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...
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| Veröffentlicht in: | Nature biotechnology Jg. 37; H. 6; S. 632 - 639 |
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| Hauptverfasser: | , , , , , , , , , , , |
| Format: | Journal Article |
| Sprache: | Englisch |
| Veröffentlicht: |
United States
Nature Publishing Group
01.06.2019
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| ISSN: | 1087-0156, 1546-1696, 1546-1696 |
| Online-Zugang: | Volltext |
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| 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. Our taxonomy tool can be automated and applied to metagenomes from any environment for virus classification. |
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| AbstractList | 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.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. 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.Classification of archaeal and bacterial viruses can be automated with an algorithm that identifies relationships on the basis of shared gene content. 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. |
| Author | Zablocki, Olivier Kropinski, Andrew M Lavigne, Rob Adriaenssens, Evelien M Krupovic, Mart Bin Jang, Ho Turner, Dann Sullivan, Matthew B Brister, J Rodney Bolduc, Benjamin Kuhn, Jens H Roux, Simon |
| Author_xml | – sequence: 1 givenname: Ho surname: Bin Jang fullname: Bin Jang, Ho organization: Department of Microbiology, Ohio State University, Columbus, OH, USA – sequence: 2 givenname: Benjamin surname: Bolduc fullname: Bolduc, Benjamin organization: Department of Microbiology, Ohio State University, Columbus, OH, USA – sequence: 3 givenname: Olivier orcidid: 0000-0001-7561-1373 surname: Zablocki fullname: Zablocki, Olivier organization: Department of Microbiology, Ohio State University, Columbus, OH, USA – sequence: 4 givenname: Jens H surname: Kuhn fullname: Kuhn, Jens H organization: Integrated Research Facility at Fort Detrick, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD, USA – sequence: 5 givenname: Simon orcidid: 0000-0002-5831-5895 surname: Roux fullname: Roux, Simon organization: US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA – sequence: 6 givenname: Evelien M orcidid: 0000-0003-4826-5406 surname: Adriaenssens fullname: Adriaenssens, Evelien M organization: Quadram Institute Bioscience, Norwich Research Park, Norwich, UK – sequence: 7 givenname: J Rodney surname: Brister fullname: Brister, J Rodney organization: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA – sequence: 8 givenname: Andrew M surname: Kropinski fullname: Kropinski, Andrew M organization: Department of Food Science, University of Guelph, Guelph, Ontario, Canada – sequence: 9 givenname: Mart orcidid: 0000-0001-5486-0098 surname: Krupovic fullname: Krupovic, Mart organization: Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Institut Pasteur, Paris, France – sequence: 10 givenname: Rob surname: Lavigne fullname: Lavigne, Rob organization: Laboratory of Gene Technology, Department of Biosystems, Faculty of BioScience Engineering, KU Leuven, Leuven, Belgium – sequence: 11 givenname: Dann orcidid: 0000-0002-0249-4513 surname: Turner fullname: Turner, Dann organization: Centre for Research in Biosciences, Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol, UK – sequence: 12 givenname: Matthew B orcidid: 0000-0001-8398-8234 surname: Sullivan fullname: Sullivan, Matthew B email: sullivan.948@osu.edu, sullivan.948@osu.edu organization: Department of Civil, Environmental and Geodetic Engineering, Ohio State University, Columbus, OH, USA. sullivan.948@osu.edu |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/31061483$$D View this record in MEDLINE/PubMed |
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| Snippet | Microbiomes from every environment contain a myriad of uncultivated archaeal and bacterial viruses, but studying these viruses is hampered by the lack of a... |
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| SubjectTerms | 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 |
| Title | Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks |
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