Identification of novel genera and subcluster classifications for mycobacteriophages

Abstract

Aim: To identify novel genera amongst mycobacteriophages (MP) and verify a hypothesised correlation between the taxonomy set by the International Committee on Taxonomy of Viruses (ICTV) and the National Centre for Biotechnology Information (NCBI) with that of the Actinobacteriophage Database, which may help formalise subcluster assignment.

Methods: A dataset of 721 MP genomes was analysed using VIRIDIC, a nucleotide alignment-based software that predicts genus assignments. Potentially novel genera were analysed using Gegenees and VICTOR, respectively. These genera were then compared to the subclusters assigned by the Actinobacteriophage Database to verify a hypothesis that one genus can be assigned to one subcluster (i.e., the genus-subcluster hypothesis).

Results: Initially, when comparing the current genus classifications of the 721 MP dataset to the Actinobacteriophage database subcluster assignments, 83.3% of subclusters supported the genus-subcluster hypothesis. Following the sequential VIRIDIC, Gegenees and VICTOR analyses, a total of 20 novel genera were identified based on a ≥ 70% and ~ 50% similarity threshold for VIRIDIC and Gegenees, respectively, and a monophyletic nature in the VICTOR output. Interestingly, these criteria also appear to support the creation of 13 novel subclusters, which would increase the support for the genus-subcluster hypothesis to 97.6%.

Conclusion: The link between genus and subcluster classifications appears robust, as most subclusters can be assigned a single genus and vice versa. By relating the taxonomic and clustering classification systems, they can be easily kept up to date to best reflect MP diversity, which could aid the rapid selection of related (or diverse) phages for research, therapeutic and diagnostic purposes.

Keywords

Mycobacteriophage / taxonomy / ICTV / actinobacteriophage database / novel genera / novel subclusters

References

[1] Saxena S,Forn-Cuní G.Drug resistance in nontuberculous mycobacteria: mechanisms and models.Biology2021;10:96 PMCID:PMC7911849

[2] Tarashi S,Fateh A.Nontuberculous mycobacterial resistance to antibiotics and disinfectants: challenges still ahead.Biomed Res Int2022;2022:8168750 PMCID:PMC8898113

[3] Field NL,Gavey L.Mycobacterium avium subspecies paratuberculosis infection in cattle - a review in the context of seasonal pasture-based dairy herds.Ir Vet J2022;75:12 PMCID:PMC9121589

[4] Allué-Guardia A,Chan J.Mycobacteriophages as potential therapeutic agents against drug-resistant tuberculosis.Int J Mol Sci2021;22:735 PMCID:PMC7828454

[5] Dedrick RM,Garlena RA.Engineered bacteriophages for treatment of a patient with a disseminated drug-resistant Mycobacterium abscessus.Nat Med2019;25:730-3 PMCID:PMC6557439

[6] Hatfull GF,Schooley RT.Phage Therapy for Antibiotic-resistant bacterial infections.Annu Rev Med2022;73:197-211

[7] Lawrence JG,Hendrix RW.Imbroglios of viral taxonomy: genetic exchange and failings of phenetic approaches.J Bacteriol2002;184:4891-905 PMCID:PMC135278

[8] Nelson D.Phage taxonomy: we agree to disagree.J Bacteriol2004;186:7029-31 PMCID:PMC523225

[9] Adriaenssens E.How to name and classify your phage: an informal guide.Viruses2017;9:70 PMCID:PMC5408676

[10] Moraru C,Kropinski AM.VIRIDIC-A novel tool to calculate the intergenomic similarities of prokaryote-infecting Viruses.Viruses2020;12:1268 PMCID:PMC7694805

[11] Adriaenssens EM.Phage diversity in the human gut microbiome: a taxonomist’s perspective.mSystems2021;6:e0079921 PMCID:PMC8407299

[12] Turner D,Adriaenssens EM.A roadmap for genome-based phage taxonomy.Viruses2021;13:506 PMCID:PMC8003253

[13] Sharma S,Chatterjee S.Isolation and characterization of a lytic bacteriophage against Pseudomonas aeruginosa.Sci Rep2021;11:19393 PMCID:PMC8481504

[14] Gorbalenya AE.Bioinformatics of virus taxonomy: foundations and tools for developing sequence-based hierarchical classification.Curr Opin Virol2022;52:48-56

[15] Rodwell EV,Pulford CV.Isolation and characterisation of bacteriophages with activity against invasive non-typhoidal salmonella causing bloodstream infection in Malawi.Viruses2021;13:478 PMCID:PMC7999457

[16] Stanton CR,Beer M,Petrovski S.Isolation and characterisation of the bundooravirus genus and phylogenetic investigation of the salasmaviridae bacteriophages.Viruses2021;13:1557 PMCID:PMC8402886

[17] Li J,Hu Y.Characterization and genomic analysis of BUCT549, a novel bacteriophage infecting vibrio alginolyticus with flagella as receptor.Front Microbiol2021;12:668319 PMCID:PMC8245777

[18] Hatfull GF.Mycobacteriophages.Microbiol Spectr2018;6 PMCID:PMC6282025

[19] Hatfull GF.Mycobacteriophages: From Petri dish to patient.PLoS Pathog2022;18:e1010602 PMCID:PMC9262239

[20] Pope WH,Russell DA.Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary SciencePhage Hunters Integrating Research and EducationMycobacterial Genetics CourseWhole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity.eLife2015;4:e06416 PMCID:PMC4408529

[21] Agren J,Håfström T.Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups.PLoS One2012;7:e39107 PMCID:PMC3377601

[22] Kyrkou I,Ellegaard-Jensen L.Isolation and characterisation of novel phages infecting Lactobacillus plantarum and proposal of a new genus, “Silenusvirus”.Sci Rep2020;10:8763 PMCID:PMC7260188

[23] Meier-Kolthoff JP.VICTOR: genome-based phylogeny and classification of prokaryotic viruses.Bioinformatics2017;33:3396-404 PMCID:PMC5860169

[24] Mavrich TN.Bacteriophage evolution differs by host, lifestyle and genome.Nat Microbiol2017;2:17112 PMCID:PMC5540316

[25] Cresawn SG,Day N,Hendrix RW.Phamerator: a bioinformatic tool for comparative bacteriophage genomics.BMC Bioinformatics2011;12:395 PMCID:PMC3233612

[26] Jacobs-sera D,Bowman C.Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) programOn the nature of mycobacteriophage diversity and host preference.Virology2012;434:187-201 PMCID:PMC3518647

[27] Grose JH.Understanding the enormous diversity of bacteriophages: the tailed phages that infect the bacterial family Enterobacteriaceae.Virology2014;468-470:421-43 PMCID:PMC4301999

[28] Demo S,Bernardino A.BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE.PLoS One2021;16:e0248418 PMCID:PMC7954295

[29] Mu A.Bacteriophage discovery to advance biotechnology and biotherapeutics.Nat Rev Microbiol2023;21:279

[30] Crane A,Hua T.Phylogenetic relationships and codon usage bias amongst cluster K mycobacteriophages.G32021;11:jkab291 PMCID:PMC8527509

[31] Hosseiniporgham S.A review on mycobacteriophages: from classification to applications.Pathogens2022;11:777 PMCID:PMC9317374