Host Phylogeny and Diet Shape Gut Microbiome and Virome in Wild Small Mammals of Gongga Mountain, China

Background: Gut microbiotas play pivotal roles in host adaptation, yet their composition and function in high-altitude small mammals remain poorly characterized. This study investigated how host phylogeny (order-level) and dietary habits shape the gut microbiome and virome of three mammalian orders (Eulipotyphla, Rodentia, Lagomorpha) in Gongga Mountain, a biodiversity hotspot on the Qinghai-Tibet Plateau. Results: Metagenomic sequencing of 219 samples from 22 species revealed order-specific microbial signatures: Eulipotyphla (carnivorous) harbored higher abundances of potential pathogens (e.g., Helicobacter, Hafnia) and Retroviridae; Lagomorpha (herbivorous) was enriched in cellulolytic bacteria (e.g., Lachnospiraceae, Prevotella) and carbohydrate-active enzymes (CAZymes); Rodentia (omnivorous) showed intermediate traits. We reconstructed 1,385 high-quality metagenome-assembled genomes (MAGs), 1,328 representing novel species, and identified 749 viral operational taxonomic units (vOTUs), >80% being Caudoviricetes. Crucially, Retroviridae abundance in Eulipotyphla suggests zoonotic risk. Phage-host network analysis indicated Caudoviricetes regulates cellulolytic bacteria in Lagomorpha. Conclusion: Host phylogeny and diet jointly drive gut microbiome divergence in small mammals. We establish the first gut microbiome and virome resource of small mammals in the high-altitude area of Gongga Mountain, highlighting Eulipotyphla as a potential vector for zoonotic pathogens.