Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease

Abstract

Idiopathic inflammatory bowel disease (IBD) is a common cause of chronic gastrointestinal (GI) disease in dogs. The combination of an underlying host genetic susceptibility, an intestinal dysbiosis, and dietary/environmental factors are suspected as main contributing factors in the pathogenesis of canine IBD. However, actual mechanisms of the hostmicrobe interactions remain elusive. The aim of this study was to compare the fecal microbiota and serum metabolite profiles between healthy dogs (n D 10) and dogs with IBD before and after 3 weeks of medical therapy (n D 12). Fecal microbiota and metabolite profiles were characterized by 454-pyrosequencing of 16 S rRNA genes and by an untargeted metabolomics approach, respectively. Significantly lower bacterial diversity and distinct microbial communities were observed in dogs with IBD compared to the healthy control dogs. While Gammaproteobacteria were overrepresented, Erysipelotrichia, Clostridia, and Bacteroidia were underrepresented in dogs with IBD. The functional gene content was predicted from the 16 S rRNA gene data using PICRUSt, and revealed overrepresented bacterial secretion system and transcription factors, and underrepresented amino acid metabolism in dogs with IBD. The serum metabolites 3-hydroxybutyrate, hexuronic acid, ribose, and gluconic acid lactone were significantly more abundant in dogs with IBD. Although a clinical improvement was observed after medical therapy in all dogs with IBD, this was not accompanied by significant changes in the fecal microbiota or in serum metabolite profiles. These results suggest the presence of oxidative stress and a functional alteration of the GI microbiota in dogs with IBD, which persisted even in the face of a clinical response to medical therapy.

Effect of an extruded animal protein‐free diet on fecal microbiota of dogs with food‐responsive enteropathy

“…These findings are similar to those of previous studies, where lower bacterial diversity and richness and different microbial communities in dogs with acute and chronic GI disease compared to those in HC dogs were reported 16, 18, 41, 42, 43, 44. At the phylum level, an increased abundance of Proteobacteria was detected, based on the univariate analyses.…”

“…In dogs with acute diarrhea, after perturbation the microbiota seemed to return to the starting condition 45. Administration of antibiotics is a strong driver to shift GI microbial composition 16, 46, 47. In 1 study, treatment with diet, with or without a probiotic strain ( Enterococcus faecium ), lead to a significantly increased richness of the fecal bacterial microbiome in dogs with FRE, similar to our results 48…”

“…Several studies have evaluated how to modulate the intestinal microbiota in dogs with GI diseases. In dogs with IBD, previous reports showed no changes in fecal microbiota after treatment with immunosuppressive drugs 16, 18, 43. In dogs with acute diarrhea, after perturbation the microbiota seemed to return to the starting condition 45.…”

“…Amplification and sequencing of the V4 variable region 16S rRNA gene was performed as previously reported 16. Raw sequence data were screened, trimmed, denoised, chimera‐depleted and filtered using QIIME pipeline version 1.8.0 31.…”

Clinical utility of currently available biomarkers in inflammatory enteropathies of dogs

“…Alterations in the fecal bacterial microbiome have been found in dogs with CIE 63, 64, 65, 66. The most significant decreases were detected in Faecalibacterium spp.…”