Diversity and community analysis of fermenting bacteria isolated from eight major Korean fermented foods using arbitrary-primed PCR and 16S rRNA gene sequencing

Abstract

Korean fermented foods are known to be beneficial for human health. Bacterial community studies have been conducted to figure out what roles the bacteria used to ferment these foods play in food fermentation. The metagenomic approach identifies both culturable and unculturable bacterial compositions, but this technique is limited in its ability to accurately determine the bacterial species from short 16S rRNA PCR products. In this study, we revisited the culture-dependent method using a relatively large number of bacterial isolates in an attempt to overcome the problem of bacterial identification, accepting that the unculturable bacterial population in each fermented food would be undetectable. Eight Korean fermented foods including kimchi, jeotgal, and meju were collected, and 1589 fermenting bacterial strains were randomly isolated. Bacteria were grouped by banding pattern using arbitrary-primed (AP) PCR prior to bacterial identification and sorted into 219 groups; 351 strains were not grouped because there was no identical AP-PCR band pattern. 16S rRNA sequence analysis identified the bacterial compositions of the fermented foods. As dominant genera, Lactobacillus and Leuconostoc strains were detected in four kimchi samples, Staphylococcus in three jeotgal samples, and Enterococcus and Bacillus in the meju sample. Interestingly, S. Equorum was most dominant in saeu-jeotgal, indicating that it is halophilic and may enhance the fermentation flavor. Further comparative analysis of this study with previous metagenomic results revealed that bacterial communities in fermented foods are highly similar at the genus level but often differ at the species level. This bacterial community study is useful for understanding the roles and functional properties of fermenting bacteria in the fermentation process of Korean fermented foods.