# Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Dann Turner, Andrey N Shkoporov, Cédric Lood, Andrew D Millard, Bas E Dutilh, Poliane Alfenas-Zerbini, Leonardo J van Zyl, Ramy K Aziz, Hanna M Oksanen, Minna M Poranen, et al.

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Dann Turner, Andrey N Shkoporov, Cédric Lood, Andrew D Millard, Bas E Dutilh, et al. Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee. Archives of Virology, 2023, 168 (2), pp.74. 10.1007/s00705-022-05694-2. pasteur-03953086

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# Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee

Dann Turner¹ ID · Andrey N. Shkoporov² ID · Cédric Lood³ ID · Andrew D. Millard⁴ · Bas E. Dutilh⁵,⁶ ID ·

Poliane Alfenas-Zerbini⁷ ID · Leonardo J. van Zyl⁸ ID · Ramy K. Aziz⁹,¹⁰ ID · Hanna M. Oksanen¹¹ ID ·

Minna M. Poranen¹¹ · Andrew M. Kropinski¹² · Jakub Barylski¹³ ID · J Rodney Brister¹⁴ ID · Nina Chanisvili¹⁵ ·

Rob A. Edwards¹⁶ ID · François Enault¹⁷ · Annika Gillis¹⁸ · Petar Knezevic¹⁹ · Mart Krupovic²⁰ ID · Ipek Kurtböke²¹ ID ·

Alla Kushkina²²,²³ ID · Rob Lavigne³ ID · Susan Lehman²⁴ ID · Malgorzata Lobocka²⁵ ID · Cristina Moraru²⁶ ID ·

Andrea Moreno Switt²⁷ · Vera Morozova²⁸ · Jesca Nakavuma²⁹ ID · Alejandro Reyes Muñoz³⁰ ID · Jānis Rūmnieks³¹ ID ·

BL Sarkar³² · Matthew B. Sullivan³³ ID · Jumpei Uchiyama³⁴ ID · Johannes Wittmann³⁵ ID · Tong Yigang³⁶ ID ·

Evelien M. Adriaenssens³⁷ ID

© The Author(s) 2023

## Abstract

This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021–March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families *Podoviridae*, *Siphoviridae*, and *Myoviridae* as well as the order *Caudovirales* were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.

## Introduction

Here, we present taxonomic changes submitted to the Bacterial Viruses Subcommittee (BVS) of the International Committee on Taxonomy of Viruses (ICTV) in 2021, assessed and approved at the ICTV Executive Committee meeting (EC53, July 2021), and ratified in 2022 by membership vote [1]. The new taxonomy release (#37) can be found on the ICTV website (https://ictv.global/) and is available for download as two Excel files, the Master Species List (MSL37) and the Virus Metadata Resource (VMR37), which links each species with an exemplar virus genome and accession number.

## Abolishment of the families *Myoviridae*, *Podoviridae*, and *Siphoviridae* and the order *Caudovirales*

The most drastic change in phage classification officialised with this release is the abolishment of the morphology-based families *Myoviridae*, *Podoviridae*, and *Siphoviridae* and the removal of the order *Caudovirales*, which is replaced by the class *Caudoviricetes* to group all tailed bacterial and archaeal viruses with icosahedral capsids and a double-stranded DNA genome. The submission of the taxonomy proposal (2021.001B) followed the publication of a manuscript describing a roadmap for phage taxonomy by the Vice Chair, former Chair, and current Chair of the BVS [2]. This change was necessary, given multiple independent assessments that these morphology-based families are polyphyletic and do not accurately reflect shared evolutionary histories [3–8].

The process of accommodating all members of the three morphology-based families into new, genomically coherent families has begun. Creating new families requires at least two genera, but ideally more, to enable definition of

Handling Editor: Sead Sabanadzovic.

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Evelien M. Adriaenssens
evelien.adriaenssens@quadram.ac.uk

Extended author information available on the last page of the article
demarcation criteria based on core gene sets and phyloge-
netic analysis. While this leaves some taxa as "unclassified"
at the levels of family and order within the class *Caudoviri-
cetes* (summarised in Supplementary Table S1), it allows for
the creation of new genome-based taxa that better reflect the
diversity and genomic relationships of these abundant and
diverse viruses in the future. At the same time, we recognise
the importance of morphological (non-taxonomic) identifi-
ers such as "podovirus", "myovirus", or "siphovirus". These
terms can be used freely to reflect these distinctive features
and retain their historical reference; however, after the 2022
ratification vote, they do not have any formal taxonomic
meaning/significance.

## Change to freeform binomial species name format

In 2020, the ICTV voted to mandate the binomial format for the naming of virus species, where the genus name and a species epithet together form a unique species name, consistent with other taxonomies in biology [9, 10]. This change was applied to 2,532 species of bacterial viruses with input from each study group chair and the members of the BVS through an online consultation. The BVS elected to implement a fully freeform format for binomial naming in which the study groups and taxonomy proposal authors were responsible for the final format of the species names. A brief description of how this binomial format was applied to bacterial viruses follows.

In most cases, the species epithet was directly inherited
from the exemplar virus name. For example, the species
*Escherichia virus T4* was renamed to *Tequatrovirus T4*,
reflecting the name of its exemplar phage T4 (also called
Enterobacteria phage T4, phage T4, or Escherichia phage
T4). Certain study groups and proposal authors elected to
define new species epithets, such as the *Leviviricetes* and
*Crassvirales* Study Groups, who proposed latinised binomi-
als for all species. For example, the model phage MS2 was
assigned to the species *Emesvirus zinderi* [11], the proto-
typical crAssphage was assigned to the species *Carjivirus
communis*, and the first isolated representative of the order
*Crassvirales*, Bacteroides phage crAss001, was assigned to
the species *Kehishuvirus primarius* [12].

The BVS implemented a number of additional ortho-
graphic rules for the creation of new species epithets that
are derived directly from the phage name. Where virus
names consisted only of numerals, the first letter of the genus
names, followed by a “v” (virus) was prepended to the spe-
cies epithet. For example, Pseudomonas phage 14 – 1 is the
exemplar virus of species *Pbunavirus pv141*. The species
epithet can be composed of a mixture of alphanumeric char-
acters in lower and upper case. For future species epithets,

we would request that only lowercase letters are used. Where
existing phage names had a mixture of upper and lower case
letters, these were retained to facilitate recognition of similar
virus names such as P2 and p2 by the bacterial virus research
community.

Where the species epithet consisted of letters only, the
consensus of the BVS was to only permit lowercase letters.
For example, Bacillus phage Deep Blue is the exemplar
virus of the species *Caeruleovirus deepblue*.

## Overview of taxonomy changes

Ninety-five taxonomy proposals were submitted to the BVS Chair and approved by the Executive Committee in 2021. The number of proposals and taxa created precludes detailed individual descriptions, but they are summarised in Supplementary Table S1, and all individual proposals are available from the ICTV website (https://ictv.global/files/proposals/approved?fid=4467#block-teamplus-page-title). Herein, we provide an overview of changes (Table 1) and a brief summary of proposals resulting in the creation of higher-ranking taxa, including new orders and families.

The class *Caudoviricetes* now contains 14 families assigned to four orders. Three of these orders encompass viruses infecting archaea [1, 13]. A further 33 families have been established but not yet been assigned to an order, in addition to 37 subfamilies and 631 genera that have yet to be classified at the rank of family or order (Fig. 1).

## New taxa in the class *Caudoviricetes*

Twenty-two new families were delineated in the class *Caudoviricetes*, 21 of which were newly established (four within the new order *Crassvirales*) and one of which was promoted from the level of subfamily (Table 1). Additional taxa (Fig. 1) were established in the class *Caudoviricetes* by the Archaeal Viruses Subcommittee [1, 13] but are not discussed in this report.

<table><caption>**Table 1** Summary of taxonomic changes for bacterial viruses for Master Species List 37, ratified in 2022. No changes were made at the class, phylum, kingdom, or realm level.</caption><thead><tr><th></th><th>Species</th><th>Genus</th><th>Subfamily</th><th>Family</th><th>Order</th></tr></thead><tbody><tr><td>Abolished</td><td>5</td><td>2</td><td>0</td><td>3</td><td>1</td></tr><tr><td>New</td><td>804</td><td>257</td><td>26</td><td>21</td><td>1</td></tr><tr><td>Moved or promoted</td><td>58</td><td>64</td><td>4</td><td>1</td><td>0</td></tr><tr><td>Renamed</td><td>2736</td><td>1</td><td>0</td><td>0</td><td>0</td></tr><tr><td>Current total</td><td>3601</td><td>1199</td><td>98</td><td>47</td><td>4</td></tr></tbody></table>
<figure><img src="image_3.png" /><figcaption>**Fig. 1** Cladogram depicting the taxonomic structure of the order *Caudoviricetes*. New bacterial and archaeal virus families created in 2021 are highlighted in green or blue, respectively, and those abolished are in red. Numbers of subfamilies, genera, and species are depicted as histograms adjacent to each family. Numbers in parentheses indicate changes recorded from ratified taxonomic proposals. Subfamilies and genera moved from the abolished families *Myoviridae*, *Podoviridae*, and *Siphoviridae* are detailed in Supplementary Table S1.</figcaption></figure>

## Order Crassvirales

The newly established order *Crassvirales*, named after the computer program crAss [14], which was used in the discovery of its founding member, comprises dsDNA tailed bacteriophages with genome sizes ranging from 83 to 106 kbp (Taxonomy Proposal 2021.021B.A.Crassvirales). Very few representatives of the order have been isolated in culture. The majority of species have been described based on analysis of metagenomically assembled genomes (MAGs) extracted from gut-associated, soil, marine, and industrial environments [15–18]. Members of the order *Crassvirales* are especially prevalent in mammalian gut microbiomes and were isolated from, or predicted to infect, bacteria of

the phylum Bacteroidota (more specifically, order Bacteroidales in the mammalian gut) [19–21].

The first representative to be discovered and reported in the literature was crAssphage, a ubiquitous and highly prevalent member of the human gut virome [19, 22]. Metagenomic sequencing reads mapped to the prototypical crAssphage from up to 73% of the human faecal metagenomic datasets, accounting for up to 90% of the reads in virus-like-particle-enriched metagenomes or 22% of the reads of the total metagenomes in extreme cases. With other members of the order included, these viruses are detectable in 98% of faecal viromes from Western cohorts and in 77% of human faecal viromes worldwide. In 8% of cases, crAss-like phages accounted for > 50% of the
virome, making this order the most abundant group of viruses of the human virome [16].

The current genome-based taxonomy of the order *Crassvirales* includes four families (*Intestiviridae*, *Crevaviridae*, *Suoliviridae*, and *Steigviridae*), 11 subfamilies, 42 genera, and 73 species. Cultured representatives only exist for the families *Intestiviridae* (species *Jahgtovirus secundus* represented by Bacteroides phage crAss002) and *Steigviridae* (species *Kehishuvirus primarius* represented by Bacteroides phage crAss001, *Wulfhauvirus bangladeshii* by Bacteroides phages DAC15 and DAC17, and *Akihdevirus balticus* by Cellulophaga phage phi14:2). *Carjivirus communis*, the species comprising the prototypical crAssphage, currently remains without cultured isolates.

## Family Peduoviridae

The family *Peduoviridae* is the formalisation of P2-like phages consisting of tailed, non-enveloped viruses that contain a set of six orthologous core genes. This group of viruses was previously a subfamily (*Peduovirinae*) in the abolished family *Myoviridae* but warranted elevation to family status when the morphology-based classification of viruses was abolished and genomic analysis revealed that the diversity among members of the *Peduovirinae* (created in 2011; Taxonomy Proposal 2009.012a-qB) is similar to that of other recently defined families in the class *Caudoviricetes*. The family includes arguably the best-studied example of a class of temperate phage commonly found in genomes of Gram-negative bacteria, P2 (isolated in 1951 by Giuseppe Bertani [23]), after which the family is named.

## Family Mesyanzhinovviridae

The family *Mesyanzhinovviridae* is named in honour of the late Vadim V. Mesyanzhinov (Shemyakin-Ovchinnikov Institute Moscow). The family encompasses seven genera comprising temperate and lytic siphoviruses infecting strains of the eubacterial genera *Bordetella*, *Pseudomonas*, and *Xanthomonas*. It consists of two subfamilies – *Bradleyvirinae*, named for David Edward Bradley, known for his research into the ultrastructure of bacteriophages (genera: *Abidjanvirus*, *Bosavirus*, *Xooduovirus*, and *Epaquintavirus*) and *Rabinowitzvirinae*, named for Genia Rabinowitz, one of the first scientists to study bacteriophages of *Bacillus pyocyaneus* sp. (genera: *Vojvodinavirus* and *Yuavirus*) – and the orphan genus *Keylargovirus*.

## Families Straboviridae and Kyanoviridae

The family *Straboviridae* is named after the Greek philosopher Strabo. The new family encompasses the previous “T4-like” phages classified within the abolished family

*Myoviridae*. The family *Straboviridae* now consists of 35 genera, with 11 newly created genera (genera: *Kagamiyamavirus*, *Angelvirus*, *Bragavirus*, *Mosugukvirus*, *Mylasvirus*, *Roskildevirus*, *Jiangsuvirus*, *Chrysonvirus*, *Cinqassovirus*, *Gualtarvirus*, and *Carettavirus*). There are 21 genera within the subfamilies *Tevenvirinae* (genera: *Dhakavirus*, *Gaprivervirus*, *Gelderlandvirus*, *Jiaodavirus*, *Kagamiyamavirus*, *Kanagawavirus*, *Karamvirus*, *Moonvirus*, *Mosigvirus*, *Mosugukvirus*, *Roskildevirus*, *Tegunavirus*, *Tequatrovirus*, and *Winklervirus*), *Emmerichvirinae* (genera: *Ishigurovirus* and *Ceceduovirus*), and *Twarogvirinae* (genera: *Lasallevirus*, *Hadassahvirus*, *Acajnonavirus*, and *Zedzedvirus*), with a further 14 floating genera (*Angelvirus*, *Biquartavirus*, *Bragavirus*, *Carettavirus*, *Chrysonvirus*, *Cinqassovirus*, *Gualtarvirus*, *Jiangsuvirus*, *Krischvirus*, *Mylasvirus*, *Pseudotevenvirus*, *Schizotequatrovirus*, *Slopevirus*, and *Tulanevirus*). The genera *Schizotequatrovirus*, *Slopevirus*, *Pseudotevenvirus*, and *Krischvirus* have been removed from the subfamily *Tevenvirinae*, as the members of these genera are not monophyletic with other members of the subfamily.

The family *Kyanoviridae* is named after the ancient Greek word *Kyanos* for “cyan/dark blue”. The family includes “T4-like” phages of the myovirus morphotype, with all representatives to date infecting cyanobacteria. While related to members of the *Straboviridae*, they are distant relatives. As such, and to be consistent with other viral families, they have been separated into a family, as they form a monophyletic group. The relationship between *Straboviridae*, *Kyanoviridae*, and other families at higher taxonomic levels has yet to be resolved. Currently there are no subfamilies, and the family consists of 26 genera previously of the abolished *Myoviridae* (*Cymopoleiavirus*, *Charybdisvirus*, *Anaposvirus*, *Nodensvirus*, *Vellamovirus*, *Kanaloavirus*, *Bellamyvirus*, *Salacisavirus*, *Mazuvirus*, *Atlauavirus*, *Libanvirus*, *Ahtivirus*, *Namakavirus*, *Pontusvirus*, *Ronodorvirus*, *Leucotheavirus*, *Thetisvirus*, *Thaumasvirus*, *Tefnutvirus*, *Neptunevirus*, *Palaemonvirus*, *Nerrivikvirus*, *Brizovirus*, *Nereusvirus*, *Acionnavirus*, and *Biquartavirus*) and 20 new genera (*Sedonavirus*, *Gibbetvirus*, *Chalconvirus*, *Potamoivirus*, *Lipsvirus*, *Lowelvirus*, *Makelovirus*, *Haifavirus*, *Nilusvirus*, *Sokavirus*, *Macariavirus*, *Greenvirus*, *Ormenosvirus*, *Shandvirus*, *Emcearvirus*, *Galenevirus*, *Glaucusvirus*, *Alisovirus*, *Neritesvirus*, and *Bristolvirus*).

## Family Naomviridae

The family *Naomviridae* consists of the single genus *Noahvirus*. The etymology of the family name comes from the Hebrew meaning of Naomi, “pleasant one/good one”. Current members of the genus *Noahvirus* have the defining characteristic of replacing deoxythymidine with deoxyuridine within their genomic DNA [24].
## Family Casjensviridae

The family *Casjensviridae*, named in honour of Sherwood R. Casjens (University of Utah), comprises the four existing genera (*Ahduovirus*, *Chivirus*, *Nazgulvirus* and *Sano-virus*) and 20 new genera (*Broinstvirus*, *Cenphatecvirus*, *Dunedinvirus*, *Enchivirus*, *Fengtaivirus*, *Gediminasvirus*, *Gwanakrovirus*, *Jacunavirus*, *Kokobelvirus*, *Lavrentiev-virus*, *Maxdohrnvirus*, *Newforgelanevirus*, *Phobosvirus*, *Redjacvirus*, *Salvovirus*, *Seodaemunguvirus*, *Sharonstreet-virus*, *Yonseivirus*, and *Zhonglingvirus*) of flagellotrophic siphoviruses, including Salmonella phage Chi (assigned to the species *Chivirus chi*) [25].

## Family Vilmaviridae

The family *Vilmaviridae* was named after clusters V, L, and M, defined in the Actinobacteriophage Database [26]. The family is composed of two subfamilies, *Lclasvirinae* (genera: *Bromdenvirus*, *Bronvirus*, *Faithunavirus*, and *Lumosvirus*) and *Mclasvirinae* (genera: *Bongovirus* and *Reyvirus*) and two unassigned genera, *Kumaovirus* and *Wildcatvirus*. The L and M cluster viruses are all temperate siphoviruses, while those belonging to cluster V are strictly lytic *Mycobacterium* siphophages.

## Family Orlajensenviridae

The family *Orlajensenviridae* formalises the classification of the cluster EE *Microbacterium* phages defined in the Actinobacteriophage Database [26]. The family is composed of a single subfamily, *Pelczarvirinae*, named after Michael Joseph Pelczar, which includes three genera: *Paopuvirus*, *Bonaevitaevirus*, and *Efekovirus*, which share 20 orthologous core genes encoding structural, morphogenesis, and DNA-binding proteins. The family is named after Sigurd Ola-Jensen, who was responsible for the initial isolation and taxonomy of the bacterial genus *Microbacterium*.

## Bacterial viruses infecting members of the bacterial class Flavobacteriia are classified within nine families

Nine new families were established, based on comparative and phylogenetic analysis of isolated bacteriophages infecting members of the bacterial class Flavobacteriia and supported by complete coding sequences from metagenomes. Each of the families forms a monophyletic group in VirClust [27] and VICTOR [28], and their members share at least eight core genes [28]. Members of these families

infect bacterial hosts of the genera *Polaribacter*, *Tenacibaculum*, *Cellulophaga*, *Winogradskyella*, and *Olleya*.

Two families are named after the islands Helgoland and Dune of the Helgoland Archipelago in the North Sea, where many of these bacterial viruses were isolated: *Helgolandviridae*, which contains a single genus (*Leefvirus*), and *Duneviridae*, which contains three genera (*Ingelinevirus*, *Labanvirus* and *Unahavirus*). The family *Forsetiviridae* is named after the god Forseti, associated with the island Hegoland in Nordic mythology, and consists of a single genus, *Freyavirus*. Derived from the Latin word *pervagus*, translated as “widely roaming”, the family *Pervagoviridae* is composed of a single genus, *Callevirus*. *Pachyviridae*, named after the Greek word *pakhús* for “thick”, consists of three genera (*Baltivirus*, *Bacelvirus*, and *Gundelvirus*). *Molycolviridae* is named after the two species in the genus *Mollyvirus*: *Mollyvirus molly* and *Mollyvirus colly*. Three genera (*Nekkelsvirus*, *Cebadecemvirus*, and *Cellubavirus*) are classified within the family *Assiduviridae*, named after the Latin word *assiduous*, meaning “constant” or “regular”. The family *Aggregaviridae*, so named because the host *Olleya* sp. are commonly found on aggregates, consists of a single genus, *Harrekavirus*. Lastly, the family *Winoviridae* is named after the host genus *Winogradskyella* and contains two genera, *Peternellavirus* and *Pippivirus*.

## Family Zierdtviridae

The family *Zierdtviridae*, named after Charles Henry Zierdt, contains two subfamilies: *Emilbogenvirinae* (genera: *Sukkupivirus*, *Kablunavirus*, *Foxborovirus*, *Pleakleyvirus*, *Sky-sandvirus*, and *Gruunavirus*) and *Toshachvirinae* (genera: *Chunghsingvirus* and *Ceetrepovirus*), comprising lytic *Gordonia* phages from cluster CR and *Corynebacterium* phages of cluster EN defined in the Actinobacteriophage Database [26]. The subfamilies were named after Sheila Toshach and Emil Bogen. Members of the family share a set of 18 core genes.

## Conclusions and future directions

The past year has seen substantial changes in the taxonomy of bacterial viruses, as the BVS and ICTV move towards a more coherent and unified system of virus classification based on genome-level relationships. For bacterial viruses, a roadmap and guidance for genomic classification have been published with recommendations for analysis of the genomes of these diverse and ubiquitous viruses [2, 29, 30]. The abolishment of the order *Caudovirales* and the families *Myoviridae*, *Siphoviridae*, and *Podoviridae* has resulted in a significant number of floating subfamilies and genera. To resolve this, concerted efforts by the BVS and the wider
community are required to establish new taxa at the ranks of family and order that accurately reflect the evolutionary relationships of these viruses. With more research, greater coverage of viral diversity, and the development of new and more-sensitive approaches for sequence analysis, we are confident that robust consensus approaches for the delineation of higher taxa will emerge.

The creation of the order *Crassvirales* and nine families of viruses infecting members of the bacterial class Flavobacteriia serves to illustrate the significance of virome datasets for establishing demarcation criteria for taxonomic classification. The inclusion of viruses identified from metagenomic data is essential to capture the true diversity of bacterial viruses and will undoubtedly lead to the expansion of existing taxa and the creation of new ones in the future. However, for inclusion within the taxonomic framework, it is necessary to incorporate appropriate checks to demonstrate that such sequences represent the complete coding region of the genome [31].

The classification of bacterial viruses unquestionably relies upon the combined efforts of the research community, and the past year has seen increasing numbers of proposals submitted from outside the BVS and its study groups. We strongly encourage such initiatives. Interested researchers can always contact the BVS and study groups for information, consultation, and engagement with the taxonomic framework. While metagenomic virus discovery efforts continue to uncover and catalogue the diversity of the virosphere, taxonomic classification will inevitably lag behind the submission of new genome sequences to databases. We hope that through the engagement of the wider community and the continued development of new tools and approaches for sequence analysis, this gap will decrease substantially in the near future.

**Supplementary Information** The online version contains supplementary material available at https://doi.org/10.1007/s00705-022-05694-2.

**Acknowledgements** We would like to acknowledge the assistance provided by colleagues at NCBI, in particular Igor Tolstoy.

**Author contribution** All authors contributed to the creation or assessment of taxonomy proposals. DT and EMA wrote the manuscript with input from AMK, ANS, ADM, BED, CL, HMO, LZ, MMP, PA-Z, RAE, and RKA. All authors evaluated and approved the final version.

**Funding** B.E.D. was supported by the European Research Council (ERC) Consolidator Grant 865694: DiversiPHI, the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860, the Alexander von Humboldt Foundation in the context of an Alexander von Humboldt Professorship funded by the German Federal Ministry of Education and Research, and the European Union's Horizon 2020 Research and Innovation Program, under the Marie Skłodowska-Curie Actions Innovative Training Networks grant agreement no. 955974 (VIROINF). Work by J.R.B. was supported by the National Center for Biotechnology Information of the National Library of Medicine (NLM), National Institutes of Health. R.A.E was supported by an

award from the National Institute of Diabetes and Digestive and Kidney Diseases of the National Institute of Health RC2DK116713 and an award from the Australian Research Council, DP220102915. R.L. is supported by the research grant PHAGEFORCE from the KU Leuven. C.L. is supported by the Research Foundation - Flanders (FWO Grant 12D8623N) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy - EXC 2051 - Project-ID 390713860. V.M. is supported by the Russian state-funded project For ICBFM SB RAS, Grant 121031300043-8. H.M.O. was supported by the University of Helsinki and Academy of Finland by funding for FINStruct and Instruct Centre Finland, Instruct-ERIC. M.M.P. acknowledges funding from the Sigrid Jusélius Foundation and the Academy of Finland (grant 331627). A.N.S is supported by a Wellcome Trust Research Career Development Fellowship [220646/Z/20/Z] and the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (Grant agreement No 101001684). E.M.A. gratefully acknowledges funding by the Bio-technology and Biological Sciences Research Council (BBSRC); this research was funded by the BBSRC Institute Strategic Programme Gut Microbes and Health BB/R012490/1 and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/000PR10356.

## Declarations

**Conflict of interest** All authors are current members of the Bacterial Viruses Subcommittee and/or Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV).

**Open Access** This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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## Authors and Affiliations

Dann Turner¹ ID • Andrey N. Shkoporov² ID • Cédric Lood³ ID • Andrew D. Millard⁴ • Bas E. Dutilh⁵,⁶ ID •

Poliane Alfenas-Zerbini⁷ ID • Leonardo J. van Zyl⁸ ID • Ramy K. Aziz⁹,¹⁰ ID • Hanna M. Oksanen¹¹ ID •

Minna M. Poranen¹¹ • Andrew M. Kropinski¹² • Jakub Barylski¹³ ID • J Rodney Brister¹⁴ ID • Nina Chanisvili¹⁵ •

Rob A. Edwards¹⁶ ID • François Enault¹⁷ • Annika Gillis¹⁸ • Petar Knezevic¹⁹ • Mart Krupovic²⁰ ID • Ipek Kurtböke²¹ ID •

Alla Kushkina²²,²³ ID • Rob Lavigne³ ID • Susan Lehman²⁴ ID • Malgorzata Lobocka²⁵ ID • Cristina Moraru²⁶ ID •

Andrea Moreno Switt²⁷ • Vera Morozova²⁸ • Jesca Nakavuma²⁹ ID • Alejandro Reyes Muñoz³⁰ ID • Jānis Rūmnieks³¹ ID •

BL Sarkar³² • Matthew B. Sullivan³³ ID • Jumpei Uchiyama³⁴ ID • Johannes Wittmann³⁵ ID • Tong Yigang³⁶ ID •

Evelien M. Adriaenssens³⁷ ID
Dann Turner
dann2.turner@uwe.ac.uk

Andrey N. Shkoporov
andrey.shkoporov@ucc.ie

Cédric Lood
cedric.lood@kuleuven.be

Andrew D. Millard
adm39@leicester.ac.uk

Bas E. Dutilh
bedutilh@gmail.com

Poliane Alfenas-Zerbini
palfenas@ufv.br

Leonardo J. van Zyl
vanzyllj@gmail.com

Ramy K. Aziz
raziz1@gmail.com

Hanna M. Oksanen
Hanna.oksanen@helsinki.fi

Minna M. Poranen
Minna.poranen@helsinki.fi

Andrew M. Kropinski
phage.canada@gmail.com

Jakub Barylski
jakub.barylski@gmail.com

J Rodney Brister
jamesbr@ncbi.nlm.nih.gov

Nina Chanisvili
Nina.chanishvili@gmail.com

Rob A. Edwards
robert.edwards@flinders.edu.au

François Enault
François.enault@univ-bpclermont.fr

Annika Gillis
annika.gillis@gmail.com

Petar Knezevic
petar.knezevic@dbe.uns.ac.rs

Mart Krupovic
mart.krupovic@gmail.com

Ipek Kurtböke
IKurtbok@usc.edu.au

Alla Kushkina
a.kushkina@gmail.com

Rob Lavigne
rob.lavigne@kuleuven.be

Susan Lehman
susan.lehman@fda.hhs.gov

Malgorzata Lobocka
lobocka@ibb.waw.pl

Cristina Moraru
liliana.cristina.moraru@uol.de

Andrea Moreno Switt
andrea.moreno@uc.cl

Vera Morozova
Vera_morozova@ngs.ru

Jesca Nakavuma
jesca.nakavuma@gmail.com

Alejandro Reyes Muñoz
a.reyes@uniandes.edu.co

Jānis Rūmnieks
j.rumnieks@biomed.lu.lv

BL Sarkar
bl_sarkar@hotmail.com

Matthew B. Sullivan
mbsulli@gmail.com

Jumpei Uchiyama
uchiyama@okayama-u.ac.jp

Johannes Wittmann
jow12@dsmz.de

Tong Yigang
tong.yigang@gmail.com

1 School of Applied Sciences, College of Health, Science and Society, University of the West of England, Bristol BS16 1QY, UK

2 Department of Medicine and APC Microbiome Ireland, School of Microbiology, University College Cork, Cork, Ireland

3 Department of Biosystems, Faculty of Bioscience Engineering, KU, Leuven, Belgium

4 Department of Genetics and Genome Biology, University of Leicester, University Road, Leicester, UK

5 Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich-Schiller-University Jena, 07743 Jena, Germany

6 Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Padualaan 8, Utrecht 3584 CH, The Netherlands

7 Departamento de Microbiologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil

8 Institute for Microbial Biotechnology and Metagenomics (IMBM), Department of Biotechnology, University of the Western Cape, 7535 Bellville, Cape Town, South Africa

9 Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, 11562 Cairo, Egypt

10 Egypt/ and Children's Cancer Hospital, 57357, 11617 Cairo, Egypt

11 Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, 00014 Helsinki, Finland

12 Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada

13 Department of Molecular Virology, Adam Mickiewicz University in Poznan, Poznan, Poland
14 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

15 The Eliava Institute of Bacteriophage, Microbiology and Virology, Tbilisi, Georgia

16 Flinders Accelerator for Microbiome Exploration, Adelaide, Australia

17 Université Clermont Auvergne, CNRS, LMGE, Clermont-Ferrand, France

18 Laboratory of Food and Environmental Microbiology, Université Catholique de Louvain, Croix du Sud 2, L7.05.12, 1348 Louvain-la-Neuve, Belgium

19 PK Lab, Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 3, Novi Sad, Serbia

20 Archaeal Virology Unit, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris 75015, France

21 School of Science, Technology and Engineering, University of the Sunshine Coast, 4558 Maroochydore, BC, QLD, Australia

22 Department of Bacteriophage molecular genetics, D.K.Zabolotny Institute of microbiology and virology, NAS of Ukraine, 154 Acad. Zabolotnoho str, 03143 Kyiv, Ukraine

23 Department of Bacterial molecular genetics, Faculty of biology, University of Gdansk, Wita Stwosza 59, 80-308 Gdansk, Poland

24 Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA

25 Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland

26 Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany

27 Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas y Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile

28 Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, Russia

29 College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda

30 Max Planck Tandem Group in Computational Biology, Departamento de Ciencias Biológicas, Universidad de los Andes, 111711 Bogotá, Colombia

31 Latvian Biomedical Research and Study Center, 1067 Riga, Latvia

32 ICMR-National Institute of Cholera and Enteric Diseases (NICED), Kolkata, India

33 Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, Ohio State University, Columbus, OH 43210, USA

34 Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University, 1-1-1, Tsushima-naka, Kita-ku, Okayama 7008530, Japan

35 Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures GmbH, Inhoffenstr. 7B, 38124 Braunschweig, Germany

36 College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China

37 Quadram Institute Bioscience, Rosalind Franklin Road, Norwich Research Park, Norwich NR4 7UQ, UK