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A metagenomic study of the rumen virome in domestic caprids

  • Samuel Namonyo
  • Maina Wagacha
  • Solomon Maina
  • Lillian Wambua
  • Morris Agaba
Brief Report

Abstract

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.

Notes

Acknowledgements

We thank BecA-ILRI Hub, its staff and that of the University of Nairobi for their support.

Compliance with ethical standards

Funding

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.

Ethical approval

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.

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Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2018

Authors and Affiliations

  • Samuel Namonyo
    • 1
    • 2
  • Maina Wagacha
    • 1
  • Solomon Maina
    • 2
  • Lillian Wambua
    • 1
    • 4
  • Morris Agaba
    • 2
    • 3
  1. 1.The University of NairobiNairobiKenya
  2. 2.BecA-ILRI HubNairobiKenya
  3. 3.The Nelson Mandela African Institute of Science and TechnologyArushaTanzania
  4. 4.International Centre for Insect Physiology and EcologyNairobiKenya

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