Biodiversity and structure of livestock-associated bacteriophage communities in Brazil and Spain

Introduction Livestock waste represents a complex microbial ecosystem in which bacteriophages can play essential roles in shaping bacterial populations and mediating gene exchange. However, comparative analyses of livestock-associated viral communities across geographic regions remain scarce. Methods We conducted a unified metagenomic analysis of 23 Brazilian and 29 Spanish livestock-waste metagenomes, encompassing broiler litter and swine manure samples. Viral operational taxonomic units (vOTUs) were identified and used to compare phage community composition across production matrices, waste-handling stages, geographic regions, and countries. Results More than 100,000 vOTUs were identified, of which over 98% were classified as bacteriophages. Brazilian samples showed distinct phage-community profiles between broiler and swine production systems, whereas Spanish swine manure samples exhibited modest regional variation at finer taxonomic resolution. Cross-country comparisons indicated broad convergence at the phage class level but substantial compositional differences at finer taxonomic resolution. Discussion These findings indicate that livestock-associated phage communities are shaped by ecological context, production matrix, and waste-management practices. This study expands current knowledge of viral biodiversity in agricultural environments and contributes to a One Health understanding of microbial dynamics in livestock-waste systems.