A metagenomic study of the rumen virome in domestic caprids
This project sought to investigate the domestic caprid rumen virome by developing a robust viral DNA isolation and enrichment protocol (utilizing membrane filtration, ultra-centrifugation, overnight PEG treatment and nuclease treatment) and using RSD-PCR and high throughput sequencing (HTS) techniques. 3.53% of the reads obtained were analogous to those of viruses denoting Siphoviridae, Myoviridae, Podoviridae, Mimiviridae, Microviridae, Poxviridae, Tectiviridae and Marseillevirus. Most of the sequenced reads from the rumen were similar to those of phages, which are critical in maintaining the rumen microbial populations under its carrying capacity. Though identified in the rumen, most of these viruses have been reported in other environments as well. Improvements in the viral DNA enrichment and isolation protocol are required to obtain data that are more representative of the rumen virome. The 102,130 unknown reads (92.31%) for the goat and 36,241 unknown reads (93.86%) for the sheep obtained may represent novel genomes that need further study.
We thank BecA-ILRI Hub, its staff and that of the University of Nairobi for their support.
Compliance with ethical standards
Funding was provided by the Africa Biosciences Challenge Fund which is financed by The Syngenta Foundation for Sustainable Agriculture, The Bill & Melinda Gates Foundation, The Australian Agency for International Development and The Swedish Ministry for Foreign Affairs through the Swedish International Development Cooperation Agency.
Conflict of interest
Samuel Namonyo, Maina Wagacha, Solomon Maina, Lillian Wambua and Morris Agaba declare that they have no conflict of interest.
All the rules and guidelines in the treatment and handling of the animals used in this study were followed as outlined by the ministry of livestock (Kenya) and the International Livestock Research Institute.
- 5.Berg Miller ME, Yeoman CJ, Chia N, Tringe SG, Angly FE, Edwards RA, Flint HJ, Lamed R, Bayer EA, White BA (2012) Phage–bacteria relationships and CRISPR elements revealed by a metagenomic survey of the rumen microbiome. Environ Microbiol 14(1):207–227. https://doi.org/10.1111/j.1462-2920.2011.02593 CrossRefPubMedGoogle Scholar
- 6.Fernando BR (2012) Metagenomic analysis of microbial communities in the bovine rumen, Ph.D. thesis. Oklahoma State University, StillwaterGoogle Scholar
- 9.Meyer F, Paarmann D, D’Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA (2008) The metagenomics RAST server—a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinform 9:386. https://doi.org/10.1186/1471-2105-9-386 CrossRefGoogle Scholar
- 14.Racaniello VR, Enquist LW (2008) Principles of virology, vol 1. Molecular biology. ASM Press, Washington, DC. ISBN 1-55581-479-4Google Scholar
- 15.Rosseel T (2015) Genome sequencing by random priming methods for viral identification, Ph.D. thesis. Ghent University, GhentGoogle Scholar
- 18.Rondon MR, August PR, Bettermann AD, Brady SF et al (2000) Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 66(6):2541–2547. https://doi.org/10.1128/AEM.66.6.2541-2547.2000 CrossRefPubMedPubMedCentralGoogle Scholar
- 26.Hayward AC (1993) The host of Xanthomonas. In: Swings JG, Civerolo LE (eds) Xanthomonas. Chapman and Hall, London, pp 51–54Google Scholar
- 27.Madigan M, Martinko T, John M (eds) (2005) Brock biology of microorganisms, 11th edn. Prentice Hall, New Jersey, pp 545–572Google Scholar
- 28.Khan N (2009) Acanthamoeba: biology and pathogenesis. Caister Academic Press, Norfolk, p 209Google Scholar
- 29.Leahy SC, Kelly WJ, Altermann E, Ronimus RS, Yeoman CJ et al (2010) The genome sequence of the rumen methanogen Methanobrevibacter ruminantium reveals new possibilities for controlling ruminant methane emissions. PLoS One 5(1):e8926. https://doi.org/10.1371/journal.pone.0008926 CrossRefPubMedPubMedCentralGoogle Scholar