Viromics approaches for the study of viral diversity and ecology in microbiomes

doi:10.1038/s41576-025-00871-w

Review

. 2025 Jul 21.

doi: 10.1038/s41576-025-00871-w. Online ahead of print.

Viromics approaches for the study of viral diversity and ecology in microbiomes

Simon Roux¹, Clement Coclet²

Affiliations

¹ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. sroux@lbl.gov.
² DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

PMID: 40691354
DOI: 10.1038/s41576-025-00871-w

Review

Viromics approaches for the study of viral diversity and ecology in microbiomes

Simon Roux et al. Nat Rev Genet. 2025.

. 2025 Jul 21.

doi: 10.1038/s41576-025-00871-w. Online ahead of print.

Authors

Simon Roux¹, Clement Coclet²

Affiliations

¹ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. sroux@lbl.gov.
² DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

PMID: 40691354
DOI: 10.1038/s41576-025-00871-w

Abstract

Viruses are found across all ecosystems and infect every type of organism on Earth. Traditional culture-based methods have proven insufficient to explore this viral diversity at scale, driving the development of viromics, the sequence-based analysis of uncultivated viruses. Viromics approaches have been particularly useful for studying viruses of microorganisms, which can act as crucial regulators of microbiomes across ecosystems. They have already revealed the broad geographic distribution of viral communities and are progressively uncovering the expansive genetic and functional diversity of the global virome. Moving forward, large-scale viral ecogenomics studies combined with new experimental and computational approaches to identify virus activity and host interactions will enable a more complete characterization of global viral diversity and its effects.

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Conflict of interest statement

Competing interests statement: The authors declare no competing interests.

References

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[1] Koonin, E. V., Kuhn, J. H., Dolja, V. V. & Krupovic, M. Megataxonomy and global ecology of the virosphere. ISME J. 18, wrad042 (2024). - PubMed - PMC

[2] Koonin, E. V., Kuhn, J. H., Dolja, V. V. & Krupovic, M. Megataxonomy and global ecology of the virosphere. ISME J. 18, wrad042 (2024). - PubMed - PMC

[3] Koonin, E. V. et al. Global organization and proposed megataxonomy of the virus world. Microbiol. Mol. Biol. Rev. 84, e00061–19 (2020). This review proposes a global genome-based viral classification framework that integrates both isolate and metagenome-assembled viral genomes. - PubMed - PMC

[4] Koonin, E. V. et al. Global organization and proposed megataxonomy of the virus world. Microbiol. Mol. Biol. Rev. 84, e00061–19 (2020). This review proposes a global genome-based viral classification framework that integrates both isolate and metagenome-assembled viral genomes. - PubMed - PMC

[5] Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007). - PubMed

[6] Suttle, C. A. Marine viruses — major players in the global ecosystem. Nat. Rev. Microbiol. 5, 801–812 (2007). - PubMed

[7] Bratbak, G., Egge, J. K. & Heldal, M. Viral mortality of the marine alga Emiliania huxleyi (Haptophyceae) and termination of algal blooms. Mar. Ecol. Prog. Ser. 93, 39–48 (1993).

[8] Bratbak, G., Egge, J. K. & Heldal, M. Viral mortality of the marine alga Emiliania huxleyi (Haptophyceae) and termination of algal blooms. Mar. Ecol. Prog. Ser. 93, 39–48 (1993).

[9] Coy, S. R., Gann, E. R., Pound, H. L., Short, S. M. & Wilhelm, S. W. Viruses of eukaryotic algae: diversity, methods for detection, and future directions. Viruses 10, 487 (2018). - PubMed - PMC

[10] Coy, S. R., Gann, E. R., Pound, H. L., Short, S. M. & Wilhelm, S. W. Viruses of eukaryotic algae: diversity, methods for detection, and future directions. Viruses 10, 487 (2018). - PubMed - PMC

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Viromics approaches for the study of viral diversity and ecology in microbiomes

Affiliations

Viromics approaches for the study of viral diversity and ecology in microbiomes

Authors

Affiliations

Abstract

Conflict of interest statement

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