title: Microbiome Survey of the Inflamed and Noninflamed Gut at Different Compartments Within the Gastrointestinal Tract of Inflammatory Bowel Disease Patients.
abstract: BACKGROUND
  We aimed to contrast the mucosal microbiota in Crohn's disease (CD) and ulcerative colitis (UC).
  
  
  METHODS
  We assessed the concept of localized dysbiosis by comparing the bacterial communities of inflamed and noninflamed mucosa of patients with inflammatory bowel disease (IBD) and by analysis of the microbiota composition at distinct gut compartments (ileum, cecum, mid-colon, and rectum). We performed 16S rDNA sequencing to analyze population structures. Quality control and operational taxonomic unit classification of reads were performed using mothur with statistical analyses executed in the R package, phyloseq.
  
  
  RESULTS
  There was no variation in any phyla or genera comparing inflamed to noninflamed mucosa within CD (or UC) or when comparing different gut compartments within CD (or UC). There were differences between the inflamed and noninflamed mucosa between CD and UC: analysis of the inflamed IBD gut at the phylum level indicated that Bacteroidetes (P = 0.002) and Fusobacteria (P < 0.05) were detected more frequently in inflamed CD mucosa than in inflamed UC mucosa. Conversely, Proteobacteria and Firmicutes (P < 0.05) were more frequently observed in the inflamed UC mucosa. At the genus level, the abundance of Faecalibacterium (P ≤ 0.05), Bacteroides (P = 0.003), and Pseudomonas (P < 0.001) were significantly different between the inflamed CD and UC and the abundance of 13 genera were significantly different within the noninflamed mucosa. The noninflamed UC mucosa was the most different from non-IBD mucosa.
  
  
  CONCLUSIONS
  Dramatic shifts of microbial communities were not observed between the noninflamed and inflamed mucosa within CD (or UC) although both the inflamed (and noninflamed) mucosa was different between CD and UC.
authors.affiliation: *Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Canada; †Bioinformatics Core, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada; and ‡Department of Internal Medicine, IBD Clinical and Research Centre, University of Manitoba, Canada.
authors.forename: Jessica D
authors.initials: JD
authors.lastname: Forbes
authors.forename: Gary
authors.initials: G
authors.lastname: Van Domselaar
authors.forename: Charles N
authors.initials: CN
authors.lastname: Bernstein
mesh_terms: D016022:Case-Control Studies; D003093:Colitis, Ulcerative / Q000145:classification / Q000235:genetics / Q000382:microbiology*; D003424:Crohn Disease / Q000145:classification / Q000235:genetics / Q000382:microbiology*; D004269:DNA, Bacterial / Q000235:genetics; D005260:Female; D005500:Follow-Up Studies; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D008297:Male; D064307:Microbiota / Q000235:genetics*; D011379:Prognosis
chemical_list: D004269:DNA, Bacterial