Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences

Lesley A. Ogilvie, Lucas D. Bowler, Jonathan Caplin, Cinzia Dedi, David Diston, Elizabeth Cheek, Huw Taylor, James E. Ebdon and Brian V. Jones ()
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Lesley A. Ogilvie: Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton
Lucas D. Bowler: Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton
Jonathan Caplin: School of Environment and Technology, University of Brighton
Cinzia Dedi: Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton
David Diston: School of Environment and Technology, University of Brighton
Elizabeth Cheek: School of Computing, Engineering and Mathematics, University of Brighton
Huw Taylor: School of Environment and Technology, University of Brighton
James E. Ebdon: School of Environment and Technology, University of Brighton
Brian V. Jones: Centre for Biomedical and Health Science Research, School of Pharmacy and Biomolecular Sciences, University of Brighton

Nature Communications, 2013, vol. 4, issue 1, 1-16

Abstract: Abstract Bacterial viruses (bacteriophages) have a key role in shaping the development and functional outputs of host microbiomes. Although metagenomic approaches have greatly expanded our understanding of the prokaryotic virosphere, additional tools are required for the phage-oriented dissection of metagenomic data sets, and host-range affiliation of recovered sequences. Here we demonstrate the application of a genome signature-based approach to interrogate conventional whole-community metagenomes and access subliminal, phylogenetically targeted, phage sequences present within. We describe a portion of the biological dark matter extant in the human gut virome, and bring to light a population of potentially gut-specific Bacteroidales-like phage, poorly represented in existing virus like particle-derived viral metagenomes. These predominantly temperate phage were shown to encode functions of direct relevance to human health in the form of antibiotic resistance genes, and provided evidence for the existence of putative ‘viral-enterotypes’ among this fraction of the human gut virome.

Date: 2013
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DOI: 10.1038/ncomms3420

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