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Background  Inflammatory bowel disease (IBD) is characterized by gut dysbiosis. To date, the large bowel microbiota has been in focus. However, the microbiota of the small intestine may also be of importance, as the small bowel is a site for the induction and control of mucosal immune responses, which can be modulated by constituents of the local microbiota.    Methods  Duodenal fluids were collected during diagnostic work-up of treatment-naïve children who were suspected of having IBD. The duodenal fluids were analyzed by pyrosequencing (average of 32,000 reads/sample, read length of 500 nucleotides). After diagnosis, the duodenal microbiota of subjects with ulcerative colitis (N = 8) or Crohn’s disease (N = 5), and non-IBD controls (N = 8) were compared.    Results  Pyrosequencing revealed that the duodenal microbiota of children with ulcerative colitis contained fewer Operational Taxonomic Units (OTUs) per individual than the duodenal microbiota of the controls ( P  = 0.005). This reduction in richness of the duodenal microbiota was seen for three major phyla:  Firmicutes ,  Actinobacteria , and  Bacteroidetes . Several bacterial genera were detected less frequently in the children with ulcerative colitis than in the non-IBD controls, including  Collinsella  ( P  = 0.001),  Lactobacillus  ( P  = 0.007), and  Bacillus  ( P  = 0.007), as well as a non-identified member of the order  Sphingobacteriales  ( P  = 0.007).    Conclusions  In this pilot study, we show that the duodenal microbiota of children with ulcerative colitis exhibits reduced overall richness, despite the fact that the inflammation is primarily localized to the colon. These results should be corroborated in a larger study.

Low-complexity microbiota in the duodenum of children with newly diagnosed ulcerative colitis