Characterization of the fecal and mucosa-associated microbiota in dogs with chronic inflammatory enteropathy

The objective of the study was the characterization of intestinal bacterial microbiota in dogs with inflammatory bowel disease. Most sequencing-based taxonomic studies have been focused on the fecal microbiota because this is the most accessible sample in the veterinary clinical setting. However, the analysis of these samples does not provide complete information regarding the composition of the small intestine, especially affected in this canine disease. Thus, our study aimed to assess the intestinal microbiota using not only fecal samples but also duodenal biopsy specimens at the diagnosis of this canine disease. Furthermore, healthy dogs (used as a control group, n=12) and IBD dogs (n=34) were characterized regarding signalment, epidemiological data, severity scores for clinical activity indices, and endoscopic and histopathological findings, allowing valuable and deeper characterization of the disease. Our study shows that the composition and diversity of fecal microbiota in dogs with IBD were significantly different from healthy dogs. However, only a few bacterial taxa shifts were observed when assessing duodenal-associated microbiota through analysis of duodenal biopsies specimens. Thus, even if the bowel inflammation mainly affects the small intestine in the IBD-affected dogs of the study, fecal specimens constitute a better sample, due not only to their easy availability but also in terms of searching for bacterial taxa as biomarkers for canine IBD. Further investigations including functionality approaches targeting the gut microbiome at both levels are warranted.