Abstract
Kimchi is a Korean traditional fermented food made of brined vegetables, with a variety of spices. Various microorganisms are associated with the kimchi fermentation process. This study was undertaken in order to apply quantitative real-time PCR targeting the 16S and 26S rRNA genes for the investigation of dynamics of bacterial, archaeal, and yeast communities during fermentation of various types of kimchi. Although the total bacterial and archaeal rRNA gene copy numbers increased during kimchi fermentation, the number of yeasts was not significantly altered. In 1 ng of bulk DNA, the mean number of rRNA gene copies for all strains of bacteria was 5.45×106 which was 360 and 50 times greater than those for archaea and yeast, respectively. The total gene copy number for each group of microorganisms differed among the different types of kimchi, although the relative ratios among them were similar. The common dominance of bacteria in the whole microbial communities of various types of kimchi suggests that bacteria play a principal role in the kimchi fermentation process.
Similar content being viewed by others
References
Bae, J.W., S.K. Rhee, J.R. Park, W.H. Chung, Y.D. Nam, I. Lee, H. Kim, and Y.H. Park. 2005. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 71, 8825–8835.
Butinar, L., S. Santos, I. Spencer-Martins, A. Oren, and N. Gunde-Cimerman. 2005. Yeast diversity in hypersaline habitats. FEMS Microbiol. Lett. 244, 229–234.
Chang, H.W., K.H. Kim, Y.D. Nam, S.W. Roh, M.S. Kim, C.O. Jeon, H.M. Oh, and J.W. Bae. 2008. Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis. Int. J. Food Microbiol. 126, 159–166.
Chelo, I.M., L. Ze-Ze, L. Chambel, and R. Tenreiro. 2004. Physical and genetic map of the Weissella paramesenteroides DSMZ 20288 chromosome and characterization of different rrn operons by ITS analysis. Microbiology 150, 4075–4084.
Cho, J., D. Lee, C. Yang, J. Jeon, J. Kim, and H. Han. 2006. Microbial population dynamics of kimchi, a fermented cabbage product. FEMS Microbiol. Lett. 257, 262–267.
de Boer, E. and R.R. Beumer. 1999. Methodology for detection and typing of foodborne microorganisms. Int. J. Food Microbiol. 50, 119–130.
Dolezel, J., J. Bartos, H. Voglmayr, and J. Greilhuber. 2003. Nuclear DNA content and genome size of trout and human. Cytometry 51, 127–128.
Furet, J.P., P. Quenee, and P. Tailliez. 2004. Molecular quantification of lactic acid bacteria in fermented milk products using real-time quantitative PCR. Int. J. Food Microbiol. 97, 197–207.
Hierro, N., B. Esteve-Zarzoso, A. Gonzalez, A. Mas, and J.M. Guillamon. 2006. Real-time quantitative PCR (QPCR) and reverse transcription-QPCR for detection and enumeration of total yeasts in wine. Appl. Environ. Microbiol. 72, 7148–7155.
Kanagawa, T. 2003. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96, 317–323.
Kim, M. and J. Chun. 2005. Bacterial community structure in kimchi, a Korean fermented vegetable food, as revealed by 16S rRNA gene analysis. Int. J. Food Microbiol. 103, 91–96.
Lee, C.W., C.Y. Ko, and D.M. Ha. 1992. Microfloral changes of the lactic acid bacteria during kimchi fermentation and identification of the isolates. Kor. J. Appl. Microbiol. Biotechnol. 20, 102.
Li, S.J., H.Y. Paik, and H. Joung. 2006. Dietary patterns are associated with sexual maturation in Korean children. Br. J. Nutr. 95, 817–823.
Loureiro, V. 2002. Spoilage yeasts in foods and beverages: characterization and ecology for improved diagnosis and control. Food Res. Int. 33, 247–256.
Martin, B., A. Jofre, M. Garriga, M. Pla, and T. Aymerich. 2006. Rapid quantitative detection of Lactobacillus sakei in meat and fermented sausages by real-time PCR. Appl. Environ. Microbiol. 72, 6040–6048.
Mheen, T.I. and T.W. Kwon. 1984. Effect of temperature and salt concentration on Kimchi fermentation. Kor. J. Food Sci. Technol. 16, 443–450.
Nan, H.M., J.W. Park, Y.J. Song, H.Y. Yun, J.S. Park, T. Hyun, S.J. Youn, Y.D. Kim, J.W. Kang, and H. Kim. 2005. Kimchi and soybean pastes are risk factors of gastric cancer. World J. Gastroenterol. 11, 3175–3181.
Oh, J.Y. and Y.S. Han. 2003. Purification and characterization of L-galactono-γ-lactone oxidase in Pichia sp. isolated from kimchi. Kor. J. Food Sci. Technol. 35, 1135–1142.
Renard, A., P. Gomez di Marco, M. Egea-Cortines, and J. Weiss. 2008. Application of whole genome amplification and quantitative PCR for detection and quantification of spoilage yeasts in orange juice. Int. J. Food Microbiol. 126, 195–201.
Reynisson, E., H.L. Lauzon, H. Magnusson, G.O. Hreggvidsson, and V.T. Marteinsson. 2008. Rapid quantitative monitoring method for the fish spoilage bacteria Pseudomonas. J. Environ. Monit. 10, 1357–1362.
Ritalahti, K.M., B.K. Amos, Y. Sung, Q. Wu, S.S. Koenigsberg, and F.E. Loffler. 2006. Quantitative PCR targeting 16S rRNA and reductive dehalogenase genes simultaneously monitors multiple Dehalococcoides strains. Appl. Environ. Microbiol. 72, 2765–2774.
Roh, S.W., Y.D. Nam, H.W. Chang, Y. Sung, K.H. Kim, H.J. Lee, H.M. Oh, and J.W. Bae. 2007. Natronococcus jeotgali sp. nov., a halophilic archaeon isolated from shrimp jeotgal, a traditional fermented seafood from Korea. Int. J. Syst. Evol. Microbiol. 57, 2129–2131.
Roh, S.W., Y.D. Nam, H.W. Chang, Y. Sung, K.H. Kim, H.M. Oh, and J.W. Bae. 2007. Halalkalicoccus jeotgali sp. nov., a halophilic archaeon from shrimp jeotgal, a traditional Korean fermented seafood. Int. J. Syst. Evol. Microbiol. 57, 2296–2298.
Ross, R.P., S. Morgan, and C. Hill. 2002. Preservation and fermentation: past, present and future. Int. J. Food Microbiol. 79, 3–16.
Suzuki, M.T. and S.J. Giovannoni. 1996. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl. Environ. Microbiol. 62, 625–630.
Takai, K. and K. Horikoshi. 2000. Rapid detection and quantification of members of the archaeal community by quantitative PCR using fluorogenic probes. Appl. Environ. Microbiol. 66, 5066–5072.
Yeates, C., M.R. Gillings, A.D. Davison, N. Altavilla, and D.A. Veal. 1998. Methods for microbial DNA extraction from soil for PCR amplification. Biol. Proc. Online 1, 40–47.
Author information
Authors and Affiliations
Corresponding author
Additional information
These authors contributed equally to this work.
Rights and permissions
About this article
Cite this article
Park, EJ., Chang, HW., Kim, KH. et al. Application of quantitative real-time PCR for enumeration of total bacterial, archaeal, and yeast populations in kimchi. J Microbiol. 47, 682–685 (2009). https://doi.org/10.1007/s12275-009-0297-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s12275-009-0297-1