Relation of fecal microbiome with the source of starch in free ranging dogs housed in a shelter.

The intestinal enzymatic feature of the modern breeds of dogs can digest starch and, accordingly, variable amounts of starchy foods can be included in the diets. Potato and rice contain a different type of starch and a dietary intervention study was conducted in dog to evaluate the variations of faecal microbiome in relation to the source of starch in home made diets.Thirty adult dogs housed in a shelter were selected and fed a diet based on a mixture of rice, pasta and fresh raw meat. For the study, a group of dogs continued to receive this diet (CD), a second group (B1) was assigned to a diet with rice as main source of starch (CB1), and the third group (B2) was fed with a diet containing potato instead of rice. Samples of faeces were collected from each dog before the morning meal at the beginning (T0) and after 15 days (T15) and analyzed for pH, ammonia N (N-NH3) and total N (TN), short chain fatty acids (SCFA) and lactic acid. Relative abundance (RA) of faecal microbiota was assessed by sequencing and annotating the V3-V4 regions of the 16S rRNA.The total amounts of starch of the diets was similar, but starch differed for in vitro rate digestion and the undigestible starch was higher in B2 than B1 and CD diets. Dog fed B2 diet (potato starch) showed lower (P<0.05) N-NH3 and pH and higher (P<0.05) molar proportion of lactic acid. The RAs (P<0.05) of Bacteroidetes and Proteobacteria were significantly higher in faeces collected at T15 in comparison to T0 samples for B1 and CD diets, but not for the B2 diet. Pairwise comparisons of the RA values of genera within diets showed an increase (P<0.05) of Megamonas for B1 diet at T15 , p-75-a5 for B1 and B2 diets at T15 and Streptococcus for B2 diet at T15. Principal components analysis (PCA) using the RA of phyla or genera as input variables explained 96.02% and 61.40% of total variance, respectively, but failed to aggregate the dogs on the basis of the diet or time of sampling.These results suggest that small changes of diet composition, providing comparable supply of nutrients, have limited effects on faecal microbiome in in healthy dogs. Furthermore, the data obtained underline the high individual variability of microbiota among dogs.