Analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis.
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.
Chang
Ho-Won
HW
Biological Resource Center, KRIBB, Daejeon 305-806, South Korea.
Kim
Kyoung-Ho
KH
Nam
Young-Do
YD
Roh
Seong Woon
SW
Kim
Min-Soo
MS
Jeon
Che Ok
CO
Oh
Hee-Mock
HM
Bae
Jin-Woo
JW
D001105:Archaea / Q000235:genetics / Q000302:isolation & purification*; D001483:Base Sequence; D001937:Brassica / Q000382:microbiology*; D016000:Cluster Analysis; D019641:DNA, Archaeal / Q000737:chemistry / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D005285:Fermentation; D005516:Food Microbiology; D006801:Humans; D007777:Lactobacillaceae / Q000235:genetics / Q000302:isolation & purification*; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D011157:Population Dynamics; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D012336:RNA, Ribosomal, 16S; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D013997:Time Factors; D015003:Yeasts / Q000235:genetics / Q000302:isolation & purification*
D019641:DNA, Archaeal; D004269:DNA, Bacterial; D004271:DNA, Fungal; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; C065096:RNA, ribosomal, 26S