Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

Abstract

This study is the first to use a metagenomics approach to characterize the phylogeny and functional capacity of the canine gastrointestinal microbiome. Six healthy adult dogs were used in a crossover design and fed a low-fiber control diet (K9C) or one containing 7.5% beet pulp (K9BP). Pooled fecal DNA samples from each treatment were subjected to 454 pyrosequencing, generating 503,280 (K9C) and 505,061 (K9BP) sequences. Dominant bacterial phyla included the Bacteroidetes/Chlorobi group and Firmicutes, both of which comprised ∼35% of all sequences, followed by Proteobacteria (13-15%) and Fusobacteria (7-8%). K9C had a greater percentage of Bacteroidetes, Fusobacteria and Proteobacteria, whereas K9BP had greater proportions of the Bacteroidetes/Chlorobi group and Firmicutes. Archaea were not altered by diet and represented ∼1% of all sequences. All archaea were members of Crenarchaeota and Euryarchaeota, with methanogens being the most abundant and diverse. Three fungi phylotypes were present in K9C, but none in K9BP. Less than 0.4% of sequences were of viral origin, with >99% of them associated with bacteriophages. Primary functional categories were not significantly affected by diet and 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 several gastrointestinal metagenomes demonstrated phylogenetic and metabolic similarity between dogs, humans and mice. More research is required to provide deeper coverage of the canine microbiome, evaluate effects of age, genetics or environment on its composition and activity, and identify its role in gastrointestinal disease.

Figure 1

Phylogenetic clustering of canine, human, mouse and chicken gastrointestinal metagenomes. A double hierarchical dendogram, using the weighted-pair group clustering method and the Manhattan distance method with no scaling, shows phylogenetic distribution of microorganisms among canine (K9C; K9BP), human (F1S; HSM), murine (LMC; OMC) and chicken (CCA) metagenomes. Dendogram linkages of the bacterial classes are not phylogenetic, but based on relative abundance of the taxonomic designations within samples. The heat map depicts the relative percentage of each class of microorganism (variables clustering on the y axis) within each sample (x axis clustering). The heat map colors represent the relative percentage of the microbial designations within each sample, with the legend indicated at the upper left corner. The samples along the x axis with Manhattan distances are indicated by branch length and an associated scale located at the upper right corner. Clustering based on Manhattan distance of the bacterial classes along the y axis and their associated scale is indicated in the lower left corner.

Figure 2

Metabolic clustering of canine, human, mouse and chicken gastrointestinal metagenomes. A double hierarchical dendogram, using the weighted-pair group clustering method and the Manhattan distance method with no scaling, shows bacteria distribution (classes) among canine (K9C; K9BP), human (F1S; HSM), murine (LMC; OMC) and chicken (CCA) metagenomes. Dendogram linkages are based on relative abundance of the metabolic classes (variables) within the samples. Clustering of the samples was similarly based on comparative abundance of the metabolic classes among individual samples. The heat map depicts the relative percentage of each metabolic class (variables clustering on y axis) within each sample (x axis clustering). The heat map colors represent the relative percentage of the metabolic classes within each sample, with the legend indicated at the upper left corner. The samples along the x axis with Manhattan distances are indicated by branch length and an associated scale located at the upper right corner. Clustering based on Manhattan distance of the metabolic classes along the y axis and their associated scale is indicated in the lower left corner.