Association between specific mucosa‐associated microbiota in Crohn's disease at the time of resection and subsequent disease recurrence: A pilot study

Crohn's disease pathogenesis involves alterations in the gut microbiota. We characterized the mucosa‐associated microbiota at the time of surgical resection and 6 months later to identify bacterial profiles associated with recurrence and remission.

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

[2]  David A W Soergel,et al.  Association of gut microbiota with post-operative clinical course in Crohn’s disease , 2013, BMC Gastroenterology.

[3]  P. Rutgeerts,et al.  Natural history of recurrent Crohn's disease at the ileocolonic anastomosis after curative surgery. , 1984, Gut.

[4]  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.

[5]  R. Blumberg,et al.  The immunology of mucosal models of inflammation. , 2002, Annual review of immunology.

[6]  Steven J Brown,et al.  925j Optimising post-operative Crohn's disease management: best drug therapy alone versus colonoscopic monitoring with treatment step-up. The POCER study. , 2013 .

[7]  T. Ko,et al.  Dietary Fiber Enhances a Tumor Suppressor Signaling Pathway in the Gut , 2006, Annals of surgery.

[8]  J. Hoheisel,et al.  Correspondence analysis applied to microarray data , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[9]  G. Macfarlane,et al.  The control and consequences of bacterial fermentation in the human colon. , 1991, The Journal of applied bacteriology.

[10]  Terence P. Speed,et al.  A comparison of normalization methods for high density oligonucleotide array data based on variance and bias , 2003, Bioinform..

[11]  Martin Hartmann,et al.  Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities , 2009, Applied and Environmental Microbiology.

[12]  K. Wilson,et al.  Ribosomal DNA Sequence Analysis of Mucosa-Associated Bacteria in Crohn’s Disease , 2004, Inflammatory bowel diseases.

[13]  D. Alland,et al.  A detailed analysis of 16S ribosomal RNA gene segments for the diagnosis of pathogenic bacteria. , 2007, Journal of microbiological methods.

[14]  Lukas Wagner,et al.  A Greedy Algorithm for Aligning DNA Sequences , 2000, J. Comput. Biol..

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

[16]  C. Szabó.  Hydrogen sulphide and its therapeutic potential , 2007, Nature Reviews Drug Discovery.

[17]  M. Helmrath,et al.  A new animal model of postsurgical bowel inflammation and fibrosis: the effect of commensal microflora , 2009, Gut.

[18]  S. Batzoglou,et al.  Bacterial flora-typing with targeted, chip-based Pyrosequencing , 2007, BMC Microbiology.

[19]  P. Rutgeerts,et al.  Therapy of metronidazole with azathioprine to prevent postoperative recurrence of Crohn's disease: a controlled randomized trial. , 2008, Gastroenterology.

[20]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[21]  E. Levy,et al.  Short-chain fatty acids: ready for prime time? , 2006, Nutrition in clinical practice : official publication of the American Society for Parenteral and Enteral Nutrition.

[22]  P. Brigidi,et al.  Antibiotic combination therapy in patients with chronic, treatment‐resistant pouchitis , 1999, Alimentary pharmacology & therapeutics.

[23]  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.

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

[25]  N. Docherty,et al.  Sulphate‐reducing bacteria and hydrogen sulphide in the aetiology of ulcerative colitis , 2009, The British journal of surgery.

[26]  R. Knight,et al.  Impact of Ileocecal Resection and Concomitant Antibiotics on the Microbiome of the Murine Jejunum and Colon , 2013, PloS one.

[27]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[28]  Mihai Pop,et al.  Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples , 2009, PLoS Comput. Biol..

[29]  S. Cucchiara,et al.  The Microbiota in Inflammatory Bowel Disease in Different Age Groups , 2009, Digestive Diseases.

[30]  J. Cameron,et al.  Patterns of ileal recurrence in Crohn's disease. A prospective randomized study. , 1992, Annals of surgery.

[31]  Zhongtang Yu,et al.  An Efficient RNA Extraction Method for Estimating Gut Microbial Diversity by Polymerase Chain Reaction , 2009, Current Microbiology.

[32]  C. Neut,et al.  Self inflicted rectal ulcer: hearing is believing , 2003, Gut.

[33]  Patrick J. Lindsey,et al.  Butyrate-Induced Transcriptional Changes in Human Colonic Mucosa , 2009, PloS one.

[34]  Rob Knight,et al.  UCHIME improves sensitivity and speed of chimera detection , 2011, Bioinform..

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

[36]  S. Schuster,et al.  Integrative analysis of environmental sequences using MEGAN4. , 2011, Genome research.

[37]  G. Macfarlane,et al.  Regulation of short-chain fatty acid production , 2003, Proceedings of the Nutrition Society.

[38]  N. Barnich,et al.  Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn's disease. , 1998, Gastroenterology.

[39]  M. Helmrath,et al.  Expansion of intestinal stem cells associated with long-term adaptation following ileocecal resection in mice. , 2007, American journal of physiology. Gastrointestinal and liver physiology.

[40]  C. Neut,et al.  Changes in the bacterial flora of the neoterminal ileum after ileocolonic resection for Crohn's disease , 2002, American Journal of Gastroenterology.

[41]  P. Rutgeerts,et al.  Controlled trial of metronidazole treatment for prevention of Crohn's recurrence after ileal resection. , 1995, Gastroenterology.

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

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

[44]  Guy Perrière,et al.  Between-group analysis of microarray data , 2002, Bioinform..

[45]  R Balfour Sartor,et al.  Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. , 2004, Gastroenterology.

[46]  J. Furne,et al.  Fecal Hydrogen Sulfide Production in Ulcerative Colitis , 1998, American Journal of Gastroenterology.

[47]  Jean Thioulouse,et al.  CO‐INERTIA ANALYSIS AND THE LINKING OF ECOLOGICAL DATA TABLES , 2003 .