Differences in prokaryotic and viral community between rumen and feces

Ruminants harbor diverse microbial communities, including prokaryotes and viruses, across their digestive tract. Rumen viruses contribute to carbohydrate metabolism; however, their persistence and host interactions in the lower gastrointestinal tract remain unclear. In this study, we investigated the prokaryotic and viral communities in the rumen and feces of the same wethers using whole-metagenomic and virus-like particle metagenomic sequencing. For prokaryotic community analysis, we reconstructed over 300 metagenome-assembled genomes, most of which were novel. These revealed strong site specificity, with distinct prokaryotic community compositions between the rumen and feces. Virome analysis recovered more than 6,000 viral genomes, including many novel viruses. Unlike prokaryotes, several viruses were found to be shared between the rumen and feces. Auxiliary metabolic genes encoding glycoside hydrolases were identified in several rumen-associated viral genomes, whereas fecal-associated viral genomes did not harbor such genes. Host-virus interaction analysis predicted that viruses predominantly infect dominant bacterial taxa and methanogens within each gastrointestinal site, although some viruses may interact with hosts across different sites. These findings highlight the strong site specificity of the prokaryotic communities and the comparatively broader distribution of viruses within the ruminant gastrointestinal tract. These insights advance understanding of virus-prokaryote-host interactions with implications for animal productivity.