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. 2021 Mar 18;13(3):506.
doi: 10.3390/v13030506.

A Roadmap for Genome-Based Phage Taxonomy

Dann Turner  1 , Andrew M Kropinski  2   3 , Evelien M Adriaenssens  4
Affiliations

A Roadmap for Genome-Based Phage Taxonomy

Dann Turner et al. Viruses. .

Abstract

Bacteriophage (phage) taxonomy has been in flux since its inception over four decades ago. Genome sequencing has put pressure on the classification system and recent years have seen significant changes to phage taxonomy. Here, we reflect on the state of phage taxonomy and provide a roadmap for the future, including the abolition of the order Caudovirales and the families Myoviridae, Podoviridae, and Siphoviridae. Furthermore, we specify guidelines for the demarcation of species, genus, subfamily and family-level ranks of tailed phage taxonomy.

Keywords: Caudovirales; Myoviridae; Podoviridae; Siphoviridae; demarcation criteria; phage classification; phage taxonomy.

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Conflict of interest statement

All authors are members of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), E.M.A. is the current Chair, D.T. is the current Vice Chair and A.M.K is the previous Chair. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Line drawing of bacteriophage morphotypes, adapted from Ackermann, 2005 [6].
Figure 2
Figure 2
Dendrogram generated by GRAViTy (http://gravity.cvr.gla.ac.uk, accessed on 5 February 2021) for DB-B: Baltimore Group Ib—Prokaryotic and archaeal dsDNA viruses (VMRv34) and annotated using iTOL [16,42]. The inside coloured ring indicates the morphotype and the outside ring the new proposed and ratified families as of 2021. The distance from tip to node, indicated by the scale rings, represents the composite generalised Jaccard distance (0–1) between two genomes calculated based on relatedness of the proteins and the genome organisation, where 0 is identical and 1 is no measurable relation between two genomes. The Jaccard distance of 0.8, unifying the majority of eukaryotic virus families is indicated in blue for illustration purposes. Bootstrap values (0–1) are indicated by branch colour on a greyscale, from light grey (0) to black (1), showing that the majority of branches are well-supported. Bootstrap values were calculated as described by Aiewsakun and Simmonds [16] by random resampling of the protein profile hidden Markov models that form the basis of the protein relatedness score, recomputing the pairwise distance matrix and then recomputing the dendrogram and repeating this 100 times.
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