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

Abstract

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.

Authors:
 [1];  [1]; ORCiD logo [1];  [2]; ORCiD logo [3]; ORCiD logo [4];  [5];  [6]; ORCiD logo [7];  [8]; ORCiD logo [9]; ORCiD logo [1]
+ Show Author Affiliations
  1. Ohio State Univ., Columbus, OH (United States)
  2. National Inst. of Health, Fort Detrick, Frederick, MD (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of Liverpool (United Kingdom); Quadram Inst. Bioscience, Norwich (United Kingdom)
  5. National Inst. of Health, Bethesda, MD (United States)
  6. Univ. of Guelph, ON (Canada)
  7. Inst. Pasteur, Paris (France)
  8. Katholieke Univ. Leuven (Belgium)
  9. Univ. of the West England, Bristol (United Kingdom)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org.:
US National Institute of Allergy and Infectious Diseases (NIAID; USDOE Office of Science (SC), Biological and Environmental Research (BER)
OSTI Identifier:
1580836
Alternate Identifier(s):
OSTI ID: 1569045
Grant/Contract Number:  
AC02-05CH11231; HHSN272200700016I; AC52-07NA27344
Resource Type:
Accepted Manuscript
Journal Name:
Nature Biotechnology
Additional Journal Information:
Journal Volume: 37; Journal Issue: 6; Journal ID: ISSN 1087-0156
Publisher:
Springer Nature
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 54 ENVIRONMENTAL SCIENCES; 60 APPLIED LIFE SCIENCES

Citation Formats

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, and Sullivan, Matthew B. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. United States: N. p., 2019. Web. doi:10.1038/s41587-019-0100-8.
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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. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. United States. https://doi.org/10.1038/s41587-019-0100-8
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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, and Sullivan, Matthew B. Mon . "Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks". United States. https://doi.org/10.1038/s41587-019-0100-8. https://www.osti.gov/servlets/purl/1580836.
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@article{osti_1580836,
title = {Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks},
author = {Bin Jang, Ho and Bolduc, Benjamin and Zablocki, Olivier and Kuhn, Jens H. and Roux, Simon and Adriaenssens, Evelien M. and Brister, J. Rodney and Kropinski, Andrew M. and Krupovic, Mart and Lavigne, Rob and Turner, Dann and Sullivan, Matthew B.},
abstractNote = {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.},
doi = {10.1038/s41587-019-0100-8},
journal = {Nature Biotechnology},
number = 6,
volume = 37,
place = {United States},
year = {Mon May 06 00:00:00 EDT 2019},
month = {Mon May 06 00:00:00 EDT 2019}
}
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Publisher's Version of Record
https://doi.org/10.1038/s41587-019-0100-8
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  • DOI: 10.25982/59912.37/1635154
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