Korean Journal of Microbiology (미생물학회지)

The Microbiological Society of Korea (한국미생물학회)
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Paenibacillus kimchicus sp. nov., an antimicrobial bacterium isolated from Kimchi

김치로부터 분리된 항균 활성 세균 Paenibacillus kimchicus sp. nov.

  • Park, A-rum (Department of Microbiology, Chungbuk National University) ;
  • Oh, Ji-Sung (Department of Microbiology, Chungbuk National University) ;
  • Roh, Dong-Hyun (Department of Microbiology, Chungbuk National University)
  • Received : 2016.06.24
  • Accepted : 2016.07.13
  • Published : 2016.09.30
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Abstract

An antimicrobial bacterium to pathogenic microorganisms, strain $W5-1^T$ was isolated from Korean fermented-food Kimchi. The isolate was Gram-staining-variable, strictly aerobic, rod-shaped, endospore-forming, and motile with peritrichous flagella. It grew at $15-40^{\circ}C$, at pH 6.0-10.0, and in the presence of 0-4% NaCl. Strain $W5-1^T$ could hydrolyze esculin and xylan, and assimilate $\small{D}$-mannose, but not $\small{D}$-mannitol. Strain $W5-1^T$ showed antimicrobial activity against Listeria monocytogens, Pseudomonas aeruginosa, Staphylococcus aureus, and Salmonella typhi. The G+C content of the DNA of strains $W5-1^T$ was 52.6 mol%. The predominant respiratory quinone was menaquinone-7 (MK-7) and the major cellular fatty acids were $C_{16:0}$, antieiso-$C_{15:0}$, $C_{18:0}$, and $C_{12:0}$. The strain contained meso-diaminopimelic acid in cell-wall peptidoglycan. On the basis of 16S rRNA gene sequence and phylogenetic analysis, the strain W5-1 was shown to belong to the family Paenibacillaceae and was most closely related to Paenibacillus pinihumi $S23^T$ (98.4% similarity) and Paenibacillus tarimensis $SA-7-6^T$ (96.4%). The DNA-DNA relatedness between the isolate and Paenibacillus pinihumi $S23^T$ was 8.5%, indicating that strain $W5-1^T$ represented a species in the genus Paenibacillus. On the basis of the evidence from this polyphasic study, it is proposed that strain $W5-1^T$ is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus kimchicus sp. nov. is proposed. The type strain is $W5-1^T$ (=KACC $15046^T$ = $LMG 25970^T$).

병원성 미생물들에 대해 항균활성을 보이는 $W5-1^T$ 균주가 한국의 발효식품인 김치에서 분리되었다. 이 분리주는 그람염색변이성, 절대호기성, 간균, 내생포자형성과 주모성의 편모를 가지고 운동성을 나타내었다. 균주는 $15-40^{\circ}C$, pH 6.0-10.0, 0-4% NaCl 조건에서 생육하였다. 균주는 esculin과 xylan을 가수분해하였고, $\small{D}$-mannose을 동화하였으나 $\small{D}$-mannitol은 동화하지 못하였다. $W5-1^T$ 균주는 Listeria monocytogens, Pseudomonas aeruginosa, Staphylococcus aureus, Salmonella typhi에 항균활성을 보였다. $W5-1^T$ 균주의 DNA의 G+C 함량은 52.6 mol%였다. 주요 호흡성 퀴논은 menaquinone-7 (MK-7)였고, 주요 세포성 지방산은 $C_{16:0}$, antieiso-$C_{15:0}$, $C_{18:0}$, and $C_{12:0}$였다. 균주는 세포벽 펩티도클리칸으로 meso-diaminopimelic acid을 함유하였다. 16S rRNA 유전자서열 분석에 근거하여 $W5-1^T$ 균주는 Paenibacillaceae 과로 분류되었으며 Paenibacillus pinihumi $S23^T$(98.4% similarity), P. tarimensis $SA-7-6^T$(96.4%) 균주와 높은 연관성을 보였다. 분리주와 P. pinihumi $S23^T$는 8.5%의 DNA-DNA 관련성을 보임으로 $W5-1^T$ 균주가 Paenibacillus 속의 한 종임을 보여주었다. 이러한 다각적 연구의 증거로 볼 때 $W5-1^T$ 균주는 Paenibacillus 속의 신종으로 사료되어 Paenibacillus kimchicus로 명명을 제안하며, 표준균주는 $W5-1^T$(=KACC $15046^T$=LMG $25970^T$)이다.

Keywords

References

  1. Ash, C., Priest, F.G., and Collins, M.D. 1993. Molecular identification of rRNA group 3 bacilli (Ash, Farrow, Wallbanks and Collins) using a PCR probe test. Proposal for the creation of a new genus Paenibacillus. Antonie van Leeuwenhoek 64, 253-260.
  2. Buck, J.D. 1982. Nonstaining (KOH) method for determination of Gram reactions of marine bacteria. Appl. Environ. Microbiol. 44, 992-993.
  3. Choi, J.H., Im, W.T., Yoo, J.S., Lee, S.M., Moon, D.S., Kim, H.J., Rhee, S.K., and Roh, D.H. 2008. Paenibacillus donghaensis sp. nov., a xylan-degrading and nitrogen-fixing bacterium isolated from East Sea sediment. J. Microbiol. Biotechnol. 18, 189-193.
  4. Chung, Y.R., Kim, C.H., Hwang, I., and Chun, J. 2000. Paenibacillus koreensis sp. nov., a new species that produces an iturin-like antifungal compound. Int. J. Syst. Evol. Microbiol. 50, 1495-1500. https://doi.org/10.1099/00207713-50-4-1495
  5. De Vos, P., Ludwig, W., Schleifer, K.H., and Whitman, W.B. 2009. Family IV. Paenibacillaceae fam. nov. In Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 3 (The Firmicutes), pp. 269. In De Vos, P., Garrity, G.M., Jones, D., Krieg, N.R., Ludwig, W., Rainey, F.A., Schleifer, K.H., and Whitman, W.B. (eds.) Springer, New York, USA.
  6. Euzeby, J.P. 1997. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int. J. Syst. Bacteriol. 47, 590-592. (List of prokaryotic names with standing in nomenclature. http://www.bacterio.net). https://doi.org/10.1099/00207713-47-2-590
  7. Ezaki, T., Hashimoto, Y., and Yabuuchi, E. 1989. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int. J. Syst. Bacteriol. 39, 224-229. https://doi.org/10.1099/00207713-39-3-224
  8. Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368-376. https://doi.org/10.1007/BF01734359
  9. Fleming, H.P., Etchells, J.L., and Costilow, R.N. 1975. Microbial inhibition by an isolate of Pediococcus from cucumber brines. Appl. Microbiol. 30, 1040-1042.
  10. Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41, 95-98.
  11. Heimbrook, M.E., Wang, W.L., and Campbell, G. 1989. Staining bacterial flagella easily. J. Clin. Microbiol. 27, 2612-2615.
  12. Hiraishi, A., Ueda, Y., Ishihara, J., and Mori, T. 1996. Comparative lipoquinone analysis of influent sewage and activated sludge by high performance liquid chromatography and photodiode array detection. J. Gen. Appl. Microbiol. 42, 457-470. https://doi.org/10.2323/jgam.42.457
  13. Kajimura, Y. and Kaneda, M. 1996. Fusaricidin A, a new depsipeptide antibiotic produced by Bacillus polymyxa KT-8. Taxonomy, fermentation, isolation, structure elucidation and biological activity. J. Antibiot. (Tokyo) 49, 129-135. https://doi.org/10.7164/antibiotics.49.129
  14. 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. https://doi.org/10.1007/BF01731581
  15. Kluge, A.G. and Farris, J.S. 1969. Quantitative phyletics and the evolution of anurans. Syst. Zool. 18, 1-32. https://doi.org/10.2307/2412407
  16. Kumar, S., Stecher, G., and Tamura, K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33, 1870-1874. https://doi.org/10.1093/molbev/msw054
  17. Kurusu, K., Ohba, K., Arai, T., and Fukushima, K. 1987. New peptide antibiotics LI-F03, F04, F05, F07, and F08, produced by Bacillus polymyxa. I. Isolation and characterization. J. Antibiot. (Tokyo) 40, 1506-1514. https://doi.org/10.7164/antibiotics.40.1506
  18. Larkin, M.A., Balckshields, G., Brown, N.P., Chenna, R., McGettigan, P.A., McWilliam, H., Valentin, F., Wallace, I.M., Wilm, A., Lopez, R., et al. 2007. Clustal W and Clustal X version 2.0. Bioinformatics 23, 2947-2948. https://doi.org/10.1093/bioinformatics/btm404
  19. 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. https://doi.org/10.1016/S0021-9673(01)83344-6
  20. Nakajima, N., Chihara, S., and Koyama, Y. 1972. A new antibiotic, gatavalin. I. Isolation and characterization. J. Antibiot. (Tokyo) 25, 243-247. https://doi.org/10.7164/antibiotics.25.243
  21. Pichard, B., Larue, J.P., and Thouvenot, D. 1995. Gavaserin and saltavalin, new peptide antibiotics produced by Bacillus polymyxa. FEMS Microbiol. Lett. 133, 215-218. https://doi.org/10.1111/j.1574-6968.1995.tb07887.x
  22. Saitou, N. and Nei, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406-425.
  23. Sasser, M. 1990. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark, DE, USA.
  24. Schaeffer, A.B. and Fulton, M.D. 1933. A simplified method of staing endospores. Science 77, 194. https://doi.org/10.1126/science.77.1990.194
  25. Schleifer, K.H. and Kandler, O. 1972. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol. Rev. 36, 407-477.
  26. Shida, O., Takagi, H., Kadowaki, K., Nakamura, L.K., and Komagata, K. 1997. Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int. J. Syst. Bacteriol. 47, 289-298. https://doi.org/10.1099/00207713-47-2-289
  27. Slepecky, R. and Hemphill, E. 1992. The genus Bacillus-nonmedical. The Prokaryotes, 2nd edn, pp. 1663-1696. In Balows, A., Truper, H.G., Dworkin, M., Harder, W., and Schleifer, K.H. (eds.). Springer, New York, USA.
  28. Smibert, R.M. and Krieg, N.R. 1994. Phenotypic characterization. Methods for General and Molecular Bacteriology, pp. 607-655. In Gerhardt, P., Murray, R.G.E., Wood, W.A., and Krieg, N.R. (eds.). American Society for Microbiology, Washington, DC, USA.
  29. Vogler, K. and Studer, R.O. 1966. The chemistry of the polymyxin antibiotics. Experientia 22, 345-354. https://doi.org/10.1007/BF01901127
  30. Wayne, L.G., Brenner, D.J., Colwell, R.R., Grimont, P.A.D., Kandler, O., Krichevsky, M.I., Moore, L.H., Moore, W.E.C., Murray, R.G.E., Stackebrandt, E., et al. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37, 463-464. https://doi.org/10.1099/00207713-37-4-463