Host Breed and Geography Shape the Antiviral Defense Landscape of the Bovine Rumen Microbiome

The rumen microbiome represents a complex, phage-rich ecosystem where microbial survival depends on both metabolic cooperation and antiviral defense. However, global and breed-associated variations in rumen prokaryotic immune systems remain poorly understood. Here, we performed the most comprehensive profile to date of antiviral defense systems in the rumen, analyzing 6,530 microbial genomes and metagenome-assembled genomes (MAGs) from diverse cattle breeds and geographic regions. In this global dataset, we identified over 90,000 defense systems, the most abundant of which were restriction-modification, PDC-S01, DNA modification systems (DMS_other), AbiE and SoFic, with variations influenced by both host the lineage and geographic region. A more in-depth analysis was performed using two complementary antiviral annotation frameworks for Nellore cattle (Bos indicus) from Brazil. Data exhibited a remarkably enriched antiviral defense repertoire, with over 15,632 defense systems encoded across 547 high-quality MAGs. These systems were densely clustered in dominant rumen lineages, such as Prevotella, and positively correlated with prophage abundance, consistent with virus–host coevolution. Notably, we also detected viral contigs encoding both antiviral defense and anti-defense genes, underscoring the arms race between the phages and their microbial hosts. Metatranscriptomic data from North America and Oceania revealed high expression levels of toxin-antitoxin modules, CRISPR components, and restriction enzymes, suggesting a basal level of antiviral activity. These findings reveal the rumen as an antiviral innovation hotspot, highlighting microbiome resilience with implications for ecology, adaptation, and phage-based interventions.