Unraveling the viral dark matter of the rumen microbiome with a new global virome database

Like in the human gut and other environments, viruses are probably also diverse and modulate the microbiome (both population and function) in the rumen of ruminants, but it remains largely unknown. Here we mined 975 published rumen metagenomes for viral sequences, created the first rumen virome database (RVD), and perform ecogenomic meta-analyses of these data. This identified 397,180 species-level viral operational taxonomic units (vOTUs) and allowed for a 10-fold increase in classification rate of rumen viral sequences compared with other databases. Most of the classified vOTUs belong to the order Caudovirales, but distinct from those in the human gut. Rumen viruses likely have ecosystem impacts as they were predicted to infect dominant fiber degraders and methane producers, and they carry diverse auxiliary metabolic genes and antibiotic resistance genes. Together, the RVD database and these findings provide a baseline framework for future research on how viruses may impact the rumen ecosystem.