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Open Access Highly Accessed Research article

Metagenomics of rumen bacteriophage from thirteen lactating dairy cattle

Elizabeth M Ross123*, Steve Petrovski12, Peter J Moate1 and Ben J Hayes123

Author Affiliations

1 Department of Environment and Primary Industries, Bundoora, VIC 3086, Australia

2 Dairy Futures Cooperative Research Centre, Bundoora, VIC 3086, Australia

3 La Trobe University, Bundoora, VIC 3086, Australia

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BMC Microbiology 2013, 13:242  doi:10.1186/1471-2180-13-242

Published: 1 November 2013

Abstract

Background

The bovine rumen hosts a diverse and complex community of Eukarya, Bacteria, Archea and viruses (including bacteriophage). The rumen viral population (the rumen virome) has received little attention compared to the rumen microbial population (the rumen microbiome). We used massively parallel sequencing of virus like particles to investigate the diversity of the rumen virome in thirteen lactating Australian Holstein dairy cattle all housed in the same location, 12 of which were sampled on the same day.

Results

Fourteen putative viral sequence fragments over 30 Kbp in length were assembled and annotated. Many of the putative genes in the assembled contigs showed no homology to previously annotated genes, highlighting the large amount of work still required to fully annotate the functions encoded in viral genomes. The abundance of the contig sequences varied widely between animals, even though the cattle were of the same age, stage of lactation and fed the same diets. Additionally the twelve animals which were co-habited shared a number of their dominant viral contigs. We compared the functional characteristics of our bovine viromes with that of other viromes, as well as rumen microbiomes. At the functional level, we found strong similarities between all of the viral samples, which were highly distinct from the rumen microbiome samples.

Conclusions

Our findings suggest a large amount of between animal variation in the bovine rumen virome and that co-habiting animals may have more similar viromes than non co-habited animals. We report the deepest sequencing to date of the rumen virome. This work highlights the enormous amount of novelty and variation present in the rumen virome.

Keywords:
Virome; Rumen; Bacteriophage; Metagenomics