Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier; Kuhn, Jens H.; Roux, Simon; Adriaenssens, Evelien M.; Brister, J. Rodney; Kropinski, Andrew M.; Krupovic, Mart; Lavigne, Rob; Turner, Dann; Sullivan, Matthew B.

doi:10.1038/s41587-019-0100-8

Title: Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

Journal Article · Mon May 06 00:00:00 EDT 2019 · Nature Biotechnology

DOI:https://doi.org/10.1038/s41587-019-0100-8· OSTI ID:1580836

Bin Jang, Ho ^[1]; Bolduc, Benjamin ^[1];

^[1]; Kuhn, Jens H. ^[2];

^[3];

^[4]; Brister, J. Rodney ^[5]; Kropinski, Andrew M. ^[6];

^[7]; Lavigne, Rob ^[8];

^[9];

^[1]

Ohio State Univ., Columbus, OH (United States)
National Inst. of Health, Fort Detrick, Frederick, MD (United States)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
Univ. of Liverpool (United Kingdom); Quadram Inst. Bioscience, Norwich (United Kingdom)
National Inst. of Health, Bethesda, MD (United States)
Univ. of Guelph, ON (Canada)
Inst. Pasteur, Paris (France)
Katholieke Univ. Leuven (Belgium)
Univ. of the West England, Bristol (United Kingdom)

Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a universal, scalable taxonomic framework. We present vConTACT v.2.0, a network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. We report near-identical (96%) replication of existing genus-level viral taxonomy assignments from the International Committee on Taxonomy of Viruses for National Center for Biotechnology Information virus RefSeq. Application of vConTACT v.2.0 to 1,364 previously unclassified viruses deposited in virus RefSeq as reference genomes produced automatic, high-confidence genus assignments for 820 of the 1,364. We applied vConTACT v.2.0 to analyze 15,280 Global Ocean Virome genome fragments and were able to provide taxonomic assignments for 31% of these data, which shows that our algorithm is scalable to very large metagenomic datasets. Finally, our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)

Sponsoring Organization:: US National Institute of Allergy and Infectious Diseases (NIAID; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; HHSN272200700016I; AC52-07NA27344

OSTI ID:: 1580836

Alternate ID(s):: OSTI ID: 1569045

Journal Information:: Nature Biotechnology, Vol. 37, Issue 6; ISSN 1087-0156

Publisher:: Springer NatureCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 252 works

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