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The gastrointestinal microbiota is considered important in inflammatory bowel disease (IBD) pathogenesis. Discoveries fromestablisheddisease cohorts report reduced bacterial diversity, changes in bacterial composition, and a protective role forFaecalibacterium prausnitziiin 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 thande-novodisease.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 macroscopicallyandmicroscopically normal colon. We utilized a dual-methodology approach with pyrosequencing (threshold >10,000 reads) and confirmatory real-time PCR (RT-PCR).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. AnincreaseinFaecalibacteriumwas observed in CD compared with controls by pyrosequencing (mean 16.7% vs. 9.1% of reads,P=0.02) and replicated by specificF. prausnitziiRT-PCR (36.0% vs. 19.0% of total bacteria,P=0.02). No disease-specific clustering was evident on principal components analysis.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 forF. prausnitziiin CD, suggesting a more dynamic role for this organism than previously described.