Exploring the RNA virus populations of the rumen and saliva of cattle

Abstract

The majority of rumen viral metagenome studies use either (1) viral DNA extracted from viral particles fractionated from rumen fluid for high throughput sequencing; (2) viral reads extracted from metagenome sequence datasets derived from DNA extracted from whole or the microbial fraction of rumen fluid; or (3) viral reads extracted from metatranscriptomes derived from RNA extracted from rumen fluid. While the latter method enables the RNA virome to be determined, viral reads may represent a very small fraction of the total sequence dataset which could result in the diversity and extent of RNA virus populations, being underestimated. In addition, there has been little research into the viral populations present in the saliva compared to those present in the rumen, despite the frequent interchange of digesta between these two body sites, during rumination.