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Understanding phage-bacterial interactions and their role in the rumen
Diverse viral communities (especially bacteriophages) are found in all ecosystems and are considered the most abundant biological entity on earth. Although viruses are commonly found in all ecosystems, the roles of viruses within these ecosystems are poorly understood, partly because no conserved gene common to all viruses exists and less than 1% of the bacterial hosts can be cultivated. As a first attempt to better understand the role and functional relationships of viruses, in particular how prophages influence rumen bacterial communities, we have investigated viral and bacterial community relationships under different dietary conditions (55% corn silage, 27% condensed distillers plus solubles (CDS), 40% modified distillers grains plus solubles (MDGS), corn based control diet) in a Latin-square design using 4 fistulated steers using a metagenomics approach. Rumen samples were collected after a 21-day adaptation period after total rumen evacuation and mixing. A total rumen evacuation was performed via the rumen cannula and samples were collected after mixing the contents. Tangential flow filtration was performed to isolate viral particles from the rumen sample. In addition to the bacterial 16S gene, the viral and bacterial metagenomes were sequenced using the Ion Torrent personnel genome machine (PGM) to identify species composition, interactions between viruses and bacteria, and to identify differences in metabolic potential under different dietary conditions. Our analysis of the rumen microbial community demonstrates intra-individual structuring of microbial communities based on diet. However, the metagenomes sequence analysis for metabolic profiles (function) exhibited a more constant pattern. Furthermore, each dietary treatment produced a unique virome, consistent with previous research on human gut environments. The rumen virome was dominated by ss DNA viruses, mainly Microviridae, Circoviridae, and unclassified ss DNA viruses. Currently, we are applying ecological theory to understand the ecological role of viruses within the gut environment in controlling bacterial diversity and maintaining ecosystem function. Improving the understanding of viral-bacterial dynamics and the impact on metabolic profiles remains important, not only for cattle health, productivity, and feed efficiency, but these models also have the potential to elicit patterns pertinent to ecological theory.
Keywords: metagenome, viral-bacterial interaction, virome