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

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...

Full description

Saved in:
Bibliographic Details
Published in:Nature biotechnology Vol. 37; no. 6; pp. 632 - 639
Main Authors: 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
Format: Journal Article
Language:English
Published: United States Nature Publishing Group 01.06.2019
Subjects:
Algorithms
Automation
Bacteriophages - genetics
Biotechnology
Classification
Cluster analysis
Clustering
Gene Regulatory Networks - genetics
Genome, Viral - genetics
Genomes
Metagenome - genetics
Metagenomics
Microbiomes
Phylogeny
Prokaryotic Cells - virology
Taxonomy
Viruses
Viruses - classification
Viruses - genetics
ISSN:1087-0156, 1546-1696, 1546-1696
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary: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. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification.
Bibliography:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
content type line 14
content type line 23
ISSN:1087-0156
1546-1696
1546-1696
DOI:10.1038/s41587-019-0100-8