A genomic strategy to identify archaeal viruses in the rumen

Summary

​Phage therapy is becoming increasingly important as a means of eradicating or controlling microbial populations and has been raised as a potential strategy to reduce methane emissions from ruminants. In this one-year project, the viral metagenome (virome) of the rumen was investigated. Virus particles were successfully purified and concentrated from relatively small volumes of bovine rumen fluid and sufficient quantities of viral DNA obtained to facilitate high-throughput sequencing, without the inclusion of additional amplification steps. Results of sequence analysis indicated that the rumen contains a highly diverse virus population, predominated by double-stranded DNA viruses (tailed bacteriophages of the order Caudovirales), with evidence of some changes occurring in the viral population in relation to the time of feeding. Viral marker genes (terminase large subunit) associated with previously sequenced archaeaphage (including the Siphoviruses, Methanobacterium phage ψM2 and Methanothermobacter phage ψM100) were detected within the virome dataset. Characterisation of the corresponding rumen microbial populations using a 16S rRNA gene approach also indicated the types of methanogens which may be infected or associated with these archaeaphage. Utilising a metagenomic approach has provided an ideal platform for identifying archaeaphage present within the rumen virome and has provided an insight into the advantages of adopting this approach for future studies examining the phage and viral populations of the rumen.
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