The Association of the Rumen Virome with Methane Emissions in Dairy Cattle - vOTUs Database

Enteric methane production in ruminants is a major environmental concern, yet its association with the ruminal virome remains largely unexplored. This study analyzed ruminal metagenomes from 448 Holstein dairy cows using Oxford Nanopore Technologies to investigate the virome and its link to methane emissions. We identified 8,933 viral operational taxonomic units (vOTUs), including bacteriophages, archaeophages, megaviruses, and virophages. Significant differences between high- and low-emitting cows were observed. Low emitters showed greater abundance (mean log-FC = 0.72, Padj≤ 0.049) of vOTUs infecting bacteria like Prevotella, whereas greater abundance (mean log-FC = 0.70, Padj ≤ 0.047) of archaeophages and megaviruses infecting Methanobrevibacter, ciliates like Paramecium, and fungi, microorganisms linked to methane production, were observed in high emitters. These findings suggest that viruses may influence methane emissions by modulating key microbial populations. Although mechanisms remain unclear, rumen viruses could serve as biomarkers for selecting low-emission animals or to develop microbial interventions.