Food Science and Biotechnology

Korean Society of Food Science and Technology (한국식품과학회)
권호 표지

Bacterial Diversity in a Korean Traditional Soybean Fermented Foods (Doenjang and Ganjang) by 16S rRNA Gene Sequence Analysis

  • Cho, Kye-Man (Division of Applied Life Science, Gyeongsang Notional University) ;
  • Seo, Weon-Taek (Department of Food Science, Jinju National University)
  • Published : 2007.04.30
Download PDF
⟨ Previous Next ⟩

Abstract

The bacterial diversity in Korean soybean-fermented foods was investigated using a PCR-based approach. 16S rRNA sequences were amplified and cloned from two different soybean-fermented foods such as doenjang (soybean paste), and ganjang (soybean sauce). Staphylococcus equorum (60.6%), Tetragenococcus halophila (21.2%), Leuconostoc mesenteroides (9.1%), Lactobacillus sakei (6.1%), and Bacillus subtilis (3.0%) were detected among clones isolated from soybean paste samples and Halanaerobium sp. (37.5%), Halanaerobium fermentans (37.5%), T. halophila (12.5%), Staphylococcus sp. (6.3%), S. equorum (3.1%), and B. subtilis (3.1%) were detected among clones isolated from soybean sauce. Our approach revealed different bacterial distributions and diversity from those previously obtained using culture-dependent methods.

Keywords

References

  1. Choi YS, Kim JH, Yoon DH. Effects of soy extract and sex on serum and liver lipid levels of the rat. Food Sci. Biotechnol. 11: 10- 13 (2002)
  2. Sung JH, Choi SJ, Lee SW, Park KH, Moon TW. Isoflavones found in Korean soybean paste as 3-hydroxy-3-methylglutaryl coenzyme a reductase inhibitors. Biosci. Biotech. Bioch. 68: 1051-1058 (2004) https://doi.org/10.1271/bbb.68.1051
  3. Kim HJ, Lee EJ, Shin OS, Ji WD, Choi MR, Kim JK. Volatile components in the soy sauce manufactured by Bacillus species and fused yeast. J. Microbiol. Biotechn. 6: 194-201 (1996)
  4. Ham SS, Choi KK, Cui CB, Lee BG, Joo DS, Lee DS. Quality characteristics of soy sauce fermented by Bacillus licheniformis NH20 isolated from traditional meju and Aspergillus oryzae. Food Sci. BioTechnol. 13: 537-543 (2004)
  5. Yoo SK, Cho WH, Kang SM, Lee SH. Isolation and identification of microorganisms in Korean traditional soybean paste and soybean sauce. Korean J. Appl. Microbiol. Biotechnol. 27: 113-117 (1999)
  6. Yun GH, Lee ET, Kim SD. Purification and characterization of a fibrinolytic enzyme produced from Bacillus amyloliquefaciens K42 isolated from Korean soy sauce. Korean J. Microbiol. BioTechnol. 31: 284-291 (2003)
  7. Choi HS, Kim MK, Kim MK, Park HS, Song GS, Lee KK, Kim TY, Kim JG. An approach to increase vitamin $D_2$ Level in doenjang (fermented soybean paste) using mushrooms. Food Sci. BioTechnol. 14: 828-831 (2005)
  8. Lim SY, Park KY, Rhee SH. Anticancer effect of doenjang in in vitro sulforhodamine B (SRB) assay. J. Korean Soc. Food Sci. Nutr. 28: 240-245 (1999)
  9. Nagata C. Ecological study of the association between soy product intake and mortality from cancer and heart disease in Japan. Int. J. Epidemiol. 29: 832-836 (2000) https://doi.org/10.1093/ije/29.5.832
  10. Cheigh HS, Park KS, Moon GS, Park KY. Antioxidative characteristics of fermented soybean paste and its extracts on the lipid oxidation. J. Korean Soc. Food Sci. Nutr. 23: 604-613 (1990)
  11. Kim MH, Im SS, Yoo YB, Kim GE, Lee JH. Antioxidative materials in domestic meju and doenjang. 4. Separation of phenolic compounds and their antioxidative activity. J. Food Sci. Nutr. 23: 792-798 (1994)
  12. Yang SO, Chang PS, Lee JH. Isoflavone distribution and uglucosidase activity in cheonggukjang, a traditional Korean whole soybean-fermented food. Food Sci. Biotechnol. 15: 96-101 (2006)
  13. Shin ZI, Ahn CW, Nam HS, Lee HJ, Moon TH. Fraction of angiotensin converting enzyme (ACE) inhibitory peptides from soybean paste. Korean J. Food Sci. Technol. 27: 230-234 (1995)
  14. Shon DH, Lee KA, Kim SH, Ahn CW, Nam HS, Lee HJ, Shin Jl, Screening of antithrombiotic peptidesfrom soybean paste by the microplate method. Korean J. Food Sci. Technol. 28: 684-688 (1996)
  15. Kim WK, Choi KH, Kim YT, Park HH, Choi JY, Lee YS, Oh HI, Kwon lB, Lee SY. Purification and characterization of a fibrinolytic enzyme produced from Bacillus sp. strain CK 11-4 screened from cheonggukjang. Appl. Environ. Mcirob. 62: 2482-2488 (1996)
  16. Kim DH, Song HP, Kim KY, Kim JO, Byun MW. A correlation between fibrinolytic activity and microflora in Korean fermented soybean products. J. Korean Soc. Food Sci. Nutr. 33: 41-46 (2004) https://doi.org/10.3746/jkfn.2004.33.1.041
  17. Ra KS, Oh SH, Kim JM, Suh HJ. Isolation of fibrinolytic enzyme and $\beta$-glucosidase producing strains from doenjang and optimum conditions of enzyme production. J. Korean Soc. Food Sci. Nutr. 33: 439-442 (2004) https://doi.org/10.3746/jkfn.2004.33.2.439
  18. Amann RI, Krumholz L, Stahl DA. Fluorescent oligonucleotide probing of whole cells for determinative, phylogenetic, and environmental studies in microbiology. J. Bacteriol. 172: 762-770 (1990) https://doi.org/10.1128/jb.172.2.762-770.1990
  19. Leckie SE. Methods of microbial community profiling and their application to forest soils. Forest Ecol. Manag. 220: 88-106 (2005) https://doi.org/10.1016/j.foreco.2005.08.007
  20. Tajima K, Aminov R, Nagamine T, Ogata K, Nakamura M, Matsui H, Beeno Y. Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol. Ecol. 29: 159-169 (1999) https://doi.org/10.1111/j.1574-6941.1999.tb00607.x
  21. Schloss PD, Hay AG, Wilson DB, Gossett JM, Walker LP. Quantifying bacterial population dynamics in compost using 16S rRNA gene probes. Appl. Microbiol. Biot. 66: 457-463 (2005) https://doi.org/10.1007/s00253-004-1727-y
  22. Coppola S, Blaiotta G, Ercolini D, Moschetti G. Molecular evaluation of microbial diversity occurring in different types of Mozzarella cheese. J. Appl. Microbiol. 90: 414-420 (2001) https://doi.org/10.1046/j.1365-2672.2001.01262.x
  23. Kim MJ, Chun JS. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis. Int. J. Food Microbiol. 103: 91-96 (2005) https://doi.org/10.1016/j.ijfoodmicro.2004.11.030
  24. Meroth CB, Walter J, Herte C, Brandt MJ, Hammes WP. Monitoring the bacterial population dynamics in sourdough fermentation process by using PCR-denaturing gradient gel electrophoresis. Appl. Environ. Microb. 69: 475-482 (2003) https://doi.org/10.1128/AEM.69.1.475-482.2003
  25. Lee JS, He, GY, Lee JW, Oh YJ, Park JA, Park YH, Pyun YR, Ahn JS. Analysis of kimchi microflora using denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 102: 143-150 (2005) https://doi.org/10.1016/j.ijfoodmicro.2004.12.010
  26. Osborn A, Moore E, Timmis K. An evaluation of terminalrestriction fragment length polymorphism (T-RFLP) analysis for the study of microbial community structure and dynamics. Environ. Microbiol. 2: 39-50 (2000) https://doi.org/10.1046/j.1462-2920.2000.00081.x
  27. Tiquia SM, Ichida JM, Keener HM, Elwell DL, Burtt EH Jr, Michel FC Jr. Bacterial community profiles on feathers during composting as determined by terminal restriction fragment length polymorphism analysis of 16S rRNA genes. Appl. Microbiol. Biot. 67: 412-419 (2005) https://doi.org/10.1007/s00253-004-1788-y
  28. Ranjard L, Poly F, Lata JC, Mougel C, Thioulouse J, Nazaret S. Characterization of bacterial and fungal soil communities by automated ribosomal intergenic spacer analysis fingerprints: biological and methodological variability. Appl. Environ. Microb. 67: 4479-4487 (2001) https://doi.org/10.1128/AEM.67.10.4479-4487.2001
  29. Seseiia S, Isabel Sanchez I, Palop L. Characterization of Lactobacillus strains and monitoring by RAPO-PCR in controlled fermentations of 'Almagro' eggplants. Int. J. Food Microbiol. 104: 325-335 (2005) https://doi.org/10.1016/j.ijfoodmicro.2005.03.013
  30. Escalante A, Wacher C, Farres A. Lactic acid bacterial diversity in the traditional Mexican fermented dough pozol as determined by 16S rDNA sequence analysis Int. J. Food Microbiol. 64: 21-31 (2001) https://doi.org/10.1016/S0168-1605(00)00428-1
  31. Pace NR, Stahl DA, Lane DJ, Olsen GJ. The analysis of natural microbial population by ribosomal RNA sequences. Adv. Microb. Ecol. 9: 1-55 (1986)
  32. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. P. Natl. Acad. Sci. USA 87: 4576-4579 (1990) https://doi.org/10.1073/pnas.87.12.4576
  33. Cho SJ, Cho KM, Shin EC, Lim WJ, Hong SY, Choi BR, Kang JM, Lee SM, Kim YH, Kim H, Yun HD. 16S rDNA analysis of bacterial diversity in three fractions of cow rumen. J. Microbiol. Biotechn. 16: 92-101 (2006)
  34. Maidak BL, Cole JR, Lilburn TG, Parker CT Jr, Saxman PR, Stredwick JM, Li GM, Garrity B, Olsen GJ, Pramanik S, Schmidt TM, Tiedje JM. The RDP (ribosomal database project) continues. Nucleic Acids Res. 28: 173-174 (2000) https://doi.org/10.1093/nar/28.1.173
  35. Madden TL, Tatusov RL, Zhang J. Application of network BLAST server. Method Enzymol. 266: 131-141 (1996) https://doi.org/10.1016/S0076-6879(96)66011-X
  36. Tompson JD, Higgins DG, Gibson TJ. CLUSTA W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680 (1994) https://doi.org/10.1093/nar/22.22.4673
  37. Saito N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425 (1987)
  38. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swing J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol. Rev. 60: 407-438 (1996)
  39. Farrelly VF, Rainey FA, Stackebrandt E. Effect of genome size and rrn gene copy number on PCR amplification of 16S rRNA genes from a mixture of bacterial species. Appl. Environ. Microb. 61: 2798-2801 (1995)
  40. Wintzingerode F, Gobel UB, Stackebrandt E. Determination of microbial diversity in environmental samples: Pitfalls of PCR-based rRNA analysis. FEMS Microbiol. Rev. 21: 213-229 (1997) https://doi.org/10.1111/j.1574-6976.1997.tb00351.x
  41. Kang SE, Rhee JH, Park C, Sung MH, Lee IH. Distribution of poly-${\gamma}$-glutamate ($\gamma$-PGA) producers in Korean fermented foods, cheonggukjang, doenjang, and kochujang. Food Sci. Biotechnol. 14: 364-372 (2005)
  42. Anonymous. Validation of the publication of new names and new combinations previously effectively published outside the lJSB. List no. 49. lnt. J. Syst. Bacteriol. 44: 370-371 (1994) https://doi.org/10.1099/00207713-44-2-370
  43. Place RB, Hiestand D, Gallmann HR, Teuber M. Staphylococcus equorum subsp. Nov., A starter culture component for surface ripened semi-hard cheeses. System. Appl. Microbiol. 26: 30-37 (2003) https://doi.org/10.1078/072320203322337281
  44. Carnio MC, Holtzel A, Rudolf M, Henle T, Jung G, Scherer S. The macrocyclic peptide antibiotic micrococcin P(1) is secreted by the food-borne bacterium Staphylococcus equorum WS 2733 and inhibits Listeria monocytogenes on soft cheese. Appl. Environ. Microb. 66: 2378-2384. (2000) https://doi.org/10.1128/AEM.66.6.2378-2384.2000
  45. Johansson G, Berdague JL, Larsson M, Tran N, Bore E. Lipolysis, proteolysis, and formation of volatile components during ripening of a fermented sausage with Pediococcus pentosaceus and Staphylococcus xylosus as starter cultures. Met. Sci. 38: 203-218 (1994)
  46. Talon R, Montel MC, Berdague JL. Production of flavour esters by lipases of Staphylococcus warneri and Staphylococcus xylosus. Enzyme Microb. Technol. 19: 620-622 (1996) https://doi.org/10.1016/S0141-0229(96)00075-0
  47. Sondergaard AK, Stahnke LH. Growth and aroma production by staphylococcus sylosus, S. carnosus and S. equorum - a comparative study in model systems. Int. J. Food Microbiol. 75: 99-109 (2002) https://doi.org/10.1016/S0168-1605(01)00729-2
  48. Kobayashi T, Okuzumi M, Fuji J. Microflora of fermented puffer fish ovaries in rice bran 'fugunoko nukazuke'. Fish Sci. 61: 291-295 (1995) https://doi.org/10.2331/fishsci.61.291
  49. Eder W, Jahnke LL, Schmidt M, Huber R. Microbial diversity of the brine-seawater interface of the Kebrit Deep, Red Sea, studied via 16S rRNA gene sequences and cultivation methods. Appl. Environ. Microb. 7: 3077-3085. (2001)
  50. Uchida K. Multiplicity in soy pediococci carbohydrate fermentation and its application for analysis of their flora. J. Gen. Appl. Microbiol. 18: 109-129 (1982) https://doi.org/10.2323/jgam.18.109
  51. Roling WFM, van Verseveld HW. Characterization of Tetragenococcus halophila populations in Indonesian soy mash (kecap) fermentation. Appl. Environ. Microb. 62: 1203-1207 (1996)
  52. Noda F, Hayashi K, Mizunuma T. Antagonism between osmophilic lactic acid bacteria and yeasts in brine fermentation of soy sauce. Appl. Environ. Microb. 40: 452-457 (1980)
  53. Paik HD, Lee SK, Heo S, Kim SY, Lee HH, Kwon TJ. Purification and characterization of the fibrinolytic enzyme produced by Bacillus subtilis KCK-7 from chunggukjang. J. Microbial. Biotechn. 14: 829-835 (2004)