A comprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods

The gut microbiome of companion animals (cats and dogs) is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we present a comprehensive analysis of cat and dog gut microbiomes, incorporating 2,423 stool shotgun metagenomes (2,056 dog and 367 cat) spanning 12 publicly available datasets (n=513) and 7 populations newly presented in this study (n=1,910). These are compared with a baseline human population of 238 gut metagenomes from the Human Microbiome Project 1-II processed in an identical manner. All microbiomes were characterized using both reference-based taxonomic and functional profiling, as well as de novo assembly and metagenomic assembled genomes (MAG) clustered into species genome bins (SGBs). The latter identified 563 SGBs from the companion animal microbiomes, 333 novel (“unknown” SGBs or uSGBs) without confident taxonomy and 230 “known” (kSGBs) that include at least one genome with prior taxonomic assignment. Companion animal and human SGBs spanned 14 phyla, with several SGBs unique or shared across host species. For instance, 47 SGBs including Bifidobacterium spp., Lactobacillus spp., Fusobacteriaceae, and novel SGBs spanning Firmicutes, Bacteroidetes, and Actinobacteria were unique to dogs. In cats, an even larger number of unique SGBs were identified (n=65) that spanned Prevotella copri clade C, Olsenella spp., Clostridia, and novel SGBs in the Veillonellaceae, Phyllobacteriaceae, Anaplasmataceae, and Ruminococcaceae families, among others. Companion animals shared several SGBs not found in humans (n=55) that included many Blautia spp., Phocaeicola spp., Sutterella wadsworthensis, and a relatively higher proportion of novel SGBs in Butyricicoccus, Mediterraneibacter, and Fusobacteriaceae. Lastly, we identified a subset of 17 SGBs found in all three hosts, including Ruminococcus gnavus, Prevotella copri clade A, Flavonifractor plautii, Lachnospiraceae, Blautia spp., and Phocaeicola vulgatus. We identified patterns of phylogenetic clustering of genomes within SGBs (i.e., strains that are shared universally vs. host-specific lineages within SGBs). For example, Prevotella copri clade A strains recovered from cat and dog gut metagenomes clustered distinctly from those found in human hosts. These phylogenetic patterns suggest genetic divergence within host species, likely with functional implications (e.g., differences in pangenome and mobile element distributions) important to companion animal health. This study provides the largest one-health microbiome resource to date of companion animal gut metagenomes, greatly improves the ability to profile additional animal gut microbiomes in the future and contributes to our understanding of how microbes are transmitted between companion animals and humans in the contexts of infectious diseases, immune modulation, and specific genetic elements such as antimicrobial resistance genes.