16S rRNA Gene Pyrosequencing Reveals Bacterial Dysbiosis in the Duodenum of Dogs with Idiopathic Inflammatory Bowel Disease

Abstract

BackgroundCanine idiopathic 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 16 S rRNA gene pyrosequencing.Methodology/Principal FindingsBiopsy samples of small intestinal mucosa were collected endoscopically from healthy dogs (n = 6) and dogs with moderate IBD (n = 7) or severe IBD (n = 7) as assessed by a clinical disease activity index. Total RNA was extracted from biopsy specimens and 454-pyrosequencing of the 16 S rRNA gene was performed on aliquots of cDNA from each dog. Intestinal inflammation was associated with significant differences in the composition of the intestinal microbiota when compared to healthy dogs. PCoA plots based on the unweighted UniFrac distance metric indicated clustering of samples between healthy dogs and dogs with IBD (ANOSIM, p<0.001). Proportions of Fusobacteria (p = 0.010), Bacteroidaceae (p = 0.015), Prevotellaceae (p = 0.022), and Clostridiales (p = 0.019) were significantly more abundant in healthy dogs. In contrast, specific bacterial genera within Proteobacteria, including Diaphorobacter (p = 0.044) and Acinetobacter (p = 0.040), were either more abundant or more frequently identified in IBD dogs.Conclusions/SignificanceIn conclusion, dogs with spontaneous IBD exhibit alterations in microbial groups, which bear resemblance to dysbiosis reported in humans with chronic intestinal inflammation. These bacterial groups may serve as useful targets for monitoring intestinal inflammation.

Fecal Microbiome in Dogs with Acute Diarrhea and Idiopathic Inflammatory Bowel Disease

“…As in humans, an interplay between the intestinal microbiota together with an underlying genetic susceptibility of the host and dietary and environmental factors, are implicated in the development of disease [7,32]. While recent studies have reported a dysbiosis in duodenal samples of dogs with IBD, limited data are available describing the fecal microbiota in these dogs [7][8][9][10].…”

“…Chimeras were excluded using the software B2C2 (http://www. researchandtesting.com/B2C2.html) [7,19]. Operational taxonomic units (OTUs) were defined as sequences with at least 97% similarity using QIIME.…”

“…The intestinal microbiota has also been implicated in the pathogenesis of various canine GI disorders, either associated with the presence of specific pathogens (e.g., enterotoxigenic C. perfringens, Salmonella, viruses, and parasites) in acute episodes of diarrhea [5,6], or a non-specific dysbiosis such as that described in dogs with idiopathic inflammatory bowel disease [7][8][9][10]. Canine idiopathic IBD is one of the most common causes of chronic GI disease in dogs and encompasses a group of chronic enteropathies of unknown cause, which are characterized by infiltration of the intestinal mucosa with inflammatory cells [11].…”

The Microbiome

“…5,17,20,38,55,88,89,115,117,119,126 These microbial changes are accompanied by underlying susceptibilities in the innate immune system of dogs and cats with chronic enteropathies, such as idiopathic IBD, further demonstrating the relationship between gut microbiota and host health. 55,62,63,78,86 It is been shown that the canine microbiota changes with diarrhea, with the most profound changes in dogs with acute hemorrhagic diarrhea (AHD), 117 and characterized by significant decreases in Blautia, Ruminococcaceae including Faecalibacterium, and Turicibacter spp., and significant increases in genus Sutterella and Clostridium perfringens compared to healthy dogs (Fig.…”

“…94 In dogs with IBD, the mucosa-adherent microbiota of the small intestine is primarily comprised of Proteobacteria, especially E. coli-like organisms 126 or Pseudomonas, 119 with lower proportions of Firmicutes and Bacteroidetes compared to healthy dogs. 115 Boxer dogs and French Bulldogs with granulomatous colitis also have dysbiosis of their intestinal microbiome. Microbiota analysis based on sequencing of 16 S rRNA genes in combination with FISH has revealed invasive E. coli bacteria present in multifocal clusters within macrophages in the colonic mucosa.…”