Comparison of the effects of two commercially available prescription diet regimens on the fecal microbiomes of client-owned healthy pet dogs

In the present study, we used next-generation sequencing to investigate the impacts of two commercially available prescription diet regimens on the fecal microbiomes of eleven client-owned healthy pet dogs. We tested an anallergenic diet on 6 dogs and a low-fat diet on 5 dogs. Before starting the study, each dog was fed a different commercial diet over 5 weeks. After collecting pre-diet fecal samples, the anallergenic or low-fat diet was administered for 5 weeks. We then collected fecal samples and compared the pre- and post-diet fecal microbiomes. In the dogs on the anallergenic diet, we found significantly decreased proportions of Bacteroides, Ruminococcaceae, and Fusobacteriaceae, belonging to the phyla Bacteroidetes, Firmicutes, and Fusobacteria, respectively. The proportion of the genus Streptococcus belonging to the phylum Firmicutes was significantly increased upon administering the anallergenic diet. In the dogs on the low-fat diet, although the phyla Actinobacteria and Bacteroidetes tended to increase (p=0.116) and decrease (p=0.147) relative to the pre-diet levels, respectively, there were no significant differences in the proportions of any phylum between the pre- and post-diet fecal microbiomes. The anallergenic diet induced a significantly lower diversity index value than that found in the pre-diet period. Principal coordinate analysis based on unweighted UniFrac distance matrices revealed separation between the pre- and post-diet microbiomes in the dogs on the anallergenic diet. These results suggest that, even in pet dogs kept indoors in different living environments, unification of the diet induces apparent changes in the fecal microbiome.