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01-03-2020 | Brief Report

Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87

Authors: Nikita Zrelovs, Elina Cernooka, Andris Dislers, Andris Kazaks

Published in: Archives of Virology | Issue 3/2020

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

Hayes S, Mahony J, Nauta A, van Sinderen D (2017) Metagenomic approaches to assess bacteriophages in various environmental niches. Viruses 9:E127CrossRef

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

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

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

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

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

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

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

10.

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

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 502:91–111CrossRef

12.

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

13.

Besemer J, Borodovsky M (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33:W451–W454CrossRef

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 11:119CrossRef

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–W9CrossRef

16.

Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244–W248CrossRef

17.

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

18.

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

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:e01557–15CrossRef

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:e0184572CrossRef

21.

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

22.

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

23.

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

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 67:1613–1617CrossRef

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–D642CrossRef

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

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 CrossRef

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 15:5360–5363CrossRef

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 31:321–322CrossRef

30.

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

31.

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

Title: Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87
Authors: Nikita Zrelovs
Elina Cernooka
Andris Dislers
Andris Kazaks
Publication date: 01-03-2020
Publisher: Springer Vienna
Published in: Archives of Virology / Issue 3/2020
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-019-04516-2

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