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.
Highlights
The names Myoviridae, Podoviridae and Siphoviridae were formally accepted by the International Committee on Taxonomy of Viruses (ICTV) in 1981 and
The most pressing issue remains the paraphyly of the tailed phage families, because they make up the majority of isolated and metagenomicallyinferred viruses, illustrated by a dendrogram of hierarchical relations of dsDNA bacterial and archaeal viruses generated by the GRAViTy pipeline (Figure 2, Figure S1) [16,17] and a network-based representation of shared genes generated by vConTACT2 (Figure S2) [15]
The classical morphotype family-level taxonomy has been enormously useful for four decades in advancing our understanding of phage diversity
Summary
Phages have been classified according to their morphology, dating from the time before the existence of PCR, sequencing or many of the molecular methods we know today [1,2,3]. (vConTACT) [14,15], a composite tool combining gene homologies and gene order (GRAViTy) [16,17], a virus domain orthologous groups approach (VDOG) [18] and a concatenated protein phylogeny of members of the order Caudovirales (CCP77) [19] Based on this evidence, the ICTV’s Bacterial and Archaeal Viruses Subcommittee started disentangling the web of overlapping and complementary groups of tailed phages by defining new, genome-based families. Majorgenomes lineagesin ofdatabases presumedrose, novel dsDNAbecame tailed apparent thatalso these three families not based monophyletic and cohesive within a monophages have been inferred andwere isolated on metagenomic/viromic assemblies, phyletic order This paraphyly was illustrated by a number of tools and publications: The including the crAssphage lineage [27,28,29], Lak megaphage [30], and multiple other lineages.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
