Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis

https://doi.org/10.1016/j.ijfoodmicro.2008.05.013Get rights and content

Abstract

Kimchi is a traditional Korean food that is fermented from vegetables such as Chinese cabbage and radish. Many bacteria are involved in kimchi fermentation and lactic acid bacteria are known to perform significant roles. Although kimchi fermentation presents a range of environmental conditions that could support many different archaea and yeasts, their molecular diversity within this process has not been studied. Here, we use PCR-denaturing gradient gel electrophoresis (DGGE) targeting the 16S and 26S rRNA genes, to characterize bacterial, archaeal and yeast dynamics during various types of kimchi fermentation. The DGGE analysis of archaea expressed a change of DGGE banding patterns during kimchi fermentation, however, no significant change was observed in the yeast DGGE banding patterns during kimchi fermentation. No significant difference was indicated in the archaeal DGGE profile among different types of kimchi. In the case of yeasts, the clusters linked to the manufacturing corporation. Haloarchaea such as Halococcus spp., Natronococcus spp., Natrialba spp. and Haloterrigena spp., were detected as the predominant archaea and Lodderomyces spp., Trichosporon spp., Candida spp., Saccharomyces spp., Pichia spp., Sporisorium spp. and Kluyveromyces spp. were the most common yeasts.

Introduction

Fermentation is a well-known and ancient technique that uses microorganisms to process and preserve food (Ross et al., 2002). Kimchi is a Korean food prepared as a result of fermentation and in recent years it has been recognized as a health-promoting functional food (Song, 2004). Since it is interesting to know what microbes are involved by kimchi fermentation, the fermentation process has been studied extensively by microbiologists with respect to its ecology, proteomics, genetics and physiology (Kim and Chun, 2005, Li et al., 2006, Nan et al., 2005). These studies have reported that kimchi is a healthy food, rich in β-carotene, chlorophylls, dietary fiber and various minerals (Park et al., 2003). It supports a wide range of microorganisms, including lactic acid bacteria (LAB), which perform significant roles during fermentation (Bae et al., 2005, Kim and Chun, 2005). Bacterial isolates from kimchi have been investigated with respect to production and characterization of beneficial enzymes such as dextransucrase and alcohol/acetaldehyde dehydrogenase (Eom et al., 2007, Koo et al., 2005), and for biodegradation of toxic compounds such as sodium nitrite and bisphenol (Oh et al., 2004, Yamanaka et al., 2007).

Several halophilic archaea have been isolated from jeotgal, traditional Korean fermented seafood used in kimchi as an ingredient (Roh et al., 2007a, Roh et al., 2007b). Since the average NaCl concentration of kimchi is 3% (Mheen and Kwon, 1984), we reasoned that it could support haloarchaea. Yeasts such as Pichia spp. have been isolated from kimchi at low pH (about pH 4) that have been fermented over a long period of time (Oh and Han, 2003). However, the overall molecular diversity of yeasts and archaea in kimchi has not yet been reported.

Molecular biology techniques are used frequently to explore the diversity and structure of microbial communities, and microorganisms are identified using certain molecular markers such as 16S or 26S rRNA. In particular, the study of microbial ecology has benefited greatly from the introduction of denaturing gradient gel electrophoresis (DGGE), which provided a molecular fingerprinting technique for studying community structure (Yeates et al., 1998). In DGGE analysis, PCR amplicons of the same size but different sequences can be separated (Muyzer and Smalla, 1998) and this technique has been applied widely for studying microbial dynamics in complex environments such as soil (Sharma et al., 2006), sea (Bowman et al., 2003), insects (Reeson et al., 2003), sludge (Xia et al., 2005) and permafrost-affected soils (Ganzert et al., 2007). This method has also been used to investigate yeast diversity in foods such as wine (Cocolin et al., 2000a), sausage (Rantsiou et al., 2005), sourdough (Meroth et al., 2003) and coffee (Masoud et al., 2004).

In the present work, we studied population dynamics in the microbial community (bacteria, archaea and yeast) during fermentation of kimchi. We compared communities from various types of kimchi using culture-independent DGGE, which analyze 16S and 26S rRNA gene markers. For the best of our knowledge, this is the first report to reveal the diversity of archaea and yeast in kimchi analyzed by DGGE.

Section snippets

Kimchi sampling

Kimchi was obtained from the distributors of commercially-available brands. Samples were taken immediately after production in the factory and then stored at 4 °C during the sampling period. Population dynamics were monitored during fermentation using a cabbage kimchi purchased from the ‘C’ corporation (designated P kimchi). P kimchi is the best-selling kimchi brand and the most representative kimchi in Korea. It is processed with a variety of ingredients such as cabbage, red pepper powder,

Change in the microbial community during fermentation of kimchi

The pH change during fermentation of P kimchi is shown in Fig. 1. The DGGE banding patterns for bacteria, archaea and yeasts, were determined for each pH phase of kimchi fermentation (Fig. 2). pH decreased between P3 and P9, ranging between pH 5.3 and 4.1. The DGGE banding patterns of bacteria changed significantly between P3 and P4, but remained unchanged after P4 (Fig. 2A). Bands B1 to B5, which corresponded to two Bacillus and three eukaryotes, were not observed after P4, at which point the

Discussion

In general, the major ingredient of kimchi is Chinese cabbage and does not require the use of a starter culture. It is ripened by lactic fermentation and alcohol fermentation, a process performed primarily by LAB at low temperatures. Its main ingredients are vegetables such as cabbage or radish, and it can include additional ingredients such as onion, garlic, ginger and pepper. Currently, kimchi is in the health food spotlight because it is rich in nutrients and is recognized as a

Acknowledgements

This work was supported by the KRIBB Research Initiative Program, the Environmental Biotechnology National Core Research Center Program (KOSEF: R15-2003-012-02002-0) and the Conservation Technology Research and Development project hosted by the National Research Institute of Cultural Heritage (of the Cultural Heritage Administration). The first author was supported by the Korea Research Foundation Grant funded by the Korean Government (MOEHRD, Basic Research Promotion Fund)

References (52)

  • BaeJ.W. et al.

    Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria

    Applied and Environmental Microbiology

    (2005)
  • BowmanJ.P. et al.

    Prokaryotic metabolic activity and community structure in Antarctic continental shelf sediments

    Applied and Environmental Microbiology

    (2003)
  • CheighH.S. et al.

    Biochemical, microbiological, and nutritional aspects of kimchi (Korean fermented vegetable products)

    Critical Reviews in Food Science and Nutrition

    (1994)
  • CocolinL. et al.

    Development of a rapid method for the identification of Lactobacillus spp. isolated from naturally fermented Italian sausages using a polymerase chain reaction-temperature gradient gel electrophoresis

    Letters in Applied Microbiology

    (2000)
  • DeLongE.F.

    Archaea in coastal marine environments

    Proceedings of the National Academy of Sciences of the United States of America

    (1992)
  • GanzertL. et al.

    Methanogenic communities in permafrost-affected soils of the Laptev Sea coast, Siberian Arctic, characterized by 16S rRNA gene fingerprints

    FEMS Microbiology Ecology

    (2007)
  • GrantW.D. et al.

    Class III. Halobacteria class. nov

  • HenckelT. et al.

    Molecular analyses of the methane-oxidizing microbial community in rice field soil by targeting the genes of the 16S rRNA, particulate methane monooxygenase, and methanol dehydrogenase

    Applied and Environmental Microbiology

    (1999)
  • KanalH. et al.

    Natronococcus amylolyticus sp. nov., a haloalkaliphilic archaeon

    International Journal of Systematic Bacteriology

    (1995)
  • KimH.J. et al.

    Effects of yeast addition as starter on fermentation of Kimchi

    Korean Journal of Food Science Technology

    (1997)
  • KooO.K. et al.

    Cloning and characterization of the bifunctional alcohol/acetaldehyde dehydrogenase gene (adhE) in Leuconostoc mesenteroides isolated from kimchi

    Biotechnology Letters

    (2005)
  • LagesF. et al.

    Active glycerol uptake is a mechanism underlying halotolerance in yeasts: a study of 42 species

    Microbiology

    (1999)
  • LeeJ.S. et al.

    Identification of Leuconostoc strains isolated from Kimchi using carbon-source utilization patterns

    Journal of Microbiology

    (1997)
  • LeeJ.S. et al.

    Weissella koreensis sp. nov., isolated from kimchi

    International Journal of Systematic and Evolutionary Microbiology

    (2002)
  • LiS.J. et al.

    Dietary patterns are associated with sexual maturation in Korean children

    British Journal of Nutrition

    (2006)
  • MasoudW. et al.

    Yeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis

    Yeast

    (2004)
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