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

• Published in: Nature communications 2013-09, Vol.4 (1), p.2420-2420, Article 2420
• Main Authors: Ogilvie, Lesley A., Bowler, Lucas D., Caplin, Jonathan, Dedi, Cinzia, Diston, David, Cheek, Elizabeth, Taylor, Huw, Ebdon, James E., Jones, Brian V.
• Format: Article
• Language: English
• Subjects: 631/326/596/2142; 692/698/2741/2135; Adult; Bacteriophages - genetics; Base Sequence; beta-Lactamases - metabolism; Chromosomes - genetics; Ecosystem; Gastrointestinal Tract - microbiology; Gastrointestinal Tract - virology; Genetic Variation; Genome, Viral - genetics; Host Specificity - genetics; Humanities and Social Sciences; Humans; Male; Metagenome - genetics; Molecular Sequence Data; multidisciplinary; Phylogeny; Proteome - genetics; Science; Science (multidisciplinary)
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms3420

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. Bacteriophages have a significant impact on microbial ecosystems, but additional tools are needed to assess viral communities. Ogilvie et al. present a new strategy to extract viral sequences from metagenomic data sets, and present new insights on their function in the gut ecosystem.