Roux, S. et al. Ecogenomics and potential biogeochemical impacts of worldwide ample ocean viruses. Nature 537, 689–693 (2016).
Google Scholar
Guidi, L. et al. Plankton networks driving carbon export within the oligotrophic ocean. Nature 532, 465–470 (2016).
Google Scholar
Zimmerman, A. E. et al. Metabolic and biogeochemical penalties of viral an infection in aquatic ecosystems. Nat. Rev. Microbiol. (2020).
Google Scholar
Emerson, J. B. et al. Host-linked soil viral ecology alongside a permafrost thaw gradient. Nat. Microbiol. 3, 870–880 (2018).
Google Scholar
Jansson, J. Ok. & Wu, R. Soil viral range, ecology and local weather change. Nat. Rev. Microbiol. 21, 296–311 (2023).
Google Scholar
Koskella, B. & Taylor, T. B. Multifaceted impacts of bacteriophages within the plant microbiome. Annu. Rev. Phytopathol. 56, 361–380 (2018).
Google Scholar
Yan, M. et al. Interrogating the viral darkish matter of the rumen ecosystem with a world virome database. Nat. Commun. 14, 5254 (2023).
Google Scholar
Yan, M. & Yu, Z. Viruses contribute to microbial diversification within the rumen ecosystem and are related to sure animal manufacturing traits. Microbiome 12, 82 (2024).
Google Scholar
Shkoporov, A. N. & Hill, C. Bacteriophages of the human intestine: the “recognized unknown” of the microbiome. Cell Host Microbe 25, 195–209 (2019).
Google Scholar
Shkoporov, A. N., Turkington, C. J. & Hill, C. Mutualistic interaction between bacteriophages and micro organism within the human intestine. Nat. Rev. Microbiol. 20, 737–749 (2022).
Google Scholar
Walker, P. J. et al. Modifications to virus taxonomy and the Statutes ratified by the Worldwide Committee on Taxonomy of Viruses (2020). Arch. Virol. 165, 2737–2748 (2020).
Google Scholar
Walker, P. J. et al. Latest adjustments to virus taxonomy ratified by the Worldwide Committee on Taxonomy of Viruses (2022). Arch. Virol. 167, 2429–2440 (2022).
Google Scholar
Zerbini, F. M. et al. Modifications to virus taxonomy and the ICTV Statutes ratified by the Worldwide Committee on Taxonomy of Viruses (2023). Arch. Virol. 168, 175 (2023).
Google Scholar
Gorbalenya, A. E. et al. The brand new scope of virus taxonomy: partitioning the virosphere into 15 hierarchical ranks. Nat. Microbiol 5, 668–674 (2020).
Google Scholar
Camargo, A. P. et al. IMG/VR v4: an expanded database of uncultivated virus genomes inside a framework of in depth practical, taxonomic, and ecological metadata. Nucleic Acids Res. 51, D733–D743 (2023).
Google Scholar
Roux, S. et al. Minimal Details about an Uncultivated Virus Genome (MIUViG): a neighborhood consensus on requirements and finest practices for describing genome sequences from uncultivated viruses. Nat. Biotechnol. 37, 29–37 (2018).
Google Scholar
Simmonds, P. et al. Consensus assertion: virus taxonomy within the age of metagenomics. Nat. Rev. Microbiol. 15, 161–168 (2017).
Google Scholar
Simmonds, P. et al. 4 rules to determine a common virus taxonomy. PLoS Biol. 21, e3001922 (2023).
Google Scholar
Dutilh, B. E. et al. Perspective on taxonomic classification of uncultivated viruses. Curr. Opin. Virol. 51, 207–215 (2021).
Google Scholar
Koonin, E. V., Senkevich, T. G. & Dolja, V. V. The traditional Virus World and evolution of cells. Biol. Direct 1, 29 (2006).
Google Scholar
Holmes, E. C. What does virus evolution inform us about virus origins? J. Virol. 85, 5247–5251 (2011).
Google Scholar
Koonin, E. V. & Dolja, V. V. Virus World as an evolutionary community of viruses and capsidless egocentric components. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014).
Google Scholar
Moraru, C. VirClust—a device for hierarchical clustering, core protein detection and annotation of (prokaryotic) viruses. Viruses 15, 1007 (2023).
Google Scholar
Aiewsakun, P. & Simmonds, P. The genomic underpinnings of eukaryotic virus taxonomy: making a sequence-based framework for family-level virus classification. Microbiome 6, 38 (2018).
Google Scholar
Pons, J. C. et al. VPF-Class: taxonomic project and host prediction of uncultivated viruses based mostly on viral protein households. Bioinformatics (2021).
Google Scholar
Camargo, A. P. et al. Identification of cell genetic components with geNomad. Nat. Biotechnol. 42, 1303–1312 (2024).
Google Scholar
Moraru, C., Varsani, A. & Kropinski, A. M. VIRIDIC—a novel device to calculate the intergenomic similarities of prokaryote-infecting viruses. Viruses 12, 1268 (2020).
Google Scholar
Bao, Y., Chetvernin, V. & Tatusova, T. Enhancements to pairwise sequence comparability (PASC): a genome-based internet device for virus classification. Arch. Virol. 159, 3293–3304 (2014).
Google Scholar
Tisza, M. J., Belford, A. Ok., Domínguez-Huerta, G., Bolduc, B. & Buck, C. B. Cenote-Taker 2 democratizes virus discovery and sequence annotation. Virus Evol. 7, veaa100 (2021).
Google Scholar
Lima-Mendez, G., Van Helden, J., Toussaint, A. & Leplae, R. Reticulate illustration of evolutionary and practical relationships between phage genomes. Mol. Biol. Evol. 25, 762–777 (2008).
Google Scholar
Bolduc, B. et al. vConTACT: an iVirus device to categorise double-stranded DNA viruses that infect Archaea and Micro organism. PeerJ 5, e3243 (2017).
Google Scholar
Bin Jang, H. et al. Taxonomic project of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632–639 (2019).
Google Scholar
Barylski, J. et al. Evaluation of Spounaviruses as a case examine for the overdue reclassification of tailed phages. Syst. Biol. 69, 110–123 (2020).
Google Scholar
Turner, D. et al. Abolishment of morphology-based taxa and alter to binomial species names: 2022 taxonomy replace of the ICTV bacterial viruses subcommittee. Arch. Virol. 168, 74 (2023).
Google Scholar
Van Dongen, S. Graph clustering by way of a discrete uncoupling course of. SIAM J. Matrix Anal. Appl. 30, 121–141 (2008).
Google Scholar
Gorbalenya, A. E. & Lauber, C. Bioinformatics of virus taxonomy: foundations and instruments for creating sequence-based hierarchical classification. Curr. Opin. Virol. 52, 48–56 (2022).
Google Scholar
Wertheim, J. O., Metal, M. & Sanderson, M. J. Accuracy in near-perfect virus phylogenies. Syst. Biol. 71, 426–438 (2022).
Google Scholar
Meier-Kolthoff, J. P. & Göker, M. VICTOR: genome-based phylogeny and classification of prokaryotic viruses. Bioinformatics 33, 3396–3404 (2017).
Google Scholar
Gregory, A. C. et al. Genomic differentiation amongst wild cyanophages regardless of widespread horizontal gene switch. BMC Genomics 17, 930 (2016).
Google Scholar
Bobay, L. & Ochman, H. Organic species within the viral world. Proc. Natl Acad. Sci. USA 115, 6040–6045 (2018).
Google Scholar
Ndovie, W. et al. Exploration of the genetic panorama of bacterial dsDNA viruses reveals an ANI hole amid in depth mosaicism. mSystems (2025).
Prepare dinner, R. et al. INfrastructure for a PHAge REference Database: identification of large-scale biases within the present assortment of cultured phage genomes. PHAGE 2, 214–223 (2021).
Google Scholar
Nelson, D. Phage taxonomy: we comply with disagree. J. Bacteriol. 186, 7029–7031 (2004).
Google Scholar
Krupovic, M., Quemin, E. R. J., Bamford, D. H., Forterre, P. & Prangishvili, D. Unification of the globally distributed spindle-shaped viruses of the Archaea. J. Virol. 88, 2354–2358 (2014).
Google Scholar
Rokyta, D. R., Burch, C. L., Caudle, S. B. & Wichman, H. A. Horizontal gene switch and the evolution of microvirid coliphage genomes. J. Bacteriol. 188, 1134–1142 (2006).
Google Scholar
Dominguez-Huerta, G. et al. Variety and ecological footprint of International Ocean RNA viruses. Science 376, 1202–1208 (2022).
Google Scholar
Gregory, A. C. et al. Marine DNA viral macro- and microdiversity from Pole to Pole. Cell 177, 1109–1123 (2019).
Google Scholar
Gregory, A. C. et al. The intestine virome database reveals age-dependent patterns of virome range within the human intestine. Cell Host Microbe 28, 724–740 (2020).
Google Scholar
Graham, E. B. et al. A world atlas of soil viruses reveals unexplored biodiversity and potential biogeochemical impacts. Nat. Microbiol. 9, 1873–1883 (2024).
Google Scholar
Nayfach, S. et al. Metagenomic compendium of 189,680 DNA viruses from the human intestine microbiome. Nat. Microbiol 6, 960–970 (2021).
Google Scholar
Shi, M. et al. Redefining the invertebrate RNA virosphere. Nature 540, 539–543 (2016).
Google Scholar
Schulz, F. et al. Big virus range and host interactions by world metagenomics. Nature 578, 432–436 (2020).
Google Scholar
Camarillo-Guerrero, L. F., Almeida, A., Rangel-Pineros, G., Finn, R. D. & Lawley, T. D. Large growth of human intestine bacteriophage range. Cell 184, 1098–1109 (2021).
Google Scholar
Rand, W. M. Goal standards for the analysis of clustering strategies. J. Am. Stat. Assoc. 66, 846–850 (1971).
Google Scholar
Strehl, A. & Ghosh, J. Cluster ensembles—a information reuse framework for combining a number of partitions. J. Mach. Study. Res. 3, 583–617 (2003).
Larralde, M. Pyrodigal: Python bindings and interface to Prodigal, an environment friendly technique for gene prediction in prokaryotes. J. Open Supply Softw. 7, 4296 (2022).
Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation website identification. BMC Bioinf. 11, 119 (2010).
Google Scholar
Virtanen, P. et al. SciPy 1.0: elementary algorithms for scientific computing in Python. Nat. Strategies 17, 261–272 (2020).
Google Scholar
Staudt, C. L., Sazonovs, A. & Meyerhenke, H. NetworKit: a device suite for large-scale complicated community evaluation. Netw. Sci. 4, 508–530 (2016).
Google Scholar
Huerta-Cepas, J., Serra, F. & Bork, P. ETE 3: reconstruction, evaluation, and visualization of phylogenomic knowledge. Mol. Biol. Evol. 33, 1635–1638 (2016).
Google Scholar
Steinegger, M. & Söding, J. MMseqs2 permits delicate protein sequence trying to find the evaluation of large knowledge units. Nat. Biotechnol. 35, 1026–1028 (2017).
Google Scholar
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: bettering the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
Google Scholar
Minh, B. Q. et al. IQ-TREE 2: New fashions and environment friendly strategies for phylogenetic inference within the genomic period. Mol. Biol. Evol. 37, 1530–1534 (2020).
Google Scholar
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. Ok. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: quick mannequin choice for correct phylogenetic estimates. Nat. Strategies 14, 587–589 (2017).
Google Scholar
Letunic, I. & Bork, P. Interactive Tree of Life (iTOL) v6: current updates to the phylogenetic tree show and annotation device. Nucleic Acids Res. 52, W78–W82 (2024).
Google Scholar
Millard, A. et al. taxmyPHAGE: Automated taxonomy of dsDNA phage genomes on the genus and species stage. Phage (New Rochelle) 6, 5–11 (2025).
Google Scholar
Bolduc, B. vConTACT3 database v.220. Zenodo (2023).
Bolduc, B. vConTACT3 database v.223. Zenodo (2024).
Bolduc, B. vConTACT3 database v.223 (software program repository). Bitbucket (2025).
Leave a Reply