Fecal Microbiome in Dogs with Acute Diarrhea

Recent molecular studies have revealed that the canine gastrointestinal tract (GIT) harbors a highly complex microbial ecosystem. Gut microbes play a very important role in the development and regulation of the immune system of the host, mediated in-part through the production of immunomodulatory metabolites (e.g., butyrate, propionate, indole). Limited information is available about potential changes in the predominant bacterial groups in dogs with acute diarrhea, and characterizing the functional gene content of the microbiome may help to understand relationships between microbiota, endogenous metabolites, and gastrointestinal disease. Therefore, the aim of this study was (1) to characterize the fecal microbiome in healthy dogs, dogs with acute non-hemorrhagic diarrhea (NHD), and dogs with acute hemorrhagic diarrhea (AHD) using 16S rRNA gene sequencing and qPCR analysis; (2) to measure fecal concentrations of short-chain fatty acids (SCFAs) and branched-chain fatty acids (BCFAs); and (3) to describe the functional gene content of the fecal microbiome.

Fecal samples were collected from healthy dogs (n=13), dogs with NHD (n=5), and dogs with AHD (n=6). The fecal microbiota were analyzed by 454-pyrosequencing of 16S rRNA genes and qPCR assays. SCFAs were quantified by gas chromatography/mass spectrometry (GC/MS). Functional genes present in the microbiome were predicted from the 16S rRNA gene data using the software PICRUSt.

The Shannon Index for bacterial diversity was significantly decreased in dogs with acute diarrhea (AD; both NHD and AHD groups combined) compared to healthy dogs (p=0.0020). Sequences belonging to Bacteroidetes were significantly decreased in dogs with AD compared to healthy dogs (p=0.0280). Sequences belonging to the genus Faecalibacterium and an unclassified genus within the family Ruminococcaceae were both significantly decreased in dogs with AD compared to healthy dogs (p=0.0319 and 0.0368, respectively). Also, a significant decrease in Blautia spp. were observed in dogs with AD compared to healthy dogs (p=0.0472). The proportions of butyric acid were significantly increased and proportions of propionic acid were significantly decreased in dogs with AD compared to healthy dogs (p<0.05 for both). Significant differences were not observed in functional categories among all dogs after adjustment for multiple comparisons.

Results of this study revealed a bacterial dysbiosis in fecal samples of dogs with NHD and dogs with AHD compared to healthy dogs. The bacterial groups that were commonly decreased during acute diarrhea are considered to be important SCFA producers and may be important for canine intestinal health. Future studies to evaluate broader metabolomic profiles in dogs with acute diarrhea are indicated.