Interrogating the viral dark matter of the rumen ecosystem with a global virome database

The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen micro biome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.

Automated summary

By mining published rumen metagenomes, we constructed a global rumen virome database (RVD) and analyzed its diversity, virus-host linkages, and potential roles in affecting rumen functions. RVD, containing 397,180 species-level viral operational taxonomic units (vOTUs), significantly improves the detection rate of rumen viruses compared with other databases. The rumen virome is predicted to infect core members of the rumen microbiome, carry diverse auxiliary metabolic genes, and likely impact the rumen ecosystem.