Momozawa et al.   Nature Communications

Mucin gel assembly is controlled by a collective action of non-mucin proteins, disulfide bridges, Ca2+-mediated links, and hydrogen bonding

(2018) Oliver W. Meldrum et al.   Scientific Reports

Calcium-activated Chloride Channel Regulator 1 (CLCA1) Controls Mucus Expansion in Colon by Proteolytic Activity

(2018) Elisabeth E.L. Nyström et al.   EBioMedicine

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

(2018) Melanie Schirmer et al.   Cell Host & Microbe

Interaction between smoking and ATG16L1T300A triggers Paneth cell defects in Crohn’s disease

(2018) Ta-Chiang Liu et al.   JOURNAL OF CLINICAL INVESTIGATION

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis

(2018) Yael Haberman et al.   Mucosal Immunology

Intestinal barrier dysfunction orchestrates the onset of inflammatory host–microbiome cross-talk in a human gut inflammation-on-a-chip

(2018) Woojung Shin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response

(2018) Yael Haberman et al.   Nature Communications

A comparative study of the gut microbiota in immune-mediated inflammatory diseases—does a common dysbiosis exist?

(2018) Jessica D. Forbes et al.   Microbiome

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

(2017) R. Balfour Sartor et al.   GASTROENTEROLOGY

Paneth Cell Alterations in the Development and Phenotype of Crohn’s Disease

(2017) Thaddeus S. Stappenbeck et al.   GASTROENTEROLOGY

Efficacy of Sterile Fecal Filtrate Transfer for Treating Patients With Clostridium difficile Infection

(2017) Stephan J. Ott et al.   GASTROENTEROLOGY

The Mucosal Antibacterial Response Profile and Fecal Microbiota Composition Are Linked to the Disease Course in Patients with Newly Diagnosed Ulcerative Colitis

(2017) Maria K. Magnusson et al.   INFLAMMATORY BOWEL DISEASES

Defective ATG16L1-mediated removal of IRE1α drives Crohn’s disease–like ileitis

(2017) Markus Tschurtschenthaler et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

(2017) Sudarshan Paramsothy et al.   LANCET

Quantitative microbiome profiling links gut community variation to microbial load

(2017) Doris Vandeputte et al.   NATURE

Host Genetics and Gut Microbiome: Challenges and Perspectives

(2017) Alexander Kurilshikov et al.   TRENDS IN IMMUNOLOGY

Diet and microbiota in inflammatory bowel disease: The gut in disharmony

(2017) Davy C M Rapozo et al.   WORLD JOURNAL OF GASTROENTEROLOGY

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Ubiquitously expressed Human Beta Defensin 1 (hBD1) forms bacteria-entrapping nets in a redox dependent mode of action

(2017) Judith Raschig et al.   PLoS Pathogens

In the Wnt of Paneth Cells: Immune-Epithelial Crosstalk in Small Intestinal Crohn’s Disease

(2017) Nicole S. Armbruster et al.   Frontiers in Immunology

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Butyrate-producing bacteria supplemented in vitro to Crohn’s disease patient microbiota increased butyrate production and enhanced intestinal epithelial barrier integrity

(2017) Annelies Geirnaert et al.   Scientific Reports

Lactobacillus reuteriincreases mucus thickness and ameliorates dextran sulphate sodium-induced colitis in mice

(2016) D. Ahl et al.   Acta Physiologica

Probiotics, fibre and herbal medicinal products for functional and inflammatory bowel disorders

(2016) Diego Currò et al.   BRITISH JOURNAL OF PHARMACOLOGY

Are We Really Vastly Outnumbered? Revisiting the Ratio of Bacterial to Host Cells in Humans

(2016) Ron Sender et al.   CELL

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Prebiotics: why definitions matter

(2016) Robert W Hutkins et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

(2016) Floris Imhann et al.   GUT

Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease

(2016) Robert Häsler et al.   GUT

Dysbiosis in intestinal inflammation: Cause or consequence

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

Nod2Deficiency Leads to a Specific and Transmissible Mucosa-associated Microbial Dysbiosis Which Is Independent of the Mucosal Barrier Defect

(2016) Ziad Al Nabhani et al.   Journal of Crohns & Colitis

Microbial Factors Associated with Postoperative Crohn’s Disease Recurrence

(2016) Emily K. Wright et al.   Journal of Crohns & Colitis

Inherited determinants of Crohn's disease and ulcerative colitis phenotypes: a genetic association study

(2016) Isabelle Cleynen et al.   LANCET

Lypd8 promotes the segregation of flagellated microbiota and colonic epithelia

(2016) Ryu Okumura et al.   NATURE

The effect of host genetics on the gut microbiome

(2016) Marc Jan Bonder et al.   NATURE GENETICS

Gram-positive bacteria are held at a distance in the colon mucus by the lectin-like protein ZG16

(2016) Joakim H. Bergström et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion

(2016) G. M. H. Birchenough et al.   SCIENCE

Nod2: A Critical Regulator of Ileal Microbiota and Crohn’s Disease

(2016) Tabasum Sidiq et al.   Frontiers in Immunology

Epithelial IL-18 Equilibrium Controls Barrier Function in Colitis

(2015) Roni Nowarski et al.   CELL

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

(2015) Jason M. Norman et al.   CELL

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization

(2015) Malin E.V. Johansson et al.   Cell Host & Microbe

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

Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates

(2015) Doris Vandeputte et al.   GUT

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

Donor Species Richness Determines Faecal Microbiota Transplantation Success in Inflammatory Bowel Disease

(2015) Severine Vermeire et al.   Journal of Crohns & Colitis

Colonic MUC2 mucin regulates the expression and antimicrobial activity of β-defensin 2

(2015) E R Cobo et al.   Mucosal Immunology

Crohn's disease-derived monocytes fail to induce Paneth cell defensins

(2015) Lioba F. Courth et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and function of the healthy pre-adolescent pediatric gut microbiome

(2015) Emily B. Hollister et al.   Microbiome

NLRP6 Inflammasome Orchestrates the Colonic Host-Microbial Interface by Regulating Goblet Cell Mucus Secretion

(2014) Marta Wlodarska et al.   CELL

Rethinking “Enterotypes”

(2014) Dan Knights et al.   Cell Host & Microbe

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

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

The composition of the gut microbiota shapes the colon mucus barrier

(2014) H. E. Jakobsson et al.   EMBO REPORTS

Inflammatory Bowel Disease as a Model for Translating the Microbiome

(2014) Curtis Huttenhower et al.   IMMUNITY

Alterations in the Intestinal Microbiome (Dysbiosis) as a Predictor of Relapse After Infliximab Withdrawal in Crohnʼs Disease

(2014) Sylvie Rajca et al.   INFLAMMATORY BOWEL DISEASES

The microbial basis of inflammatory bowel diseases

(2014) Sushila R. Dalal et al.   JOURNAL OF CLINICAL INVESTIGATION

Paneth cell α-defensin 6 (HD-6) is an antimicrobial peptide

(2014) B O Schroeder et al.   Mucosal Immunology

Microbial sensing by goblet cells controls immune surveillance of luminal antigens in the colon

(2014) K A Knoop et al.   Mucosal Immunology

Fecal Microbial Composition of Ulcerative Colitis and Crohn’s Disease Patients in Remission and Subsequent Exacerbation

(2014) Edgar S. Wills et al.   PLoS One

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbial-induced meprin   cleavage in MUC2 mucin and a functional CFTR channel are required to release anchored small intestinal mucus

(2014) A. Schutte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Reprogrammed and transmissible intestinal microbiota confer diminished susceptibility to induced colitis in TMF−/−mice

(2014) Shai Bel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intestinal barrier in inflammatory bowel disease

(2014) Lena Antoni   WORLD JOURNAL OF GASTROENTEROLOGY

Complex host genetics influence the microbiome in inflammatory bowel disease

(2014) Dan Knights et al.   Genome Medicine

Studies of mucus in mouse stomach, small intestine, and colon. I. Gastrointestinal mucus layers have different properties depending on location as well as over the Peyer's patches

(2013) Anna Ermund et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Antimicrobial Activity of High-Mobility-Group Box 2: a New Function to a Well-Known Protein

(2013) Robert Küchler et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent

(2013) Laura Wrzosek et al.   BMC BIOLOGY

Antimicrobial peptides and gut microbiota in homeostasis and pathology

(2013) Maureen J. Ostaff et al.   EMBO Molecular Medicine

Genetic Variants Synthesize to Produce Paneth Cell Phenotypes That Define Subtypes of Crohn's Disease

(2013) Kelli L. VanDussen et al.   GASTROENTEROLOGY

Bacteria penetrate the normally impenetrable inner colon mucus layer in both murine colitis models and patients with ulcerative colitis

(2013) Malin E V Johansson et al.   GUT

Impact of Ethnicity, Geography, and Disease on the Microbiota in Health and Inflammatory Bowel Disease

(2013) Lani Prideaux et al.   INFLAMMATORY BOWEL DISEASES

NOD2-mediated dysbiosis predisposes mice to transmissible colitis and colorectal cancer

(2013) Aurélie Couturier-Maillard et al.   JOURNAL OF CLINICAL INVESTIGATION

Human colonic mucus is a reservoir for antimicrobial peptides

(2013) Lena Antoni et al.   Journal of Crohns & Colitis

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Bacteria Regulate Intestinal Epithelial Cell Differentiation Factors Both In Vitro and In Vivo

(2013) Svetlana Becker et al.   PLoS One

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

Regulation of antimicrobial peptide gene expression by nutrients and by-products of microbial metabolism

(2012) Yan Campbell et al.   EUROPEAN JOURNAL OF NUTRITION

Abnormal Activation of Autophagy-Induced Crinophagy in Paneth Cells From Patients With Crohn's Disease

(2012) Élodie Thachil et al.   GASTROENTEROLOGY

More than a marine propeller – the flagellum of the probiotic Escherichia coli strain Nissle 1917 is the major adhesin mediating binding to human mucus

(2012) Anja Troge et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Loss of TMF/ARA160 Protein Renders Colonic Mucus Refractory to Bacterial Colonization and Diminishes Intestinal Susceptibility to Acute Colitis

(2012) Shai Bel et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Host Genes Related to Paneth Cells and Xenobiotic Metabolism Are Associated with Shifts in Human Ileum-Associated Microbial Composition

(2012) Tianyi Zhang et al.   PLoS One

Lactobacillus reuteri Maintains a Functional Mucosal Barrier during DSS Treatment Despite Mucus Layer Dysfunction

(2012) Johan Dicksved et al.   PLoS One

Inflammation Drives Dysbiosis and Bacterial Invasion in Murine Models of Ileal Crohn’s Disease

(2012) Melanie Craven et al.   PLoS One

Calcium and pH-dependent packing and release of the gel-forming MUC2 mucin

(2012) D. Ambort et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human  -Defensin 6 Promotes Mucosal Innate Immunity Through Self-Assembled Peptide Nanonets

(2012) H. Chu et al.   SCIENCE

An ex vivo method for studying mucus formation, properties, and thickness in human colonic biopsies and mouse small and large intestinal explants

(2011) Jenny K. Gustafsson et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

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

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

(2011) M. Joossens et al.   GUT

Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn's disease

(2011) J. L. Benjamin et al.   GUT

Reduction of disulphide bonds unmasks potent antimicrobial activity of human β-defensin 1

(2011) Bjoern O. Schroeder et al.   NATURE

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Mucin dynamics and enteric pathogens

(2011) Michael A. McGuckin et al.   NATURE REVIEWS MICROBIOLOGY

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Tolerance exists towards resident intestinal flora but is broken in active inflammatory bowel disease (IBD)

(2010) R. DUCHMANN et al.   CLINICAL AND EXPERIMENTAL IMMUNOLOGY

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

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Paneth's disease

(2010) Jan Wehkamp et al.   Journal of Crohns & Colitis

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

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

Peroxisome proliferator-activated receptor gamma activation is required for maintenance of innate antimicrobial immunity in the colon

(2010) L. Peyrin-Biroulet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Defective Paneth Cell—Mediated Host Defense in Pediatric Ileal Crohn's Disease

(2009) Gøri Perminow et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Crohn's disease-associated adherent-invasiveE. coliare selectively favoured by impaired autophagy to replicate intracellularly

(2009) Pierre Lapaquette et al.   CELLULAR MICROBIOLOGY

TMF/ARA160 downregulates proangiogenic genes and attenuates the progression of PC3 xenografts

(2009) Galya Abrham et al.   INTERNATIONAL JOURNAL OF CANCER

Proteomic Analyses of the Two Mucus Layers of the Colon Barrier Reveal That Their Main Component, the Muc2 Mucin, Is Strongly Bound to the Fcgbp Protein

(2009) Malin E. V. Johansson et al.   JOURNAL OF PROTEOME RESEARCH

Enteric defensins are essential regulators of intestinal microbial ecology

(2009) Nita H Salzman et al.   NATURE IMMUNOLOGY

A randomized controlled trial on the efficacy of synbiotic versus probiotic or prebiotic treatment to improve the quality of life in patients with ulcerative colitis

(2009) Shunji Fujimori et al.   NUTRITION

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

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

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

Microbial Influences in Inflammatory Bowel Diseases

(2008) R. Balfour Sartor   GASTROENTEROLOGY

Reduced  -defensin expression is associated with inflammation and not NOD2 mutation status in ileal Crohn's disease

(2008) L A Simms et al.   GUT

Secreted enteric antimicrobial activity localises to the mucus surface layer

(2008) U Meyer-Hoffert et al.   GUT

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

(2008) Johan Dicksved et al.   ISME Journal

Is there a link between food and intestinal microbes and the occurrence of Crohn's disease and ulcerative colitis?

(2008) Hitoshi Asakura et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

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

The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria

(2008) M. E. V. Johansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Early-life exposures associated with antibiotic use and risk of subsequent Crohn's disease

(2008) Hans Hildebrand et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY