The Analysis of Bacterial Community in Fall-harvested Chinese Cabbage from Various Regions in Korea

Abstract

Chinese cabbage (Brassica rapa subsp. pekinensis) is one of the most popular vegetables in northeast Asia and its consumption is increasing worldwide. Although foodborne outbreaks by consumption of Chinese cabbage have increased, the investigation of the microbiome on Chinese cabbage has been limited. To study the phyllosphere of Chinese cabbage, 54 samples were collected from 18 South Korean farms in autumn. The Illumina Miseq sequencing technology was employed to measure the structure of bacterial community associated with Chinese cabbages. In this study, microbiome on Chinese cabbage and its potential risks as foodborne pathogens were investigated in association with geographical variations. To amplify the V5-V6 regions of bacterial 16S rRNA genes and minimize the contamination of chloroplast and plant mitochondria, three different forward primer sets were tested and primer combination of 799F-mod6/1114R was selected for this study. The results indicated that Proteobacteria and Bacteroidetes were dominant phyla on the Chinese cabbage. The most abundant genera on the Chinese cabbages were Chryseobacterium, Aurantimonadaceae, Sphingomonas and Pseudomonas. Diverse potential pathogens, such as Pantoea, Erwinia, Klebsiella, Yersinia, Bacillus, Staphylococcus, Salmonella and Clostridium were also detected from the samples tested. Geographical comparisons of the Illumina sequencing data revealed that Pseudomonas, Flavobacterium, Pantoea, Enterobacteriaceae_g and Oxalobacteraceae_g from samples obtained from Jeolla-do were more abundant than those from Gangwon-do, while the abundance of the Aurantimonadaceae_g and Sphingobacterium were less abundant. The microbiomes of the three groups were clustered by three dimensional Principal Coordinates Analysis (PCoA) plot, and the microbial communities of the Gangwon-do and Chungcheong-do was closely associated. Overall, the results of this study revealed that diverse bacterial communities that reside on the Chinese cabbage. Also, our data suggest that various environmental factors, especially geographic location, affect the microbiome of Chinese cabbage.