Analysis of Bacterial Diversity in Fermented Skate Using Culture-dependent and Culture-independent Approaches
2010
Lee, E.J., Paichai University, Daejeon, Republic of Korea | Kim, T.H., Paichai University, Daejeon, Republic of Korea | Kim, H.K., Paichai University, Daejeon, Republic of Korea | Lee, J.K., Paichai University, Daejeon, Republic of Korea | Kwak, H.S., Paichai University, Daejeon, Republic of Korea | Lee, J.S., Paichai University, Daejeon, Republic of Korea
Fermented skate is a traditional Korean food popular in Southwestern area of Korea. It has a characteristic flavor and alkaline pH. In this study we tried to determine the microbial flora in fermented skate using two different approaches. In culture-independent method, we amplified V2 region of 16S rRNA gene by PCR and cloned them into pUC18 plasmid to construct 16S rDNA fragment library. BLAST searches for the sequences obtained from this library revealed that uncultured bacterium clone 054E11.b was the most dominant flora in this fermented fish. In culture-dependent method, we diluted suspension of skate and spreaded on MRS, PCA, and MacConkey plates. We identified colonies grown on those plates by using PCR amplification of V2 region of 16S rRNA and DNA sequencing. BLAST searches of those DNA sequences resulted in totally different species with the observations from the 16S rDNA library analysis. Discrepancies of results obtained from both approaches suggest that the agar plates used in culture-dependent method may be different from the real condition of fermented skate. Therefore, results from culture-independent approach using 16S rDNA fragment library analysis may reflect real microbial flora in fermented skate.
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