A global livestock virome catalog links viruses with resistome assembly

Livestock manure is a prominent One Health setting for antimicrobial resistance (AMR), yet the contribution of viruses to resistome assembly remains unresolved. Here we compile the Livestock Manure Virus Database (LMVD), a global catalog of 1,330,372 viral operational taxonomic units reconstructed from 4,017 metagenomes. Livestock manure viral communities exhibit restricted biogeographic distributions, and antibiotic use and farming scale show the highest relative predictive importance for viral diversity. Viral genomes contained 78 antibiotic resistance gene (ARG) subtypes, representing 9.1% of resistome diversity in livestock manure, but virus-encoded ARGs were infrequent. Bacteriophages instead showed extensive predicted links to bacterial hosts, with nearly all antibiotic-resistant bacteria linked to viruses, predominantly temperate viruses, and enrichment in pathogenic antibiotic-resistant bacteria. Together, these findings place bounds on the contribution of viruses to direct ARG dissemination and indicate that lysogenic interactions with resistant hosts may shape AMR risk.