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Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87

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Abstract

The novel bacterial virus Mimir87, infecting the salt-tolerant bacterium Virgibacillus halotolerans, was isolated from worker honey bees. Mimir87 has an elongated head and a long non-contractile tail consistent with members of the Siphoviridae phage family. The phage genome comprises 48,016 base pairs and encodes 68 predicted proteins, to 34 of which a function could be assigned from homology analysis. The phage encodes two metabolism-related transporter proteins previously not observed in bacteriophage genomes. Mimir87 displays some relatedness to several Bacillus and Paenibacillus viruses; however, the overall sequence dissimilarity suggests Mimir87 to be a representative of a new phage genus.

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References

  1. Hatfull GF (2015) Dark matter of the biosphere: the amazing world of bacteriophage diversity. J Virol 89:8107–8110

    Article  CAS  Google Scholar 

  2. Hayes S, Mahony J, Nauta A, van Sinderen D (2017) Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9:E127

    Article  Google Scholar 

  3. Salmond GP, Fineran PC (2015) A century of the phage: past, present and future. Nat Rev Microbiol 13:777–786

    Article  CAS  Google Scholar 

  4. Abedon ST, García P, Mullany P, Aminov R (2017) Editorial: phage therapy: past, present and future. Front Microbiol 8:981

    Article  Google Scholar 

  5. Bradley DE (1967) Ultrastructure of bacteriophage and bacteriocins. Bacteriol Rev 31:230–314

    Article  CAS  Google Scholar 

  6. Green MR, Sambrook J (2017) Isolation of high-molecular-weight DNA using organic solvents. Cold Spring Harb Protoc 2017:pdb.prot093450

  7. Andrews S (2017) FastQC: a quality control tool for high throughput sequence data. 2010

  8. Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  9. Chevreux B, Wetter T, Suhai S (1999) Genome sequence assembly using trace signals and additional sequence information. Comput Sci Biol Proc Ger Conf Bioinform 99:45–56

    Google Scholar 

  10. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP (2011) Integrative genomics viewer. Nat Biotechnol 29:24–26

    Article  CAS  Google Scholar 

  11. Casjens SR, Gilcrease EB (2009) Determining DNA packaging strategy by analysis of the termini of the chromosomes in tailed-bacteriophage virions. Methods Mol Biol 502:91–111

    Article  CAS  Google Scholar 

  12. Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679

    Article  CAS  Google Scholar 

  13. Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454

    Article  CAS  Google Scholar 

  14. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119

    Article  Google Scholar 

  15. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36:W5–W9

    Article  CAS  Google Scholar 

  16. Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244–W248

    Article  Google Scholar 

  17. Laslett D, Canback B (2004) ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res 32:11–16

    Article  CAS  Google Scholar 

  18. Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  Google Scholar 

  19. Yang Y, Zhan L, Chen J, Zhang Y, Sun Y, Yang Z, Jiang L, Zhu H, Zhang Y, Lu Y, Mei L (2016) Genome sequence of Bacillus cereus phage vB_BceS-MY192. Genome Announc 4:e01557–15

    Article  Google Scholar 

  20. Geng P, Tian S, Yuan Z, Hu X (2017) Identification and genomic comparison of temperate bacteriophages derived from emetic Bacillus cereus. PLoS One 12:e0184572

    Article  Google Scholar 

  21. Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27:1009–1010

    Article  CAS  Google Scholar 

  22. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703

    Article  CAS  Google Scholar 

  23. Janda JM, Abbott SL (2007) 16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls. J Clin Microbiol 45:2761–2764

    Article  CAS  Google Scholar 

  24. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617

    Article  CAS  Google Scholar 

  25. Cole JR, Wang Q, Fish JA, Chai B, McGarrell DM, Sun Y, Brown CT, Porras-Alfaro A, Kuske CR, Tiedje JM (2014) Ribosomal Database Project: data and tools for high throughput rRNA analysis. Nucleic Acids Res 42:D633–D642

    Article  CAS  Google Scholar 

  26. Sánchez-Porro C, de la Haba RR, Ventosa A (2014) The Genus Virgibacillus. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The prokaryotes. Springer, Berlin, pp 455–465

    Google Scholar 

  27. Heyrman J, De Vos P, Logan N (2015) Virgibacillus. In: Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J, De Vos P, Hedlund B, Dedysh S (eds) Bergey’s manual of systematics of archaea and bacteria. Hoboken, New Jersey. https://doi.org/10.1002/9781118960608.gbm00545

    Chapter  Google Scholar 

  28. Na JS, Kim TH, Kim HS, Park SH, Song HS, Cha SW, Yoon HJ (2009) Liver abscess and sepsis with Bacillus pantothenticus in an immunocompetent patient: a first case report. World J Gastroenterol 15:5360–5363

    Article  Google Scholar 

  29. Ümit EG, Ümit HC, Kuloğlu F, Demir AM (2014) Multiple liver and muscle abscesses and sepsis with Bacillus pantothenticus in a leukemia patient. Turk J Haematol 31:321–322

    Article  Google Scholar 

  30. Seiler H, Wenning M (2013) Virgibacillus halotolerans sp. nov., isolated from a dairy product. Int J Syst Evol Microbiol 63:3358–3363

    Article  CAS  Google Scholar 

  31. Wang CX, Li X (2018) JMT-1: a novel, spherical lytic halotolerant phage isolated from Yuncheng saline lake. Braz J Microbiol 49:262–268

    Article  CAS  Google Scholar 

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Acknowledgements

We would like to express our gratitude for the valuable feedback and advice given on the draft version of the manuscript to Professor Rob Lavigne (Katholieke Universiteit Leuven). We also sincerely thank Dr. Janis Rumnieks (Latvian Biomedical Research and Study Centre) for his critical review of the final version of the manuscript.

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Correspondence to Andris Kazaks.

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Zrelovs, N., Cernooka, E., Dislers, A. et al. Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87. Arch Virol 165, 737–741 (2020). https://doi.org/10.1007/s00705-019-04516-2

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  • DOI: https://doi.org/10.1007/s00705-019-04516-2

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