16S rRNA gene sequencing of the duodenal microbiota in dogs with inflammatory bowel disease

J.S. Suchodolski, SE Dowd, V. Wilke, J.M. Steiner, , , A.E. Jergens Canine inflammatory bowel disease (IBD) is believed to be caused by a complex interaction of genetic, immunologic, and microbial factors. While mucosa-associated bacteria have been implicated in the pathogenesis of canine IBD, detailed studies investigating the enteric microbiota using deep sequencing techniques are lacking. The objective of this study was to evaluate mucosa-adherent microbiota in the duodenum of dogs with spontaneous idiopathic IBD using 16S rRNA gene pyrosequencing. Samples of intestinal mucosa were collected endoscopically from dogs diagnosed with moderate-to-severe IBD (n=18) and healthy dogs (n=6), respectively. Total RNA was extracted from biopsy specimens and 454-pyrosequencing of the 16S rRNA gene was performed on aliquots of cDNA from each dog. Gastrointestinal signs and intestinal inflammation in IBD dogs were accompanied by significant differences in the composition of the intestinal microbiota. The proportions of sequences belonging to the members of Bacteroidales and Clostridiales, including the genera Faecalibacterium, Ruminococcus, and Dorea within the Clostridium clusters IV and XIVa, were significantly reduced in the IBD dogs (P<0.01). In contrast, proportions of Proteobacteria, including ß-, ?- and d-Proteobacteria were significantly higher in the IBD dogs (P=0.012). In conclusion, dogs with IBD exhibit alterations in microbial diversity which bear resemblance to dysbiosis reported in humans with chronic? intestinal inflammation. These bacterial groups may serve as useful targets for diagnosis and potentially development of better treatment modalities of canine IBD.