title: Microbiota of de-novo pediatric IBD: increased Faecalibacterium prausnitzii and reduced bacterial diversity in Crohn's but not in ulcerative colitis.
abstract: OBJECTIVE
  The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries from established disease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role for Faecalibacterium prausnitzii in Crohn's disease (CD). The majority of studies to date are however potentially confounded by the effect of treatment and a reliance on established rather than de-novo disease.
  
  
  METHODS
  Microbial changes at diagnosis were examined by biopsying the colonic mucosa of 37 children: 25 with newly presenting, untreated IBD with active colitis (13 CD and 12 ulcerative colitis (UC)), and 12 pediatric controls with a macroscopically and microscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR).
  
  
  RESULTS
  Threshold pyrosequencing output was obtained on 34 subjects (11 CD, 11 UC, 12 controls). No significant changes were noted at phylum level among the Bacteroidetes, Firmicutes, or Proteobacteria. A significant reduction in bacterial α-diversity was noted in CD vs. controls by three methods (Shannon, Simpson, and phylogenetic diversity) but not in UC vs. controls. An increase in Faecalibacterium was observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads, P=0.02) and replicated by specific F. prausnitzii RT-PCR (36.0% vs. 19.0% of total bacteria, P=0.02). No disease-specific clustering was evident on principal components analysis.
  
  
  CONCLUSIONS
  Our results offer a comprehensive examination of the IBD mucosal microbiota at diagnosis, unaffected by therapeutic confounders or changes over time. Our results challenge the current model of a protective role for F. prausnitzii in CD, suggesting a more dynamic role for this organism than previously described.
authors.affiliation: Gastrointestinal Research Group, Division of Applied Medicine, University of Aberdeen, Aberdeen, UK.
authors.forename: Richard
authors.initials: R
authors.lastname: Hansen
authors.forename: Richard K
authors.initials: RK
authors.lastname: Russell
authors.forename: Caroline
authors.initials: C
authors.lastname: Reiff
authors.forename: Petra
authors.initials: P
authors.lastname: Louis
authors.forename: Freda
authors.initials: F
authors.lastname: McIntosh
authors.forename: Susan H
authors.initials: SH
authors.lastname: Berry
authors.forename: Indrani
authors.initials: I
authors.lastname: Mukhopadhya
authors.forename: W Michael
authors.initials: WM
authors.lastname: Bisset
authors.forename: Andy R
authors.initials: AR
authors.lastname: Barclay
authors.forename: Jon
authors.initials: J
authors.lastname: Bishop
authors.forename: Diana M
authors.initials: DM
authors.lastname: Flynn
authors.forename: Paraic
authors.initials: P
authors.lastname: McGrogan
authors.forename: Sabarinathan
authors.initials: S
authors.lastname: Loganathan
authors.forename: Gamal
authors.initials: G
authors.lastname: Mahdi
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
authors.forename: Emad M
authors.initials: EM
authors.lastname: El-Omar
authors.forename: Georgina L
authors.initials: GL
authors.lastname: Hold
mesh_terms: D000293:Adolescent; D002648:Child; D003013:Clostridium / Q000235:genetics / Q000302:isolation & purification*; D003093:Colitis, Ulcerative / Q000382:microbiology*; D015169:Colony Count, Microbial; D003424:Crohn Disease / Q000382:microbiology*; D005260:Female; D006801:Humans; D015212:Inflammatory Bowel Diseases / Q000382:microbiology; D008297:Male; D060888:Real-Time Polymerase Chain Reaction