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Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee

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Archives of Virology
Taxonomy ofprokaryotic viruses: 2017 update fromtheICTV Bacterial
andArchaeal Viruses Subcommittee
EvelienM.Adriaenssens1 · JohannesWittmann2 · JensH.Kuhn3 · DannTurner4 · MatthewB.Sullivan5 ·
BasE.Dutilh6,7 · HoBinJang5· LeonardoJ.vanZyl8 · JochenKlumpp9 · MalgorzataLobocka10 ·
AndreaI.MorenoSwitt11 · JanisRumnieks12· RobertA.Edwards13 · JumpeiUchiyama14 ·
PolianeAlfenas‑Zerbini15 · NicolaK.Petty16 · AndrewM.Kropinski17 · JakubBarylski18 · AnnikaGillis19 ·
MarthaR.C.Clokie20 · DavidPrangishvili21 · RobLavigne22 · RamyKaramAziz23 · SiobainDuy24 ·
MartKrupovic21 · MinnaM.Poranen25 · PetarKnezevic26 · FrancoisEnault27 · YigangTong28 ·
HannaM.Oksanen25 · J.RodneyBrister29
Received: 1 December 2017 / Accepted: 15 January 2018
© Springer-Verlag GmbH Austria, part of Springer Nature 2018
The prokaryotic virus community is represented at the Inter-
national Committee on Taxonomy of Viruses (ICTV) by the
Bacterial and Archaeal Viruses Subcommittee. Since our
last report [5], the committee composition has changed,
and a large number of taxonomic proposals (TaxoProps)
were submitted to the ICTV Executive Committee (EC) for
1. Changes in subcommittee membership. During the
past year we have lost two members. Dr. Hans-Wolfgang
Ackermann, a life member of the ICTV, the father of cau-
dovirus taxonomy [1] and an electron microscopist extraor-
dinaire [24], lamentably died and will be gravely missed.
In addition, Dr. Jens H. Kuhn, who, in spite of protestations
about not being a genuine phage biologist, proved invaluable
Handling Editor: Sead Sabanadzovic.
Electronic supplementary material The online version of this
article (http s:// /s007 05-018-3723 -z) contains
supplementary material, which is available to authorized users.
* Andrew M. Kropinski
1 Institute ofIntegrative Biology, University ofLiverpool,
LiverpoolL697ZB, UnitedKingdom
2 Leibniz-Institut DSMZ-Deutsche Sammlung
von Mikroorganismen und Zellkulturen GmbH,
38124Braunschweig, Germany
3 Integrated Research Facility atFort Detrick, National
Institute ofAllergy andInfectious Diseases, National
Institutes ofHealth, Fort Detrick, Frederick, MD21702,
4 Faculty ofHealth andApplied Sciences, UWE Bristol,
Frenchay Campus, BristolBS161QY, UnitedKingdom
5 Department ofMicrobiology, The Ohio State University,
Columbus, OH43210, USA
6 Theoretical Biology andBioinformatics, Utrecht University,
Utrecht, TheNetherlands
7 Centre forMolecular andBiomolecular Informatics,
Radboud University Medical Centre, Nijmegen,
8 Department ofBiotechnology, Institute forMicrobial
Biotechnology andMetagenomics (IMBM), University
oftheWestern Cape, Bellville, Cape Town, 7535,
9 Institute ofFood, Nutrition andHealth, ETH Zurich,
8092Zurich, Switzerland
10 Department ofMicrobial Biochemistry, Institute
ofBiochemistry andBiophysics ofthePolish Academy
ofSciences, 02-106, Warsaw, Poland
11 Faculty ofEcology andNatural Resources School,
Universidad Andres Bello, 8370146Santiago, Chile
12 Latvian Biomedical Research andStudy Center,
RigaLV-1067, Latvia
13 Departments ofComputer Science andBiology, San Diego
State University, SanDiego, CA92182, USA
E. M. Adriaenssens etal.
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to our discussions and preparation of TaxoProps and manu-
scripts, resigned from the Subcommittee. Both Hans and
Jens are acknowledged for their significant contributions
to prokaryotic virus taxonomy. Furthermore, a number
of current members have new responsibilities; and, in an
effort to increase the geographical diversity of members,
we appointed representatives from South America, Africa,
and Asia (Table1).
2. Changing the names of prokaryotic virus genera. A
significant number of prokaryotic virus genera have either
unpronounceable names (e.g., Pocjvirus, Rdjlvirus) or incor-
porated numerals (e.g., T4virus, D3112virus). In the first
case, these names contravene The International Code of
Virus Classification and Nomenclature (ICVCN, April 2017)
Rule 3.12, which states “Names for taxa shall be easy to use
and easy to remember. Euphonious names are preferred.”
In the latter case, pronunciation is a problem. For example,
is D3112virus pronounced “Dee+three thousand one hun-
dred and twelve+virus” or “Dee+thirty one+twelve+virus”
or “Dee+three+one+one+two+virus”? In addition, this
nomenclature differs drastically from that for other virus
taxa; and, would be incompatible with a Linnaean system
of nomenclature [13]. We identified all prokaryotic taxon
names that are problematic in the ICTV Master Species
List (http s://talk .ictv onli s/mast er-spec ies-list s/m/
msl/6776 ) and suggested alternative names (Supplementary
data file S1). These changes will be proposed officially at the
next meeting of the ICTV EC in 2018.
3. Re-evaluation of the SPO1-like virus taxonomy.
Over the past two years, members of the subcommittee have
re-evaluated the taxonomy of a subset of myoviruses related
to Bacillus phage SPO1. This group, made up of members
of the subfamily Spounavirinae [10] and several genera of
Bacillus-infecting viruses, was represented as a distinct
Table 1 List of current
subcommittee members who
have new responsibilities (*),
along with new members of the
Name Country Position
Evelien Adriaenssens* United Kingdom Chair, Caudovirales phage study group
Dann Turner United Kingdom Chair, Acinetobacter phage study group
Jakub Barylski* Poland Chair, Bacillus phage study group
Jochen Klumpp* Switzerland Chair, Listeria phage study group
Małgorzata Łobocka Poland Chair, Staphylococcus phage study group
Poliane Alfenas-Zerbini Brazil Member
Ramy Aziz Egypt Member
Andrea Moreno Switt Chile Member
Yigang Tong People’s Republic of China Member
Leonardo van Zyl South Africa Member
Jumpei Uchiyama Japan Member
Nicola K. Petty Australia Member
14 School ofVeterinary Medicine, Azabu University, Fuchinobe
1-7-71, Chuo-ku Sagamihara-shi, Kanagawa252-0206, Japan
15 Laboratory ofIndustrial Microbiology,Instituto de
Biotecnologia Aplicada à Agropecuária, Universidade
Federal de Viçosa, Viçosa, MinasGerais, Brazil
16 The ithree institute, University ofTechnology Sydney,
Sydney, NSW2007, Australia
17 Departments ofFood Science, andPathobiology, University
ofGuelph, 50 Stone Rd E, Guelph, ONN1G2W1, Canada
18 Department ofMolecular Virology, Institute ofExperimental
Biology, Adam Mickiewicz University, Poznan, Poland
19 Laboratory ofFood andEnvironmental Microbiology,
Université Catholique de Louvain, 1348Louvain-la-Neuve,
20 Department ofInfection, Immunity andInflammation,
University ofLeicester, LeicesterLE19HN, UnitedKingdom
21 Unit ofMolecular Biology oftheGene inExtremophiles,
Department ofMicrobiology, Institut Pasteur, 75015Paris,
22 Laboratory ofGene Technology, KU Leuven, 3001Leuven,
23 Department ofMicrobiology andImmunology, Faculty
ofPharmacy, Cairo University, Qasr El-Ainy St,
11562Cairo, Egypt
24 Department ofEcology, Evolution andNatural Resources,
Rutgers University, NewBrunswick, NJ08901, USA
25 Department ofBiosciences, University ofHelsinki, Helsinki,
26 Department ofBiology andEcology, Faculty ofSciences,
University ofNovi Sad, NoviSad, Serbia
27 Université Clermont Auvergne, CNRS, LMGE,
63000Clermont-Ferrand, France
28 Beijing Institute ofMicrobiology andEpidemiology, State
Key Laboratory ofPathogen andBiosecurity, Beijing,
29 National Center forBiotechnology Information, National
Library ofMedicine, National Institutes ofHealth, Bethesda,
MD20894, USA
Taxonomy of prokaryotic viruses: 2017 update from the ICTV Bacterial and Archaeal Viruses Subcommittee
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Table 2 Taxonomy proposals (TaxoProps) proposing new taxa (families, subfamilies, genera, species) submitted to the ICTV Executive Com-
mittee in 2017
*taxon established, **previously known as Tectivirus, ***Number in parenthesis indicates the total number of viral species in this genus
Family Subfamily Genus Type species No. of species
in genus***
Ackermannviridae Aglimvirinae Ag3virus Shigella virus AG3 1 (2)
Ackermannviridae Aglimvirinae Limestonevirus Dickeya virus Limestone 1 (2)
Ackermannviridae Cvivirinae Cba120virus Escherichia virus CBA120 4 (9)
Ackermannviridae Cvivirinae Vi1virus* Salmonella virus ViI (5)
Ackermannviridae unassigned unassigned Erwinia virus Ea2809, Serratia virus MAM1, Ser-
ratia virus IME250, Klebsiella virus 0507KN21 4
Myoviridae* Arvunavirus Arthrobacter virus ArV1 2
Myoviridae* Eah2virus Erwinia virus EaH2 2
Myoviridae* Machinavirus Erwinia virus Machina 1
Myoviridae* Ntreusvirus Salmonella virus SPN3US 1
Myoviridae* Svunavirus Geobacillus virus GBSV1 2
Myoviridae* Ampvirinae Chippewavirus Arthrobacter virus BarretLemon 1
Myoviridae* Ampvirinae Jawnskivirus Arthrobacter virus Jawnski 2
Myoviridae* Ampvirinae Sonnyvirus Arthrobacter virus Sonny 3
Podoviridae* Dfl12virus Dinoroseobacter virus DFL12phi1 1
Podoviridae* Jwalphavirus Achromobacter virus JWAlpha 2
Podoviridae* P22virus* Salmonella virus P22 1 (5)
Podoviridae* Sp58virus Salmonella virus SP058 3
Portogloboviridae Alphaportoglobovirus Sulfolobus alphaportoglobovirus 1 1
Siphoviridae* Anatolevirus Propionibacterium virus Anatole 2
Siphoviridae* Attisvirus Gordonia virus Attis 1
Siphoviridae* Doucettevirus Propionibacterium virus Doucette 4
Siphoviridae* Hk97virus Escherichia virus HK97* 9 (11)
Siphoviridae* Lambdavirus* Escherichia virus Lambda 3 (4)
Siphoviridae* Pfr1virus Propionibacterium virus PFR1 1
Siphoviridae* Tp84virus Geobacillus virus TP84 1
Siphoviridae* Trigintaduovirus Mycobacterium virus 32HC 1
Siphoviridae* Wizardvirus Gordonia virus Wizard 2
Siphoviridae* Chebruvirinae Brujitavirus Mycobacterium virus Brujita (2)
Siphoviridae* Chebruvirinae Che9cvirus* Mycobacterium virus Che9c 1 (2)
Siphoviridae* Dclasvirinae Hawkeyevirus Mycobacterium virus Hawkeye 1
Siphoviridae* Dclasvirinae Plotvirus Mycobacterium virus PLot 1
Siphoviridae* Mccleskeyvirinae Lmd1virus Leuconostoc virus Lmd1 6
Siphoviridae* Mccleskeyvirinae Una4virus Leuconostoc virus 1A4 6
Siphoviridae* Nclasvirinae Buttersvirus Mycobacterium virus Butters 2
Siphoviridae* Nclasvirinae Charlievirus Mycobacterium virus Charlie 2 (3)
Siphoviridae* Nclasvirinae Redivirus Mycobacterium virus Redi 3 (4)
Siphoviridae* Nymbaxtervirinae Baxtervirus Gordonia virus BaxterFox 2
Siphoviridae* Nymbaxtervirinae Nymphadoravirus Gordonia virus Nymphadora 3
Cystoviridae* Cystovirus* Pseudomonas virus phi6 6 (7)
Tectiviridae* Alphatectivirus** Pseudomonas virus PRD1 1 (2)
Tectiviridae* Betatectivirus Bacillus virus Bam35 2 (4)
E. M. Adriaenssens etal.
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module in various network analyses published recently [8,
9]. Using a combination of genomic, proteomics, and phylo-
genetic approaches, we have shown that this group of phages
represents a new family, comprising five subfamilies and 13
genera [7]. We therefore suggest that these viruses be moved
from their current taxonomic position in the family Myo-
viridae to a new family included in the order Caudovirales.
4. New taxa. Table2 lists of all new taxa proposed at the
ICTV EC49 meeting in Singapore in 2017. In total, two new
families, eight new subfamilies, 34 new genera, and 91 new
species were proposed. Two significant items are on this
list. The first item is the introduction of two new families of
prokaryotic viruses: Ackermannviridae and Portogloboviri-
dae. With the acceptance of changes to ICVCN Rule 3.11,
the second item is the application of the names of eminent
phage scientists, specifically Hans-Wolfgang Ackermann
(Université Laval) and Charles Shelton McCleskey (Loui-
siana State University) as prefixes for taxon name stems.
5. Updates to taxonomy. As the readership may be
aware, “Virus Taxonomy: The Classification and Nomen-
clature of Viruses - The Online (10th) Report of the ICTV”
is freely accessible at http ://ictv .glob al/repo rt. We would like
to acknowledge the hard work of Hanna M. Oksanen (Corti-
coviridae), Dennis H. Bamford (Pleolipoviridae), and Minna
M. Poranen (Cystoviridae) for completing updates to their
sections. The family Pleolipoviridae is now recognized as
the first virus taxon in the newly established ICTV category
for ssDNA/dsDNA Viruses. The summaries of the ICTV
Report chapters are published in The Journal of General
Virology [6, 11, 12].
Acknowledgements The committee would like to thank Dr. Gra-
ham Hatfull (University of Pittsburgh) for permitting us to use Act-
inobacteriophage Database electron micrographs in 2017’s taxonomy
proposals. The authors thank Laura Bollinger (National Institutes of
Health/National Institute of Allergy and Infectious Diseases, Integrated
Research Facility at Fort Detrick, Frederick, MD, USA) for editing
this paper.
Compliance with ethical standards
The views and conclusions contained in this document are those of the
authors and should not be interpreted as necessarily representing the
official policies, either expressed or implied, of the US Department
of Health and Human Services or of the institutions and companies
affiliated with the authors.
Funding This work was funded in part through Battelle Memorial
Institute’s prime contract with the US National Institute of Allergy and
Infectious Diseases (NIAID) under Contract No. HHSN272200700016I
(J.H.K.). B.E.D. was supported by the Netherlands Organization for
Scientific Research (NWO), Vidi Grant 864.14.004. R.A.E was sup-
ported by grant MCB-1330800 from the National Science Founda-
tion. J.R.B. was supported by the Intramural Research Program of
the National Institutes of Health, National Library of Medicine. R.L.
is a member of the phagebiotics research community, supported by
FWO Vlaanderen. M.M.P. was supported by the Academy of Finland
(272507). A.G. was supported by the National Fund for Scientific
Research (FNRS). H.M.O. was supported by University of Helsinki
funding for Instruct-F1 research infrastructure.
Conflict of interest The authors declare that they have no conflict of
Ethical approval The authors did not perform any studies with human
participants or animals in this article.
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... A pairwise comparison with ≥ 95 % average nucleotide identity (ANI) across ≥ 85 % alignment coverage [58,59] was used to assess genome similarity in the viral community of parviglumis and B73. Viral contigs ≥10 Kbp are described as a vMAG [60]. ...
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Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two different genotypes of Zea mays parviglumis and Z. mays genotype B73 in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as apply 16S rRNA gene amplicon sequencing and genome resolved metagenomics to identify the rhizobiome microbial and viral community. Our results demonstrate that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both, the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n =7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vMAG) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbor genes capable of contributing to carbon cycling in the rhizosphere.
... In the present study, we characterized four closely related bacteriophages infecting Enterobacter and Cronobacter. The phages belonged to the subfamily Tevenvirinae which is extremely widespread group currently containing eleven genera and its members differ significantly in their host range (Grose and Casjens, 2014;Adriaenssens et al., 2018). The newly isolated phages showed high genome similarity to Escherichia phage CC31 and Enterobacter phage PG7, two previously described phages of Karamvirus genus (Petrov et al., 2010;Grose and Casjens, 2014). ...
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Bacteria belonging to Cronobacter and Enterobacter genera are opportunistic pathogens responsible for infections in immunocompromised patients including neonates. Phage therapy offers a safe method for pathogen elimination, however, phages must be well characterized before application. In the present study we isolated four closely related bacteriophages from the subfamily Tevenvirinae infecting Cronobacter and Enterobacter strains. Bacteriophage Pet-CM3-4 which was isolated on C. malonaticus strain possessed broader host specificity than other three phages with primary Enterobacter hosts. Based on genome sequences all these phages have been assigned to the genus Karamvirus. We also studied factors influencing the host specificity of Pet-CM3-4 phage and its host range mutant Pet-CM3-1 and observed that a lysine to glutamine substitution in the long tail fiber adhesin was the reason of the Pet-CM3-1 reduced host specificity. By characterization of phage-resistant mutants from transposon library of C. malonaticus KMB-72 strain we identified that LPS is the receptor of both phages. C. malonaticus O:3 antigen is the receptor of Pet-CM3-1 phage and the Pet-CM3-4 phage binds to structures of the LPS core region. Obtained results will contribute to our understanding of biology and evolution of Tevenvirinae phages.
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... Cyanophages usually contain a double-stranded DNA (dsDNA) genome, most belonging to the order of Caudovirales, which are generally classified into Myoviridae, Siphoviridae, and Podoviridae families according to the tail morphology [22,23]. Although the first cyanophage-LPP-1 was isolated from a freshwater pond in 1963 [24], the majority of studies have been focused on the marine cyanophages to date. ...
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Background As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications. Results Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu. Conclusions We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth.
... According to Abedon et al. (2011), the total count of bacteriophages on the earth is about 10 times the total bacterial host thriving in different environments, which accounts for about 10 30-31 . The International Committee on the Taxonomy of Viruses (ICTV) is responsible for the typing of phages and they have classified bacteriophages into 19 families, among which a few are well characterized including Microviridae, Myoviridae, Inoviridae, Podoviridae and Siphoviridae (Simmonds et al. 2017;Adriaenssens et al. 2018;Walker et al. 2019). The vast abundance and diversity of phages in the biosphere provides an already equipped resource to mine for the potential phages for a variety of purposes (Nikolich and Filippov 2020). ...
In the present scenario, the development of drug-resistant bacteria poses a global threat to all living kinds including aquatic animals. The phenomenon calls for prompt action, through development and timely adoption of alternative strategies in order to sustain the quality as well as to ensure safety of the aquatic produce. In view of antimicrobial resistance especially antibiotic abuse, efforts made towards the advancement of the biological control approaches such as probiotic, symbiotic, and bacteriophage have been accelerated. In recent times, the employment of the biocontrol approach through the applications of lytic bacteriophages for therapy of bacterial infection have leaped over other bioagents. Bacteriophages are bacteria-specific viruses that precisely infect host bacteria and ultimately kill them. Ever since their discovery in the early nineteenth century, the phage therapy enjoyed fleeting popularity in western countries owing to exploratory researches and scientific explanation with regard to their successful clinical trials. In the post antibiotic discovery era, the significance of the phage was ignored. However, after the emergence of antimicrobial resistance, a new craze for therapy was appeared either as prophylactic or therapeutic approach including the aquaculture industry. Most of the therapy in aquaculture is still in the laboratory stage, and is limited to in vitro characterisation and lab-based efficacy which have emerged as the major obstacle in its adoption at the farm level. In this chapter, an effort has been made to draw a connecting line between the current state of information about bacteriophages and what could be the possible strategies for the development of field-based therapy towards the sustenance of aquaculture.
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Soil bacterial predators that use the biomass of bacterial hosts for growth (multiplication), energy, or replication have the potential to reduce bacterial populations in the wide variety of terrestrial ecosystems in which they are found. Bacterial predators , including bacteria-feeding nematodes, protists, bacteria (Bdellovibrio and like organisms, Lysobacter, and myxobacteria), and bacteriophages are responsible for bacterial turnover in soils that lead to many ecosystem services. The demonstrated breadth and specificity of bacterial host ranges for these predators make them interesting targets for the management of bacterial plant and human pathogens. However, there remain significant gaps in knowledge that will need to be filled in order to effectively utilize these predators for disease management. Here, we compared predatory strategies of the major groups of soil bacterial predators and outlined the gaps in knowledge or techniques that are limiting research. We offered specific needs and next steps for integrating analyses of predator identity and impact into studies of soil ecosystems in natural and applied settings.
Recent advances in metavirome technology have provided new insights into viral diversity and function. The bioinformatic process of metavirome study is generally divided into two (or three) steps: assembly and taxonomic profiling including nucleotide alignment. Moreover, k-mer size and contig length are known to considerably affect the results of the assembly and consequently those of taxonomic profiling; however, the optimal k-mer size and contig length have not been established. In the present study, we analyzed marine virus DNA datasets with three different k-mer sizes using different assemblers: 1 k-mer (20) in the CLC Genomics Workbench, and 4 (21, 33, 55, and 77) and 5 (21, 33, 55, 77, and 99) k-mers in metaSPAdes. The use of large k-mers had the advantage of resolving more repeat regions, with higher N50 values and average contig lengths. The contig length helps reduce the error of continuous sequences and determine the number of viral operational taxonomic units. Our analysis suggested that 300 bp may be an appropriate minimum contig length, depending on the characteristics of viral samples. Based on the assembly result using metaSPAdes, we analyzed the DNA virus community using three taxonomic profiling tools: MG-RAST online server, the taxonomic profiling tools function in the CLC microbial module, and customized taxonomic assignment coding (CUTAXAC) using RStudio based on the BLASTn analysis. CUTAXAC showed the most diverse viral composition at the family and species levels along with the highest Shannon diversity index and fastest analysis time.
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Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.
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Members of the family Pleolipoviridae (termed pleolipoviruses) are pseudo-spherical and pleomorphic archaeal viruses. The enveloped virion is a simple membrane vesicle, which encloses different types of DNA genomes of approximately 7-16 kbp (or kilonucleotides). Typically, virions contain a single type of transmembrane (spike) protein at the envelope and a single type of membrane protein, which is embedded in the envelope and located in the internal side of the membrane. All viruses infect extremely halophilic archaea in the class Halobacteria (phylum Euryarchaeota). Pleolipoviruses have a narrow host range and a persistent, non-lytic life cycle. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Pleolipoviridae which is available at
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The Corticoviridae is a family of icosahedral, internal-membrane-containing viruses with double-stranded circular DNA genomes of approximately 10 kb. Only one species, Pseudoalteromonas virus PM2, has been recognized. Pseudoalteromonas virus PM2 infects Gram-negative bacteria and was isolated from seawater in 1968. Pseudoalteromonas virus PM2 is the first bacterial virus in which the presence of lipids in the virion has been demonstrated. Viral lipids are acquired selectively during virion assembly from the host cytoplasmic membrane. The outer protein capsid is an icosahedron with a pseudo T=21 symmetry. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Corticoviridae, which is available at
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The family Cystoviridae includes enveloped viruses with a tri-segmented dsRNA genome and a double-layered protein capsid. The innermost protein shell is a polymerase complex responsible for genome packaging, replication and transcription. Cystoviruses infect Gram-negative bacteria, primarily plant-pathogenic Pseudomonas syringae strains. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Cystoviridae, which is available at
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Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome ‘sequence space’ that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
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Taxonomic classification of archaeal and bacterial viruses is challenging, yet also fundamental for developing a predictive understanding of microbial ecosystems. Recent identification of hundreds of thousands of new viral genomes and genome fragments, whose hosts remain unknown, requires a paradigm shift away from traditional classification approaches and towards the use of genomes for taxonomy. Here we revisited the use of genomes and their protein content as a means for developing a viral taxonomy for bacterial and archaeal viruses. A network-based analytic was evaluated and benchmarked against authority-accepted taxonomic assignments and found to be largely concordant. Exceptions were manually examined and found to represent areas of viral genome 'sequence space' that are under-sampled or prone to excessive genetic exchange. While both cases are poorly resolved by genome-based taxonomic approaches, the former will improve as viral sequence space is better sampled and the latter are uncommon. Finally, given the largely robust taxonomic capabilities of this approach, we sought to enable researchers to easily and systematically classify new viruses. Thus, we established a tool, vConTACT, as an app at iVirus, where it operates as a fast, highly scalable, user-friendly app within the free and powerful CyVerse cyberinfrastructure.
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Botanical, mycological, zoological, and prokaryotic species names follow the Linnaean format, consisting of an italicized Latinized binomen with a capitalized genus name and a lower-case species epithet (e.g., Homo sapiens). Virus species names, however, do not follow a uniform format, and even when binomial, are not Linnaean in style. In this thought exercise, we attempted to convert all currently official names of species included in the virus family Arenaviridae and the virus order Mononegavirales to Linnaean binomials, and to identify and address associated challenges and concerns. Surprisingly, this endeavor was not as complicated or time-consuming as even the authors of this article expected when conceiving the experiment.
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Unlabelled: Virus genomes are prone to extensive gene loss, gain, and exchange and share no universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome network analyses can complement traditional phylogenetics. We performed an exhaustive comparative analysis of the genomes of double-stranded DNA (dsDNA) viruses by using the bipartite network approach and found a robust hierarchical modularity in the dsDNA virosphere. Bipartite networks consist of two classes of nodes, with nodes in one class, in this case genomes, being connected via nodes of the second class, in this case genes. Such a network can be partitioned into modules that combine nodes from both classes. The bipartite network of dsDNA viruses includes 19 modules that form 5 major and 3 minor supermodules. Of these modules, 11 include tailed bacteriophages, reflecting the diversity of this largest group of viruses. The module analysis quantitatively validates and refines previously proposed nontrivial evolutionary relationships. An expansive supermodule combines the large and giant viruses of the putative order "Megavirales" with diverse moderate-sized viruses and related mobile elements. All viruses in this supermodule share a distinct morphogenetic tool kit with a double jelly roll major capsid protein. Herpesviruses and tailed bacteriophages comprise another supermodule, held together by a distinct set of morphogenetic proteins centered on the HK97-like major capsid protein. Together, these two supermodules cover the great majority of currently known dsDNA viruses. We formally identify a set of 14 viral hallmark genes that comprise the hubs of the network and account for most of the intermodule connections. Importance: Viruses and related mobile genetic elements are the dominant biological entities on earth, but their evolution is not sufficiently understood and their classification is not adequately developed. The key reason is the characteristic high rate of virus evolution that involves not only sequence change but also extensive gene loss, gain, and exchange. Therefore, in the study of virus evolution on a large scale, traditional phylogenetic approaches have limited applicability and have to be complemented by gene and genome network analyses. We applied state-of-the art methods of such analysis to reveal robust hierarchical modularity in the genomes of double-stranded DNA viruses. Some of the identified modules combine highly diverse viruses infecting bacteria, archaea, and eukaryotes, in support of previous hypotheses on direct evolutionary relationships between viruses from the three domains of cellular life. We formally identify a set of 14 viral hallmark genes that hold together the genomic network.
This review summarizes the electron microscopical descriptions of prokaryote viruses. Since 1959, nearly 6300 prokaryote viruses have been described morphologically, including 6196 bacterial and 88 archaeal viruses. As in previous counts, the vast majority (96.3 %) are tailed, and only 230 (3.7 %) are polyhedral, filamentous, or pleomorphic. The family Siphoviridae, whose members are characterized by long, noncontractile tails, is by far the largest family (over 3600 descriptions, or 57.3 %). Prokaryote viruses are found in members of 12 bacterial and archaeal phyla. Archaeal viruses belong to 15 families or groups of family level and infect members of 16 archaeal genera, nearly exclusively hyperthermophiles or extreme halophiles. Tailed archaeal viruses are found in the Euryarchaeota only, whereas most filamentous and pleomorphic archaeal viruses occur in the Crenarchaeota. Bacterial viruses belong to 10 families and infect members of 179 bacterial genera, mostly members of the Firmicutes and γ-proteobacteria.