The gut microbiota in IBD

IBD—ulcerative colitis and Crohn's disease—is emerging as a worldwide epidemic. An association between the increased incidence of IBD and environmental factors linked to socioeconomic development has been persistently detected in different parts of the world. The lifestyle in developed countries might impair the natural patterns of microbial colonization of the human gut. The interaction of microbes with mucosal immune compartments in the gut seems to have a major role in priming and regulating immunity. In IBD, mucosal lesions are generated by an excessive or dysregulated immune response against commensal microbes in the gut. In individuals with a genetic susceptibility to IBD, abnormal microbial colonization of the gastrointestinal tract might be the origin of such dysregulation. Developments in gene-sequencing technologies, as well as increased availability of powerful bioinformatic tools, have enabled novel insights into the microbial composition of the human gut microbiota and the effect of microbial communities on human physiology and disease. Studies that used these technologies indicate that dysbiosis (that is, abnormal microbiota composition) and decreased complexity of the gut microbial ecosystem are common features in patients with Crohn's disease or ulcerative colitis. Whether such changes are a cause or a consequence of the disease remains to be elucidated.

[1]  S. Pender.  Do metalloproteinases contribute to tissue destruction or remodeling in the inflamed gut? , 2008, Inflammatory bowel diseases.

[2]  R. Knight,et al.  Bacterial Community Variation in Human Body Habitats Across Space and Time , 2009, Science.

[3]  James R. Cole,et al.  The Ribosomal Database Project: improved alignments and new tools for rRNA analysis , 2008, Nucleic Acids Res..

[4]  S. Mazmanian,et al.  The gut microbiota shapes intestinal immune responses during health and disease , 2009, Nature Reviews Immunology.

[5]  N. Borruel,et al.  Unstable Composition of the Fecal Microbiota in Ulcerative Colitis During Clinical Remission , 2008, The American Journal of Gastroenterology.

[6]  N. Pace,et al.  Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases , 2007, Proceedings of the National Academy of Sciences.

[7]  N. Borruel,et al.  Increased mucosal tumour necrosis factor α production in Crohn’s disease can be downregulated ex vivo by probiotic bacteria , 2002, Gut.

[8]  C. Filippo.  Impact of diet in shaping gut microbiota , 2012 .

[9]  N. Borruel,et al.  Effects of Nonpathogenic Bacteria on Cytokine Secretion by Human Intestinal Mucosa , 2003, American Journal of Gastroenterology.

[10]  E. K. Kemsley,et al.  Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota , 2010, BMC gastroenterology.

[11]  C. Manichanh,et al.  Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach , 2005, Gut.

[12]  Subrata Ghosh,et al.  Increasing incidence and prevalence of the inflammatory bowel diseases with time, based on systematic review. , 2012, Gastroenterology.

[13]  Tarah Lynch,et al.  Invasive potential of gut mucosa‐derived fusobacterium nucleatum positively correlates with IBD status of the host , 2011, Inflammatory bowel diseases.

[14]  T. Ohkusa,et al.  Induction of experimental ulcerative colitis by Fusobacterium varium isolated from colonic mucosa of patients with ulcerative colitis , 2003, Gut.

[15]  J. Doré,et al.  Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray , 2010, Inflammatory bowel diseases.

[16]  Eoin L. Brodie,et al.  Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB , 2006, Applied and Environmental Microbiology.

[17]  P. Brandtzaeg.  Mucosal Immunity: Induction, Dissemination, and Effector Functions , 2009, Scandinavian journal of immunology.

[18]  V. Mai,et al.  Monitoring of Stool Microbiota in Subjects with Diarrhea Indicates Distortions in Composition , 2006, Journal of Clinical Microbiology.

[19]  N. Nielsen,et al.  Cesarean section and offspring's risk of inflammatory bowel disease: A national cohort study , 2012, Inflammatory bowel diseases.

[20]  R Balfour Sartor,et al.  Microbial influences in inflammatory bowel diseases. , 2008, Gastroenterology.

[21]  C. Bernstein,et al.  Disorders of a modern lifestyle: reconciling the epidemiology of inflammatory bowel diseases , 2008, Gut.

[22]  S. Mazmanian,et al.  A microbial symbiosis factor prevents intestinal inflammatory disease , 2008, Nature.

[23]  N. Borruel,et al.  Lactobacillus casei downregulates commensals' inflammatory signals in Crohn's disease mucosa , 2009, Inflammatory bowel diseases.

[24]  B. Chassaing,et al.  The commensal microbiota and enteropathogens in the pathogenesis of inflammatory bowel diseases. , 2011, Gastroenterology.

[25]  L. Proctor,et al.  The Human Microbiome Project in 2011 and beyond. , 2011, Cell host & microbe.

[26]  Miguel Pignatelli,et al.  Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota , 2011, PloS one.

[27]  Henrik Svanström,et al.  Antibiotic use and inflammatory bowel diseases in childhood , 2010, Gut.

[28]  J. Cummings,et al.  The contribution of sulphate reducing bacteria and 5-aminosalicylic acid to faecal sulphide in patients with ulcerative colitis , 2000, Gut.

[29]  N. Borruel,et al.  Modulation of apoptosis in intestinal lymphocytes by a probiotic bacteria in Crohn's disease , 2006, Journal of leukocyte biology.

[30]  P. Mannon,et al.  The fundamental basis of inflammatory bowel disease. , 2007, The Journal of clinical investigation.

[31]  G. Oppenheimer,et al.  REGIONAL ILEITIS: A PATHOLOGIC AND CLINICAL ENTITY , 1932 .

[32]  J. Coffey,et al.  Desulfovibrio Bacterial Species Are Increased in Ulcerative Colitis , 2010, Diseases of the colon and rectum.

[33]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[34]  I. Forgacs,et al.  Mucosal antibodies in inflammatory bowel disease are directed against intestinal bacteria. , 1996, Gut.

[35]  J. Doré,et al.  Low counts of Faecalibacterium prausnitzii in colitis microbiota , 2009, Inflammatory bowel diseases.

[36]  J. Hampe,et al.  Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease , 2004, Gut.

[37]  Ateequr Rehman,et al.  Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. , 2011, Gastroenterology.

[38]  P. Brigidi,et al.  Modulation of human dendritic cell phenotype and function by probiotic bacteria , 2004, Gut.

[39]  E. Purdom,et al.  Diversity of the Human Intestinal Microbial Flora , 2005, Science.

[40]  T. Ohkusa,et al.  Fusobacterium varium localized in the colonic mucosa of patients with ulcerative colitis stimulates species‐specific antibody , 2002, Journal of gastroenterology and hepatology.

[41]  C R Woese,et al.  Classification of methanogenic bacteria by 16S ribosomal RNA characterization. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[42]  J. Jansson,et al.  Molecular analysis of the gut microbiota of identical twins with Crohn's disease , 2008, The ISME Journal.

[43]  C. Manichanh,et al.  Colonisation by Faecalibacterium prausnitzii and maintenance of clinical remission in patients with ulcerative colitis , 2013, Alimentary pharmacology & therapeutics.

[44]  F. Guarner,et al.  Mechanisms of Disease: the hygiene hypothesis revisited , 2006, Nature Clinical Practice Gastroenterology &Hepatology.

[45]  J. Blanco,et al.  Molecular diversity of Escherichia coli in the human gut: New ecological evidence supporting the role of adherent‐invasive E. coli (AIEC) in Crohn's disease , 2009, Inflammatory bowel diseases.

[46]  Matthew W. Johnson,et al.  The Bacteriology of Pouchitis: A Molecular Phylogenetic Analysis Using 16S rRNA Gene Cloning and Sequencing , 2010, Annals of surgery.

[47]  N. Pace,et al.  Gastrointestinal microbiology enters the metagenomics era , 2008, Current opinion in gastroenterology.

[48]  P. Bork,et al.  A human gut microbial gene catalogue established by metagenomic sequencing , 2010, Nature.

[49]  H. Schiöth,et al.  Adhesion GPCRs are widely expressed throughout the subsections of the gastrointestinal tract , 2012, BMC Gastroenterology.

[50]  G. Rook.  Review series on helminths, immune modulation and the hygiene hypothesis: The broader implications of the hygiene hypothesis , 2009, Immunology.

[51]  Laurent Beaugerie,et al.  High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn's disease. , 2004, Gastroenterology.

[52]  Anders F. Andersson,et al.  A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes. , 2010, Gastroenterology.

[53]  W. Babidge,et al.  Colonic Sulfide in Pathogenesis and Treatment of Ulcerative Colitis , 1997, Digestive Diseases and Sciences.

[54]  S. Pettersson,et al.  Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-γ and RelA , 2004, Nature Immunology.

[55]  F. Bushman,et al.  Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes , 2011, Science.

[56]  W. Selby,et al.  Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn's disease. , 2007, Gastroenterology.

[57]  P. Rutgeerts,et al.  Early lesions of recurrent Crohn's disease caused by infusion of intestinal contents in excluded ileum. , 1998, Gastroenterology.

[58]  J. Doré,et al.  Biodiversity of the Mucosa‐Associated Microbiota Is Stable Along the Distal Digestive Tract in Healthy Individuals and Patients With Ibd , 2005, Inflammatory bowel diseases.

[59]  B. Haas,et al.  A Catalog of Reference Genomes from the Human Microbiome , 2010, Science.

[60]  Fiona Powrie,et al.  An innately dangerous balancing act: intestinal homeostasis, inflammation, and colitis-associated cancer , 2010, The Journal of experimental medicine.

[61]  J. Doré,et al.  Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients , 2008, Proceedings of the National Academy of Sciences.

[62]  J. Doré,et al.  Temperature Gradient Gel Electrophoresis of Fecal 16S rRNA Reveals Active Escherichia coli in the Microbiota of Patients with Ulcerative Colitis , 2006, Journal of Clinical Microbiology.

[63]  R. Knight,et al.  Moving pictures of the human microbiome , 2011, Genome Biology.

[64]  Peer Bork,et al.  Enterotypes of the human gut microbiome , 2011, Nature.

[65]  K. Honda,et al.  Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species , 2011, Science.

[66]  B. Fleischer,et al.  Reactivity of infiltrating T lymphocytes with microbial antigens in Crohn's disease , 1991, The Lancet.

[67]  J. Barrett,et al.  New IBD genetics: common pathways with other diseases , 2011, Gut.

[68]  F. Shanahan,et al.  Culture-Independent Analyses of Temporal Variation of the Dominant Fecal Microbiota and Targeted Bacterial Subgroups in Crohn's Disease , 2006, Journal of Clinical Microbiology.

[69]  Sallie W. Chisholm,et al.  Whole Genome Amplification and De novo Assembly of Single Bacterial Cells , 2009, PloS one.

[70]  C. Manichanh,et al.  Colonization by Faecalibacterium Prausnitzii and Maintenance of Clinical Remission in Patients With Ulcerative Colitis , 2011 .

[71]  J. Hugot,et al.  Crohn disease--associated adherent-invasive E. coli bacteria target mouse and human Peyer's patches via long polar fimbriae. , 2011, The Journal of clinical investigation.

[72]  Manfred Dietel,et al.  Mucosal flora in inflammatory bowel disease. , 2002, Gastroenterology.

[73]  J. Handelsman,et al.  Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. , 1998, Chemistry & biology.

[74]  F. Guarner.  What is the role of the enteric commensal flora in IBD? , 2008, Inflammatory bowel diseases.

[75]  M. Levings,et al.  TH17 Cells in Autoimmunity and Immunodeficiency: Protective or Pathogenic? , 2012, Front. Immun..

[76]  N. Borruel,et al.  Antiinflammatory Effects of Enterically Coated Amoxicillin‐Clavulanic Acid in Active Ulcerative Colitis , 1998, Inflammatory bowel diseases.

[77]  B. Shen,et al.  Acute and chronic pouchitis—pathogenesis, diagnosis and treatment , 2012, Nature Reviews Gastroenterology &Hepatology.

[78]  W. Ludwig,et al.  SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB , 2007, Nucleic acids research.