Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi

Abstract

A Gram-stain-positive, halophilic, rod-shaped, non-motile, spore forming bacterium, strain NKC1-2T, was isolated from kimchi, a Korean fermented food. Comparative analysis based on 16S rRNA gene sequence demonstrated that the isolated strain was a species of the genus Virgibacillus. Strain NKC1-2T exhibited high level of 16S rRNA gene sequence similarity with the type strains of Virgibacillus xinjiangensis SL6-1T (96.9%), V. sediminis YIM kkny3T (96.8%), and V. salarius SA-Vb1T (96.7%). The isolate grew at pH 6.5–10.0 (optimum, pH 8.5–9.0), 0.0–25.0% (w/v) NaCl (optimum, 10–15% NaCl), and 15–50°C (optimum, 37°C). The major menaquinone in the strain was menaquinone-7, and the main peptidoglycan of the strain was meso-diaminopimelic acid. The predominant fatty acids of the strain were iso-C14:0, anteisio-C15:0, iso- C15:0, and iso-C16:0 (other components were < 10.0%). The polar lipids consisted of diphosphatidylglycerol and phosphatidylglycerol. The genomic DNA G + C content of NKC1-2T was 42.5 mol%. On the basis of these findings, strain NKC1-2T is proposed as a novel species in the genus Virgibacillus, for which the name Virgibacillus kimchii sp. nov. is proposed (=KACC 19404T =JCM 32284T). The type strain of Virgibacillus kimchii is NKC1-2T.

This is a preview of subscription content, access via your institution.

References

  1. Arahal, D.R., Marquez, M.C., Volcani, B.E., Schleifer, K.H., and Ventosa, A. 1999. Bacillus marismortui sp. nov., a new moderately halophilic species from the Dead Sea. Int. J. Syst. Bacteriol. 49, 521–530.

    Article  PubMed  Google Scholar 

  2. Bousfield, G.R., Sugino, H., and Ward, D.N. 1985. Demonstration of a COOH-terminal extension on equine lutropin by means of a common acid-labile bond in equine lutropin and equine chorionic gonadotropin. J. Biol. Chem. 260, 9531–9533.

    CAS  PubMed  Google Scholar 

  3. Carrasco, I.J., Marquez, M.C., and Ventosa, A. 2009. Virgibacillus salinus sp. nov., a moderately halophilic bacterium from sediment of a saline lake. Int. J. Syst. Evol. Microbiol. 59, 3068–3073.

    CAS  Article  PubMed  Google Scholar 

  4. Collins, M. and Jones, D. 1981. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol. Rev. 45, 316.

    CAS  PubMed  PubMed Central  Google Scholar 

  5. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376.

    CAS  Article  PubMed  Google Scholar 

  6. Guan, L., Cho, K.H., and Lee, J.H. 2011. Analysis of the cultivable bacterial community in jeotgal, a Korean salted and fermented seafood, and identification of its dominant bacteria. Food Microbiol. 28, 101–113.

    CAS  Article  PubMed  Google Scholar 

  7. Heyndrickx, M., Lebbe, L., Kersters, K., De Vos, P., Forsyth, G., and Logan, N. 1998. Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus. Int. J. Syst. Evol. Microbiol. 48, 99–106.

    Google Scholar 

  8. Heyndrickx, M., Lebbe, L., Kersters, K., Hoste, B., De Wachter, R., De Vos, P., Forsyth, G., and Logan, N. 1999. Proposal of Virgibacillus proomii sp. nov. and emended description of Virgibacillus pantothenticus (Proom and Knight 1950) Heyndrickx et al. 1998. Int. J. Syst. Evol. Microbiol. 49, 1083–1090.

    CAS  Google Scholar 

  9. Heyrman, J., Logan, N.A., Busse, H.J., Balcaen, A., Lebbe, L., Rodriguez-Diaz, M., Swings, J., and De Vos, P. 2003. Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus. Int. J. Syst. Evol. Microbiol. 53, 501–511.

    CAS  Article  PubMed  Google Scholar 

  10. Jeon, C.O., Kim, J.M., Park, D.J., Xu, L.H., Jiang, C.L., and Kim, C.J. 2009. Virgibacillus xinjiangensis sp. nov., isolated from a Salt Lake of Xin-jiang Province in China. J. Microbiol. 47, 705–709.

    Article  PubMed  Google Scholar 

  11. Kim, E.Y. 2013. World Institute of Kimchi as a leading global institute of fermented foods. Biotechnol. J. 8, 759–760.

    CAS  Article  PubMed  Google Scholar 

  12. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120.

    CAS  Article  PubMed  Google Scholar 

  13. Kimura, M. 1983. The neutral theory of molecular evolution. Cambridge University Press, Cambridge, UK.

    Book  Google Scholar 

  14. Lee, S.Y., Kang, C.H., Oh, T.K., and Yoon, J.H. 2012. Virgibacillus campisalis sp. nov., from a marine solar saltern. Int. J. Syst. Evol. Microbiol. 62, 347–351.

    CAS  Article  PubMed  Google Scholar 

  15. Mesbah, M. and Whitman, W.B. 1989. Measurement of deoxyguanosine/ thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine + cytosine of DNA. J. Chromatogr. 479, 297–306.

    CAS  Article  PubMed  Google Scholar 

  16. Nei, M., Kumar, S., and Takahashi, K. 1998. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc. Natl. Acad. Sci. USA 95, 12390–12397.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  17. Niederberger, T.D., Steven, B., Charvet, S., Barbier, B., and Whyte, L.G. 2009. Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic. Int. J. Syst. Evol. Microbiol. 59, 2219–2225.

    CAS  Article  PubMed  Google Scholar 

  18. Oh, Y.J., Lee, H.W., Lim, S.K., Kwon, M.S., Lee, J., Jang, J.Y., Lee, J.H., Park, H.W., Nam, Y.D., Seo, M.J., et al. 2016a. Lentibacillus kimchii sp. nov., an extremely halophilic bacterium isolated from kimchi, a Korean fermented vegetable. Antonie van Leeuwenhoek 109, 869–876.

    CAS  Article  PubMed  Google Scholar 

  19. Oh, Y.J., Lee, H.W., Lim, S.K., Kwon, M.S., Lee, J., Jang, J.Y., Park, H.W., Nam, Y.D., Seo, M.J., and Choi, H.J. 2016b. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J. Microbiol. 54, 588–593.

    CAS  Article  PubMed  Google Scholar 

  20. Park, E.J., Chun, J., Cha, C.J., Park, W.S., Jeon, C.O., and Bae, J.W. 2012. Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing. Food Microbiol. 30, 197–204.

    CAS  Article  PubMed  Google Scholar 

  21. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.

    CAS  PubMed  Google Scholar 

  22. Sans-Serramitjana, E., Fusté, E., Martínez-Garriga, B., Merlos, A., Pastor, M., Pedraz, J., Esquisabel, A., Bachiller, D., Vinuesa, T., and Viñas, M. 2016. Killing effect of nanoencapsulated colistin sulfate on Pseudomonas aeruginosa from cystic fibrosis patients. J. Cyst. Fibros. 15, 611–618.

    CAS  Article  PubMed  Google Scholar 

  23. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI, Newark, USA.

    Google Scholar 

  24. Song, H.J. and Lee, H.J. 2014. Consumption of kimchi, a salt fermented vegetable, is not associated with hypertension prevalence. J. Ethn. Foods 1, 8–12.

    Article  Google Scholar 

  25. Tamura, K., Stecher, G., Peterson, D., Filipski, A., and Kumar, S. 2013. MEGA6: Molecular evolutionary genetics analysis version 6.0. Mol. Biol. Evol. 30, 2725–2729.

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Tindall, B.J., Tomlinson, G.A., and Hochstein, L.I. 1987. Polar lipid composition of a new halobacterium. Syst. Appl. Microbiol. 9, 6–8.

    CAS  Article  PubMed  Google Scholar 

  27. Tittsler, R.P. and Sandholzer, L.A. 1936. The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575.

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Yoon, S.H., Ha, S.M., Kwon, S., Lim, J., Kim, Y., Seo, H., and 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  PubMed  PubMed Central  Google Scholar 

  29. Yoon, J.H., Weiss, N., Lee, K.C., Lee, I.S., Kang, K.H., and Park, Y.H. 2001. Jeotgalibacillus alimentarius gen. nov., sp. nov., a novel bacterium isolated from jeotgal with L-lysine in the cell wall, and reclassification of Bacillus marinus Ruger 1983 as Marinibacillus marinus gen nov., comb. nov. Int. J. Syst. Evol. Microbiol. 51, 2087–2093.

    CAS  Article  PubMed  Google Scholar 

  30. Zhang, D.C., Schumann, P., Wu, J., Franca, L., Neuner, K., and Margesin, R. 2015. Virgibacillus flavescens sp. nov. isolated from sediment of the Yellow Sea in China. Int. J. Syst. Evol. Microbiol. 66, 1138–1143.

    Article  PubMed  Google Scholar 

Download references

Author information

Affiliations

Authors

Corresponding author

Correspondence to Hak-Jong Choi.

Additional information

Supplemental material for this article may be found at http://www.springerlink.com/content/120956.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Oh, Y.J., Jang, JY., Lim, S.K. et al. Virgibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol. 55, 933–938 (2017). https://doi.org/10.1007/s12275-017-7386-3

Download citation

Keywords

  • Virgibacillus kimchii sp. nov.
  • halophile
  • kimchi
  • taxonomy