Analysis of microbial diversity in shrimp- and fish-jeotgal by cultivation-independent and -dependent methods

Abstract

Cultivation-based techniques have traditionally been the primary tools utilized for studying the microbiology of food environments. Recently, nucleic acid-based methods have been employed to further characterize the microbial diversity in food. In Jeotgal sampes, both in fish and shrimp, pH was low 5.5-7.5, so more than 70% microbial population belongs to the Firmicutes bacteria and they might have major role in lactic acid production. By using both cultivation-dependent and -independent methods, it was proved that both methods are working together and to understand the true picture of microbial diversity in food, we have to improve the culture method so that with less labour and time consuming, it might be able to grow more and more bacteria. Culture method supported the fast growing bacteria but by changing the traditional method and with the combination of molecular methods, this can be a good technique to understand the microbial ecology of any environment. Random cloning helped to see not only uncultured bacteria but many new groups in prokaryotes and eukaryotes which could not be cultivated in cultivation method, so this method showed superiority to culture method. Although T-RFLP has shown the clear peak difference among the samples, but there is still extensive need to improve the method of DNA extraction especially in food, which has lot of inhibitors for PCR reaction. During the DNA extraction, a lot of DNA is lost; it should be saved by improvement. During the analysis of bacterial diversity, a lot of cultureable group appeared in both cultivation-dependent and -independent methods, e.g. Bacillus, Staphylococcus, Tetragenococcus, Atopostipes, Haloanaerobium, Carnobacterium and some other group which are not studied at all or very little in other foods and there is no describable reference for them. Some of them can be grown on the wide range of temperature, NaCl, and pH, like Bacillus and Staphylococcus. They can be tried as a starter and then by low...