Phylogenetic and gene‐centric metagenomics of the canine gastrointestinal microbiome reveals similarities with human and mouse gut metagenomes

Our objective was to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gut microbiome. Six healthy adult dogs were used in a crossover design and fed diets containing 0% (K9C) or 7.5% beet pulp (K9BP). Pooled fecal DNA samples from dogs fed each diet were subjected to 454 pyrosequencing. Dominant phyla included Bacteroides/Chlorobi and Firmicutes, both of which comprised ~35% of sequences, followed by Proteobacteria (13–15%) and Fusobacteria (7–8%). K9C had greater Bacteroidetes, Fusobacteria, and Proteobacteria, while K9BP had greater Bacteroidetes/Chlorobi and Firmicutes. Archaea, all Crenarchaeota and Euryarhaeota, represented ~1% of all sequences. Three fungal phylotypes, all Dikarya, were present in K9C, but none in K9BP. Viruses represented < 0.4% of sequences, with >99% associated with bacteriophage. Primary functional categories were associated with carbohydrates; protein metabolism; DNA metabolism; cofactors, vitamins, prosthetic groups, and pigments; amino acids and derivatives; cell wall and capsule; and virulence. Hierarchical clustering of our data and that of other gut metagenomes demonstrated high phylogenetic and metabolic similarity between dogs, humans, and mice. More research is needed to provide deeper coverage of the canine microbiome and identify its role in gastrointestinal disease.