The Cat Gut Microbial Genome Collection reveals global structure of the feline gut microbiome

The gut microbiome is a critical determinant of mammalian health, yet our understanding is largely derived from humans and laboratory models. The ecological principles governing the microbiome of globally important companion animals, such as cats, remain poorly defined. We generated the Cat Gut Microbial Genome Collection (CGMGC), a comprehensive resource encompassing over 40,000 microbial genomes. This collection spans 874 prokaryotic species, 6 fungal species, and 5543 viral operational taxonomic units, derived from feline gut samples across diverse geographical regions. Our analysis reveals that the cat gut microbiome is a highly host-specific ecosystem whose structure is primarily driven by geography rather than host genetics or diet. Over 50% of the identified prokaryotic species are unique to felines and contain novel taxonomic lineages. Functionally, the virome encodes a vast repertoire of auxiliary metabolic genes, indicating pervasive inter-kingdom control over bacterial hosts. Surprisingly, the feline gut shares significantly more microbial species with humans than with laboratory mice, suggesting convergent evolution in cohabiting species. The core ecological principles of the feline gut are profound host-specificity, geographic structuring, and pervasive viral modulation of bacterial function. This work redefines the feline microbiome as a unique model for host-microbe co-evolution and establishes a genomic foundation for a new era of evidence-based veterinary medicine.