Journal of Microbiology

, Volume 53, Issue 5, pp 337–342 | Cite as

Genome sequence analysis of potential probiotic strain Leuconostoc lactis EFEL005 isolated from kimchi

  • Jin Seok Moon
  • Hye Sun Choi
  • So Yeon Shin
  • Sol Ji Noh
  • Che Ok Jeon
  • Nam Soo Han
Systems and Synthetic Microbiology and Bioinformatics


Leuconostoc lactis EFEL005 (KACC 91922) isolated from kimchi showed promising probiotic attributes; resistance against acid and bile salts, absence of transferable genes for antibiotic resistance, broad utilization of prebiotics, and no hemolytic activity. To expand our understanding of the species, we generated a draft genome sequence of the strain and analyzed its genomic features related to the aforementioned probiotic properties. Genome assembly resulted in 35 contigs, and the draft genome has 1,688,202 base pairs (bp) with a G+C content of 43.43%, containing 1,644 protein-coding genes and 50 RNA genes. The average nucleotide identity analysis showed high homology (≥ 96%) to the type strain L. lactis KCTC3528, but low homology (≤ 95%) to L. lactis KCTC3773 (formerly L. argentinum). Genomic analysis revealed the presence of various genes for sucrose metabolism (glucansucrases, invertases, sucrose phosphorylases, and mannitol dehydrogenase), acid tolerance (F1F0 ATPases, cation transport ATPase, branched-chain amino acid permease, and lysine decarboxylase), vancomycin response regulator, and antibacterial peptide (Lactacin F). No gene for production of biogenic amines (histamine and tyramine) was found. This report will facilitate the understanding of probiotic properties of this strain as a starter for fermented foods.


lactic acid bacteria Leuconostoc lactis probiotics kimchi draft genome 


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  1. Altschul, S.F., Madden, T.L., Schäffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. 1997. Gapped BLAST and PSIBLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389–3402.CrossRefPubMedCentralPubMedGoogle Scholar
  2. Ammor, M.S. and Mayo, B. 2007. Selection criteria for lactic acid bacteria to be used as functional starter cultures in dry sausage production: An update. Meat Sci. 76, 138–146.CrossRefPubMedGoogle Scholar
  3. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. 2014. GenBank. Nucleic Acids Res. 42, 32–37.CrossRefGoogle Scholar
  4. De Bruyne, K., Schillinger, U., Caroline, L., Boehringer, B., Cleenwerck, I., Vancanneyt, M., De Vuyst, L., Franz, C.M.A.P., and Vandamme, P. 2007. Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes from delineation of Leuconostoc species. Int. J. Syst. Evol. Microbiol. 57, 2952–2959.CrossRefPubMedGoogle Scholar
  5. Delcher, A.L., Bratke, K.A., Powers, E.C., and Salzberg, S.L. 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679.CrossRefPubMedCentralPubMedGoogle Scholar
  6. Den Hengst, C.D., Van Hijum, S.A.F.T., Geurts, J.M.W., Nauta, A., Kok, J., and Kuipers, O.P. 2005. The Lactococcus lactis CodY regulon: Identification of a conserved cis-regulatory element. J. Biol. Chem. 280, 34332–34342.CrossRefGoogle Scholar
  7. Disz, T., Akhter, S., Cuevas, D., Olson, R., Overbeek, R., Vonstein, V., Stevens, R., and Edwards, R.A. 2010. Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics 11, 319.CrossRefPubMedCentralPubMedGoogle Scholar
  8. Felsenstein, J. 1985. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 39, 783–791.CrossRefGoogle Scholar
  9. Gardan, L., Shafik, H., Belouin, S., Broch, R., Grimont, F., and Grimont, P.A.D. 1999. DNA relatedness among the pathovars of Pseudomonas syringae and description of Pseudomonas tremae sp. nov. and Pseudomonas cannabina sp. nov. (ex Sutic and Dowson 1959). Int. J. Syst. Evol. Microbiol. 49, 469–478.Google Scholar
  10. Garvie, E.I. 1986. Genus Leuconostoc van Tieghem 1878, pp. 1071–1075. In Sneath, N.S., Mair, H.A., Sharpe, M.E., and Holt, J.G. (eds.), Bergey's Manual of Systematic Bacteriology, 8th ed. The Williams & Wilkins Co. Baltimore, Maryland, USA.Google Scholar
  11. Goris, J., Konstantinidis, K.T., Klappenbach, J.A., Coenye, T., Vandamme, P., and Tiedje, J.M. 2007. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int. J. Syst. Evol. Microbiol. 57, 81–91.CrossRefPubMedGoogle Scholar
  12. Hemme, D. and Foucaud-Scheunemann, C. 2004. Leuconostoc, characteristics, use in dairy technology and prospects in functional foods. Int. Dairy J. 14, 467–494.CrossRefGoogle Scholar
  13. Johansson, P., Paulin, L., Säde, E., Salovuori, N., Alatalo, E.R., Björkroth, K.J., and Auvinen, P. 2011. Genome sequence of a food spoilage lactic acid bacterium, Leuconostoc gasicomitatum LMG 18811T, in association with specific spoilage reactions. Appl. Environ. Microbiol. 77, 4344–4351.CrossRefPubMedCentralPubMedGoogle Scholar
  14. Jung, J.Y., Lee, S.H., and Jeon, C.O. 2012a. Complete genome sequence of Leuconostoc carnosum strain JB16, isolated from kimchi. J. Bacteriol. 194, 6672–6673.CrossRefPubMedCentralPubMedGoogle Scholar
  15. Jung, J.Y., Lee, S.H., and Jeon, C.O. 2012b. Complete genome sequence of Leuconostoc gelidum strain JB7, isolated from kimchi. J. Bacteriol. 194, 6665.CrossRefPubMedCentralPubMedGoogle Scholar
  16. Jung, J.Y., Lee, S.H., Lee, S.H., and Jeon, C.O. 2012c. Complete genome sequence of Leuconostoc mesenteroides subsp. mesenteroides strain J18, isolated from kimchi. J. Bacteriol. 194, 730–731.CrossRefPubMedCentralPubMedGoogle Scholar
  17. Kim, J.F., Jeong, H., Lee, J.S., Choi, S.H., Ha, M., Hur, C.G., Kim, J.S., Lee, S., Park, H.S., Park, Y.H., et al. 2008. Complete genome sequence of Leuconostoc citreum KM20. J. Bacteriol. 190, 3093–3094.CrossRefPubMedCentralPubMedGoogle Scholar
  18. 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. 2012. Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int. J. Syst. Evol. Microbiol. 62, 716–721.CrossRefPubMedGoogle Scholar
  19. Kullen, M.J. and Klaenhammer, T.R. 1999. Identification of the pHinducible, proton-translocating F1F0-ATPase (atpBEFHAGDC) operon of Lactobacillus acidophilus by differential display: Gene structure, cloning and characterization. Mol. Microbiol. 33, 1152–1161.CrossRefPubMedGoogle Scholar
  20. Lane, D.J. 1991. 16S/23S rRNA sequencing, pp. 115–175. In Stackebrandt, E. and Goodfellow, M.D. (eds.), Nucleic Acid Techniques in Bacterial Systematics. John Wiley and Sons, New York, N.Y., USA.Google Scholar
  21. Lee, S.H., Jung, J.Y., Lee, S.H., and Jeon, C.O. 2011. Complete genome sequence of Leuconostoc kimchii strain C2, isolated from kimchi. J. Bacteriol. 193, 5548.CrossRefPubMedCentralPubMedGoogle Scholar
  22. Lowe, T.M. and Eddy, S.R. 1997. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964.CrossRefPubMedCentralPubMedGoogle Scholar
  23. Makarova K., Slesarev, A., Wolf, Y., Sorokin, A., Mirkin, B., Koonin, E., Pavlov, A., Pavlova, N., Karamychev, V., Polouchine, N., et al. 2006. Comparative genomics of the lactic acid bacteria. Proc. Natl. Acad. Sci. USA 103, 15611–15616.CrossRefPubMedCentralPubMedGoogle Scholar
  24. Nam, S.H., Choi, S.H., Kang, A., Kim, D.W., Kim, R.N., Kim, A., and Park, H.S. 2010. Genome sequence of Leuconostoc argentinum KCTC 3773. J. Bacteriol. 192, 6490–6491.CrossRefPubMedCentralPubMedGoogle Scholar
  25. Noh, S.J. 2015. Master’s thesis. Chungbuk National University, Cheongju, Chungbuk, Korea.Google Scholar
  26. Oh, H.M., Cho, Y.J., Kim, B.K., Roe, J.H., Kang, S.O., Nahm, B.H., Jeong, G., Han, H.U., and Chun, J. 2010. Complete genome sequence analysis of Leuconostoc kimchii IMSNU 11154. J. Bacteriol. 192, 3844–3845.CrossRefPubMedCentralPubMedGoogle Scholar
  27. Overbeek, R., Begley, T., Butler, R.M., Choudhuri, J.V., Chuang, H.Y., Cohoon, M., de Crécy-Lagard, V., Diaz, N., Disz, T., Edwards, R., et al. 2005. The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes. Nucleic Acids Res. 33, 5691–5702.CrossRefPubMedCentralPubMedGoogle Scholar
  28. Pagani, I., Liolios, K., Jansson, J., Chen, I.M.A., Smirnova, T., Nosrat, B., Markowitz, V.M., and Kyrpides, N.C. 2012. The Genomes OnLine Database (GOLD) v.4: Status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res. 40, 571–579.CrossRefGoogle Scholar
  29. Park, Y.K., Bearson, B., Bang, S.H., Bang, I.S., and Foster, J.W. 1996. Internal pH crisis, lysine decarboxylase and the acid tolerance response of Salmonella typhimurium. Mol. Microbiol. 20, 605–611.CrossRefPubMedGoogle Scholar
  30. Pruitt, K.D., Tatusova, T., Klimke, W., and Maglott, D.R. 2009.NCBI reference sequences: Current status, policy and new initiatives. Nucleic Acids Res. 37, 32–36.CrossRefGoogle Scholar
  31. Richter, M. and Rosselló-Móra, R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106, 19126–19131.CrossRefPubMedCentralPubMedGoogle Scholar
  32. Saitou, N. and Nei, M. 1987. The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425.PubMedGoogle Scholar
  33. Tamura, K., Dudley, J., 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.CrossRefPubMedCentralPubMedGoogle Scholar
  34. Tatusov, R.L., Galperin, M.Y., Natale, D.A., and Koonin, E.V. 2000. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 28, 33–36.CrossRefPubMedCentralPubMedGoogle Scholar
  35. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., and Higgins, D.G. 1997. The CLUSTAL X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25, 4876–4882.CrossRefPubMedCentralPubMedGoogle Scholar
  36. Ventura, M., Canchaya, C., Zink, R., Fitzgerald, G.F., and Van Sinderen, D. 2004. Characterization of the groEL and groES loci in Bifidobacterium breve UCC 2003: Genetic, transcriptional, and phylogenetic analyses. Appl. Environ. Microbiol. 70, 6197–6209.CrossRefPubMedCentralPubMedGoogle Scholar
  37. Yu, C., Zavaljevski, N., Desai, V., and Reifman, J. 2009. Genomewide enzyme annotation with precision control: Catalytic families (CatFam) databases. Proteins Struct. Funct. Bioinforma. 74, 449–460.CrossRefGoogle Scholar

Copyright information

© The Microbiological Society of Korea and Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Jin Seok Moon
    • 1
  • Hye Sun Choi
    • 2
  • So Yeon Shin
    • 1
  • Sol Ji Noh
    • 1
  • Che Ok Jeon
    • 3
  • Nam Soo Han
    • 1
  1. 1.Brain Korea 21 Center for Bio-Resource Development, Division of Animal, Horticultural, and Food SciencesChungbuk National UniversityCheongjuKorea
  2. 2.Department of Agro-food ResourceNational Academy of Agricultural Science, RDAJeonjuKorea
  3. 3.Department of Life ScienceChung-Ang UniversitySeoulKorea

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