In the intricate world of microbiology, the classification and understanding of viruses that affect prokaryotic cells—archaea and bacteria—remains a significant scientific challenge. A recent breakthrough published in ‘Nature Biotechnology’ has cast a bright light on this somewhat shadowy field. A team of researchers led by the Department of Microbiology at Ohio State University has unveiled vConTACT v.2.0, a powerful network-based application crafted to decipher the taxonomic standing of uncultivated prokaryotic viruses through genome gene-sharing networks (DOI: 10.1038/s41587-019-0100-8).
Understanding the Innovation: vConTACT v.2.0
Viruses that target prokaryotes, commonly known as phages, play an essential role in shaping microbial communities, driving evolution, and even impacting ecosystem functions. However, cataloging these viruses has historically been hindered by the absence of a comprehensive and scalable taxonomic framework.
The newly developed vConTACT v.2.0 stakes its claim as a solution to this problem. It leverages whole genome gene-sharing profiles and integrates both distance-based hierarchical clustering and confidence scores to render accurate taxonomic predictions. The application represents an evolution from previous versions and offers a more streamlined and automated approach to phage taxonomy.
Near-Identical Replication and High-Confidence Assignments
Remarkably, vConTACT v.2.0 demonstrated near-identical replication of existing genus-level viral taxonomy assignments by the International Committee on Taxonomy of Viruses (ICTV) for the National Center for Biotechnology Information (NCBI) virus RefSeq database—with an impressive 96% accuracy. When applied to 1,364 unclassified viruses deposited in virus RefSeq, the tool automatically produced high-confidence genus assignments for 60% of these viruses. This notable success reveals vConTACT v.2.0 as a potentially indispensable asset within the virology community.
Scaling the Tool for Global Use: The Ocean Virome Project
The real test for any large-scale analytical tool is its ability to maintain accuracy and efficiency when dealing with enormous datasets. vConTACT v.2.0 was put through its paces by being applied to 15,280 genome fragments from the Global Ocean Virome, an extensive collection of metagenomic datasets. Astonishingly, it provided taxonomic assignments for 31% of these data, showcasing both the tool’s scalability and durability when faced with vast, real-world biological information.
Leads of the Innovation: The Ohio State University Microbiology Team
The team, captained by Matthew B. Sullivan from the Department of Microbiology and Civil, Environmental, and Geodetic Engineering at Ohio State University, has demonstrated a keen commitment to advancing our understanding of viral taxonomy. Their work is underpinned by collaborative efforts with several international researchers, highlighting the project’s global scientific impact.
Supporting and Funding the Taxonomic Tool
Research of this magnitude is reliant on robust backing and funding. Sullivan’s team’s efforts were buoyed by support from the National Institutes of Health, United States Department of Energy Joint Genome Institute, and the Biotechnology and Biological Sciences Research Council of the United Kingdom. These partnerships ensure the continual development of such valuable tools.
References for Further Exploration
1. Ho, B. J., Bolduc, B., Zablocki, O., Kuhn, J. H., Roux, S., Adriaenssens, E. M., … & Sullivan, M. B. (2019). Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nature Biotechnology, 37(6), 632-639. DOI: 10.1038/s41587-019-0100-8
2. Roux, S., Brum, J. R., Dutilh, B. E., Sunagawa, S., Duhaime, M. B., Loy, A., … & Sullivan, M. B. (2016). Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses. Nature, 537(7622), 689-693. DOI: 10.1038/nature19366
3. Koonin, E. V., & Dolja, V. V. (2013). A virocentric perspective on the evolution of life. Current Opinion in Virology, 3(5), 546-557. DOI: 10.1016/j.coviro.2013.06.008
4. Paez-Espino, D., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Thomas, A. D., Huntemann, M., Mikhailova, N., … & Kyrpides, N. C. (2017). Uncovering Earth’s virome. Nature, 536(7617), 425-430. DOI: 10.1038/nature19094
5. Adriaenssens, E. M., & Brister, J. R. (2017). How to name and classify your phage: An informal guide. Viruses, 9(4), 70. DOI: 10.3390/v9040070
Keywords
1. Prokaryotic Virus Taxonomy
2. vConTACT v2.0
3. Archaeal Bacterial Viruses
4. Metagenomics
5. Phage Classification Tool
Closing Remarks:
The development of vConTACT v.2.0 heralds a new era in viral taxonomy, particularly for the uncultivated prokaryotic viruses that elude traditional study. By offering a rigorous, automated, and scalable methodology, it paves the way for deeper understanding and exploration of the vast viral communities that populate diverse environments. This innovative tool not only heightens our scientific comprehension but also bolsters the fundamental frameworks upon which microbial ecology and evolution are understood.