canine and feline gut metagenomic samples Raw sequence reads

We comprehensively profiled canine and feline gut microbiomes by incorporating stool shotgun metagenomes from 7 new study populations (n=1,909) with publicly available companion animal datasets. Human gut metagenomes were also included for comparison. Microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes (MAGs) clustered into species-level genome bins (SGBs). Both universally carried and host-unique SGBs were identified. Notably, we applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g., differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the 'One Health' concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.