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Archives of Virology

, Volume 164, Issue 10, pp 2627–2630 | Cite as

Genome characterization of the novel lytic Vibrio parahaemolyticus phage vB_VpP_BA6

  • Meiyan Yang
  • Yongjian Liang
  • Runbin Su
  • Hanfang Chen
  • Jing Wang
  • Jumei Zhang
  • Yu Ding
  • Li Kong
  • Haiyan Zeng
  • Liang Xue
  • Haoming Wu
  • Qingping WuEmail author
Annotated Sequence Record

Abstract

A lytic bacteriophage, designated Vibrio phage vB_VpP_BA6, was isolated from sewage collected in Guangzhou, China. The double-stranded DNA genome of phage BA6 is composed of 50,520 bp with a G+C content of 41.77%. It possesses 64 open reading frames relating to phage structure, packaging, host lysis, DNA metabolism, and additional functions. Three tRNAs genes (encoding Pro, Ile and Trp) were detected. Comparison of its genomic features and phylogenetic analysis revealed that phage BA6 is a novel member of the family Podoviridae. This phage may represent a potential therapeutic agent against multidrug-resistant Vibrio parahaemolyticus.

Notes

Acknowledgements

The authors are grateful to the National Key R&D Program of China (2017YFC1601201), the GDAS’ Project of Science and Technology Development (No. 2019GDASYL-0103011), the Key Project of Natural Science Foundation of China (31730070) and GDAS’ Special Project of Science and Technology Development (2017GDASCX-0201) for financial support.

Supplementary material

705_2019_4351_MOESM1_ESM.tif (2 mb)
Supplementary Fig. S1 Transmission electron microscopy image of vB_VpP_BA6
705_2019_4351_MOESM2_ESM.tif (3.4 mb)
Supplementary Fig. S2 Terminal sequence determination in the vB_VpP_BA6 genome. The panels show the run-off sequencing spectrograms of the phage vB_VpP_BA6 genome using a forward primer (Forward: 5’-CTGGTGGAAGAACT GTAGAA-3′) and a reverse primer (Reverse: 5’-ATACCCGTTGCTTATCATC-3’). (A) The 3’-terminal sequence. (B) The 5’-terminal sequence
705_2019_4351_MOESM3_ESM.xlsx (10 kb)
Supplementary Table S1 Lytic spectra of vB_VpP_BA6 based on 30 bacterial strains of Vibrio parahaemolyticus. Clear lysis zone (+), no lysis zone (−)
705_2019_4351_MOESM4_ESM.xlsx (23 kb)
Supplementary Table S2 Open reading frames in the phage vB_VpP_BA6 genome

References

  1. 1.
    Lin SJ, Hsu KC, Wang HC (2017) Structural insights into the cytotoxic mechanism of Vibrio parahaemolyticus PirA(vp) and PirB(vp) Toxins. Mar Drugs 15(12):1–12Google Scholar
  2. 2.
    Kalatzis PG, Castillo D, Katharios P et al (2018) Bacteriophage interactions with marine pathogenic Vibrios: implications for phage therapy. Antibiotics (Basel) 7(1):1–23Google Scholar
  3. 3.
    Xie T, Wu Q, Zhang J et al (2017) Comparison of Vibrio parahaemolyticus isolates from aquatic products and clinical by antibiotic susceptibility, virulence, and molecular characterisation. Food Control 71:315–321CrossRefGoogle Scholar
  4. 4.
    Xie T, Wu Q, Xu X et al (2015) Prevalence and population analysis of Vibrio parahaemolyticus in aquatic products from South China markets. FEMS Microbiol Lett 362(22):v178CrossRefGoogle Scholar
  5. 5.
    Xie T, Xu X, Wu Q et al (2016) Prevalence, molecular characterization, and antibiotic susceptibility of Vibrio parahaemolyticus from ready-to-eat foods in China. Front Microbiol 7:1–10Google Scholar
  6. 6.
    Kazi M, Annapure US (2016) Bacteriophage biocontrol of foodborne pathogens. J Food Sci Technol 53(3):1355–1362CrossRefGoogle Scholar
  7. 7.
    Van Twest R and Kropinski AM (2009) Bacteriophage enrichment from water and soil.  Methods Mol Biol 501:15-21CrossRefGoogle Scholar
  8. 8.
    Kutter E (2009) Phage host range and efficiency of plating. Methods Mol Biol 501:141–149CrossRefGoogle Scholar
  9. 9.
    Xing S, Zhang X, Sun Q et al (2017) Complete genome sequence of a novel, virulent Ahjdlikevirus bacteriophage that infects Enterococcus faecium. Adv Virol 162(12):3843–3847Google Scholar
  10. 10.
    Zeng H, He W, Li C, et al (2018) Complete genome analysis of a novel phage GW1 lysing Cronobacter. Arch Virol 164(2):625–628CrossRefGoogle Scholar
  11. 11.
    Kearse M, Moir R, Wilson A et al (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649CrossRefGoogle Scholar
  12. 12.
    Seemann T (2014) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30(14):2068–2069CrossRefGoogle Scholar
  13. 13.
    Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402CrossRefGoogle Scholar
  14. 14.
    Sullivan MJ, Petty NK, Beatson SA (2011) Easyfig: a genome comparison visualizer. Bioinformatics 27(7):1009–1010CrossRefGoogle Scholar
  15. 15.
    Kumar S, Stecher G, Li M et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549CrossRefGoogle Scholar
  16. 16.
    Zhang X, Wang Y, Li S et al (2015) A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini. BMC Genomics 16:414CrossRefGoogle Scholar
  17. 17.
    Adriaenssens E, Brister JR (2017) How to name and classify your phage: an informal guide. Viruses 9(4):1–9CrossRefGoogle Scholar
  18. 18.
    Zhao X, Chen C, Shen W et al (2016) Global transcriptomic analysis of interactions between Pseudomonas aeruginosa and bacteriophage PaP3. Sci Rep 6:1–12CrossRefGoogle Scholar
  19. 19.
    Kropinski AM, Lingohr EJ, Ackermann HW (2011) The genome sequence of enterobacterial phage 7-11, which possesses an unusually elongated head. Adv Virol 156(1):149–151Google Scholar
  20. 20.
    Han F, Li M, Lin H et al (2014) The novel Shewanella putrefaciens-infecting bacteriophage Spp001: genome sequence and lytic enzymes. J Ind Microbiol Biotechnol 41(6):1017–1026CrossRefGoogle Scholar
  21. 21.
    Katharios P, Kalatzis PG, Kokkari C et al (2017) Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves. PLoS One 12(12):e190083CrossRefGoogle Scholar
  22. 22.
    Li M, Jin Y, Lin H et al (2018) Complete genome of a novel lytic Vibrio parahaemolyticus phage VPp1 and characterization of its endolysin for antibacterial activities. J Food Prot 81(7):1117–1125CrossRefGoogle Scholar
  23. 23.
    Li F, Xing S, Fu K et al (2019) Genomic and biological characterization of the Vibrio alginolyticus-infecting “Podoviridae” bacteriophage, vB_ValP_IME271. Virus Genes 55(2):218–226CrossRefGoogle Scholar
  24. 24.
    Magill DJ, Shaburova OV, Chesnokova EN et al (2015) Complete nucleotide sequence of phiCHU: a Luz24likevirus infecting Pseudomonas aeruginosa and displaying a unique host range. FEMS Microbiol Lett 362(9):1–3CrossRefGoogle Scholar
  25. 25.
    Shen X, Li M, Zeng Y et al (2012) Functional identification of the DNA packaging terminase from Pseudomonas aeruginosa phage PaP3. Adv Virol 157(11):2133–2141Google Scholar
  26. 26.
    Glukhov AS, Krutilina AI, Shlyapnikov MG et al (2012) Genomic analysis of Pseudomonas putida phage tf with localized single-strand DNA interruptions. PLoS One 7(12):e51163CrossRefGoogle Scholar
  27. 27.
    Fouts DE, Klumpp J, Bishop-Lilly KA et al (2013) Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity. Virol J 10:1–13CrossRefGoogle Scholar
  28. 28.
    Hardies SC, Hwang YJ, Hwang CY et al (2013) Morphology, physiological characteristics, and complete sequence of marine bacteriophage varphiRIO-1 infecting Pseudoalteromonas marina. J Virol 87(16):9189–9198CrossRefGoogle Scholar
  29. 29.
    Nobrega FL, Vlot M, de Jonge PA et al (2018) Targeting mechanisms of tailed bacteriophages. Nat Rev Microbiol 16(12):760–773CrossRefGoogle Scholar
  30. 30.
    Katharios P, Kalatzis PG, Kokkari C et al (2017) Isolation and characterization of a N4-like lytic bacteriophage infecting Vibrio splendidus, a pathogen of fish and bivalves. PLoS One 12(12):e190083CrossRefGoogle Scholar
  31. 31.
    Dwivedi B, Xue B, Lundin D et al (2013) A bioinformatic analysis of ribonucleotide reductase genes in phage genomes and metagenomes. BMC Evol Biol 13:1–17CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Meiyan Yang
    • 1
    • 2
  • Yongjian Liang
    • 1
    • 2
  • Runbin Su
    • 2
  • Hanfang Chen
    • 2
  • Jing Wang
    • 2
  • Jumei Zhang
    • 1
  • Yu Ding
    • 3
  • Li Kong
    • 1
  • Haiyan Zeng
    • 1
  • Liang Xue
    • 1
  • Haoming Wu
    • 1
  • Qingping Wu
    • 1
    Email author
  1. 1.State Key Laboratory of Applied Microbiology Southern China, Guangdong Provincial Key Laboratory of Microbiology Culture Collection and Application, Guangdong Open Laboratory of Applied MicrobiologyGuangdong Institute of MicrobiologyGuangzhouChina
  2. 2.College of AgricultureSouth China Agricultural UniversityGuangzhouChina
  3. 3.Department of Food Science and TechnologyJinan UniversityGuangzhouChina

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