Skip to main content
SpringerLink
Log in

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

  • Published:
Journal of Microbiology Aims and scope Submit manuscript

Abstract

A novel halophilic bacterium, strain K7T, was isolated from kimchi, a traditional Korean fermented food. The strain is Gram-positive, motile, and produces terminal endospores. The isolate is facultative aerobic and grows at salinities of 0.0–25.0% (w/v) NaCl (optimum 10–15% NaCl), pH 5.5–8.5 (optimum pH 7.0–7.5), and 15–42°C (optimum 37°C). The predominant isoprenoid quinone in the strain is menaquinone-7 and the peptidoglycan of the strain is meso-diaminopimelic acid. The major fatty acids of the strain are anteisio-C15:0, iso-C15:0, and, C16:0 (other components were < 10.0%), while the major polar lipids are diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, and three unidentified lipids. A phylogenetic analysis of 16S rRNA gene sequence similarity showed that the isolated strain was a cluster of the genus Gracilibacillus. High levels of gene sequence similarity were observed between strain K7T and Gracilibacillus orientalis XH-63T (96.5%), and between the present strain and Gracilibacillus xinjiangensis (96.5%). The DNA G+C content of this strain is 37.7 mol%. Based on these findings, strain K7T is proposed as a novel species: Gracilibacillus kimchii sp. nov. The type strain is K7T (KACC 18669T; JCM 31344T).

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Ahmed, I., Yokota, A., and Fujiwara, T. 2007. Gracilibacillus boraciitolerans sp. nov., a highly boron-tolerant and moderately halotolerant bacterium isolated from soil. Int. J. Syst. Evol. Microbiol. 57, 796–802.

    Article  CAS  PubMed  Google Scholar 

  • 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 

  • Carrasco, I.J., Marquez, M.C., Yanfen, X., Ma, Y., Cowan, D.A., Jones, B.E., Grant, W.D., and Ventosa, A. 2006. Gracilibacillus orientalis sp. nov., a novel moderately halophilic bacterium isolated from a salt lake in inner Mongolia, China. Int. J. Syst. Evol. Microbiol. 56, 599–604.

    Article  CAS  PubMed  Google Scholar 

  • Chamroensaksri, N., Tanasupawat, S., Akaracharanya, A., Visessanguan, W., Kudo, T., and Itoh, T. 2010. Gracilibacillus thailandensis sp. nov., from fermented fish (pla-ra). Int. J. Syst. Evol. Microbiol. 60, 944–948.

    Article  PubMed  Google Scholar 

  • Chen, Y.G., Cui, X.L., Zhang, Y.Q., Li, W.J., Wang, Y.X., Xu, L.H., Peng, Q., Wen, M.L., and Jiang, C.L. 2008a. Gracilibacillus halophilus sp. nov., a moderately halophilic bacterium isolated from saline soil. Int. J. Syst. Evol. Microbiol. 58, 2403–2408.

    Article  CAS  PubMed  Google Scholar 

  • Chen, Y.G., Cui, X.L., Zhang, Y.Q., Li, W.J., Wang, Y.X., Xu, L.H., Peng, Q., Wen, M.L., and Jiang, C.L. 2008b. Gracilibacillus quinghaiensis sp. nov., isolated from salt-lake sediment in the Qaidam Basin, north-west China. Syst. Appl. Microbiol. 31, 183–189.

    Article  CAS  PubMed  Google Scholar 

  • Collins, M.D. and Jones, D. 1981. A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J. Appl. Bacteriol. 51, 129–134.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Gao, M., Liu, Z.Z., Zhou, Y.G., Liu, H.C., Ma, Y.C., Wang, L., Chen, S.F., and Ji, X.C. 2012. Gracilibacillus kekensis sp. nov., a moderate halophile isolated from Keke Salt Lake. Int. J. Syst. Evol. Microbiol. 62, 1032–1036.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • Hirota, K., Hanaoka, Y., Nodasaka, Y., and Yumoto, I. 2014. Gracilibacillus alcaliphilus sp. nov., a facultative alkaliphile isolated from indigo fermentation liquor for dyeing. Int. J. Syst. Evol. Microbiol. 64, 3174–3180.

    Article  CAS  PubMed  Google Scholar 

  • Huang, H.Q., Wang, Y., Yuan, W.D., Xiao, C., Ye, J.J., Liu, M., Zhu, J., Sun, Q.G., and Bao, S.X. 2013. Gracilibacillus marinus sp. nov., isolated from the northern South China Sea. Antonie van Leeuwenhoek 104, 695–701.

    Article  CAS  PubMed  Google Scholar 

  • Huo, Y.Y., Xu, X.W., Cui, H.L., and Wu, M. 2010. Gracilibacillus ureilyticus sp. nov., a halotolerant bacterium from a saline-alkaline soil. Int. J. Syst. Evol. Microbiol. 60, 1383–1386.

    Article  CAS  PubMed  Google Scholar 

  • Jeon, C.O., Lim, J.M., Jang, H.H., Park, D.J., Xu, L.H., Jiang, C.L., and Kim, C.J. 2008. Gracilibacillus lacisalsi sp. nov., a halophilic Gram-positive bacterium from a salt lake in China. Int. J. Syst. Evol. Microbiol. 58, 2282–2286.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Kim, O.S., Cho, Y.J., Lee, K., Yoon, S.H., Kim, M., Na, H., Park, S.C., Jeon, Y.S., Lee, J.H., Yi, H., et al. 2012a. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716–721.

    Article  CAS  PubMed  Google Scholar 

  • Kim, P., Lee, J.C., Park, D.J., Shin, K.S., Kim, J.Y., and Kim, C.J. 2012b. Gracilibacillus bigeumensis sp. nov., a moderately halophilic bacterium from solar saltern soil. Int. J. Syst. Evol. Microbiol. 62, 1857–1863.

    Article  CAS  PubMed  Google Scholar 

  • Kimura, M. 1983. The neutral theroy of molecular evolution. Cambride University Press, Cambridge, UK.

    Book  Google Scholar 

  • Lane, D.J. 1991. 16S/23S rRNA sequencing. In Goodfellow, M. (ed.), Nucleic acid techniques in bacterial systematics, pp. 115–175. John Wiley & Sons. Wiley, Chichester, UK.

    Google Scholar 

  • Lee, J.J., Kang, M.S., Joo, E.S., Kim, M.K., Im, W.T., Jung, H.Y., and Srinivasan, S. 2015. Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil. J. Microbiol. 53, 429–434.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • MIDI. 1999. Sherlock microbial identification system operating manual, version 3.0. MIDI, Newark, USA.

    Google Scholar 

  • Namwong, S., Tanasupawat, S., Smitinont, T., Visessanguan, W., Kudo, T., and Itoh, T. 2005. Isolation of Lentibacillus salicampi strains and Lentibacillus juripiscarius sp. nov. from fish sauce in Thailand. Int. J. Syst. Evol. Microbiol. 55, 315–320.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Pakdeeto, A., Tanasupawat, S., Thawai, C., Moonmangmee, S., Kudo, T., and Itoh, T. 2007. Lentibacillus kapialis sp. nov., from fermented shrimp paste in Thailand. Int. J. Syst. Evol. Microbiol. 57, 364–369.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

  • 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 

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

    Google Scholar 

  • Schaeffer, A.B. and Fulton, M.D. 1933. A simplified method of staining endospores. Science 77, 194.

    Article  CAS  PubMed  Google Scholar 

  • Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M., and Kumar, S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731–2739.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tanasupawat, S., Namwong, S., Kudo, T., and Itoh, T. 2007. Piscibacillus salipiscarius gen. nov., sp. nov., a moderately halophilic bacterium from fermented fish (pla-ra) in Thailand. Int. J. Syst. Evol. Microbiol. 57, 1413–1417.

    Article  PubMed  Google Scholar 

  • Tanasupawat, S., Pakdeeto, A., Namwong, S., Thawai, C., Kudo, T., and Itoh, T. 2006. Lentibacillus halophilus sp. nov., from fish sauce in Thailand. Int. J. Syst. Evol. Microbiol. 56, 1859–1863.

    Article  CAS  PubMed  Google Scholar 

  • Tang, S.K., Wang, Y., Lou, K., Mao, P.H., Jin, X., Jiang, C.L., Xu, L.H., and Li, W.J. 2009. Gracilibacillus saliphilus sp. nov., a moderately halophilic bacterium isolated from a salt lake. Int. J. Syst. Evol. Microbiol. 59, 1620–1624.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Tittsler, R.P. and Sandholzer, L.A. 1936. The use of semi-solid agar for the detection of bacterial motility. J. Bacteriol. 31, 575–580.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wainø, M., Tindall, B.J., Schumann, P., and Ingvorsen, K. 1999. Gracilibacillus gen. nov., with description of Gracilibacillus halotolerans gen. nov., sp. nov.; transfer of Bacillus dipsosauri to Gracilibacillus dipsosauri comb. nov., and Bacillus salexigens to the genus Salibacillus gen. nov., as Salibacillus salexigens comb. nov. Int. J. Syst. Bacteriol. 49, 821–831.

    Article  PubMed  Google Scholar 

  • Yang, N., Ren, B., Dai, H., Liu, Z., Zhou, Y., Song, F., and Zhang, L. 2013. Gracilibacillus xinjiangensis sp. nov., a new member of the genus Gracilibacillus isolated from Xinjiang region, China. Antonie van Leeuwenhoek 104, 809–816.

    Article  CAS  PubMed  Google Scholar 

  • 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.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Microbiology and Functionality Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea

    Young Joon Oh, Seul Ki Lim, Min-Sung Kwon, Jieun Lee, Ja-Young Jang & Hak-Jong Choi

  2. Hygienic Safety and Analysis Center, World Institute of Kimchi, Gwangju, 61755, Republic of Korea

    Hae-Won Lee

  3. Advanced Process Technology Research Group, World Institute of Kimchi, Gwangju, 61755, Republic of Korea

    Hae Woong Park

  4. Research Group of Gut Microbiome, Korea Food Research Institute, Seongnam, 13539, Republic of Korea

    Young-Do Nam

  5. Division of Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea

    Myung-Ji Seo

Authors
  1. Young Joon Oh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Hae-Won Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Seul Ki Lim
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Min-Sung Kwon
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Jieun Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ja-Young Jang
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Hae Woong Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Young-Do Nam
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Myung-Ji Seo
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Hak-Jong Choi
    View author publications

    You can also search for this author in PubMed Google Scholar

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

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Oh, Y.J., Lee, HW., Lim, S.K. et al. Gracilibacillus kimchii sp. nov., a halophilic bacterium isolated from kimchi. J Microbiol. 54, 588–593 (2016). https://doi.org/10.1007/s12275-016-6349-4

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12275-016-6349-4

Keywords

Search

Navigation