Metagenomic Analysis of Kimchi, a Traditional Korean Fermented Food

Abstract

Kimchi, a traditional food in the Korean culture, is made from vegetables by fermentation. In this study, metagenomic approaches were used to monitor changes in bacterial populations, metabolic potential, and overall genetic features of the microbial community during the 29-day fermentation process. Metagenomic DNA was extracted from kimchi samples obtained periodically and was sequenced using a 454 GS FLX Titanium system, which yielded a total of 701,556 reads, with an average read length of 438 bp. Phylogenetic analysis based on 16S rRNA genes from the metagenome indicated that the kimchi microbiome was dominated by members of three genera: Leuconostoc, Lactobacillus, and Weissella. Assignment of metagenomic sequences to SEED categories of the Metagenome Rapid Annotation using Subsystem Technology (MG-RAST) server revealed a genetic profile characteristic of heterotrophic lactic acid fermentation of carbohydrates, which was supported by the detection of mannitol, lactate, acetate, and ethanol as fermentation products. When the metagenomic reads were mapped onto the database of completed genomes, the Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 and Lactobacillus sakei subsp. sakei 23K genomes were highly represented. These same two genera were confirmed to be important in kimchi fermentation when the majority of kimchi metagenomic sequences showed very high identity to Leuconostoc mesenteroides and Lactobacillus genes. Besides microbial genome sequences, a surprisingly large number of phage DNA sequences were identified from the cellular fractions, possibly indicating that a high proportion of cells were infected by bacteriophages during fermentation. Overall, these results provide insights into the kimchi microbial community and also shed light on fermentation processes carried out broadly by complex microbial communities.

Multifactorial diversity sustains microbial community stability

“…However its use for simpler communities is not straightforward as the resolution beyond the species level is lost. The metagenomic analysis of a simple community that is involved in Kimchi fermentation revealed the domination of community by members of the genera Leuconostoc, Lactobacillus and Weissella, however, the resolution at the strain level was not achieved (Jung et al, 2011). In the approach presented here, the resolution was enhanced with the quantification of lineage-specific OGs that were determined from the genome sequences of distinct lineages.…”

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

“…To the author's knowledge, only two studies reported metagenome shotgun sequencing from food. One investigated the microbiota of marinated and unmarinated broiler meat (53), and the other reported the metagenome sequencing of kimchi, a traditional Korean fermented food (54). Although the studies of metagenomes from food have great potential, a current limitation is the database availability due to the many genomes of food-related bacteria still to be sequenced.…”

Methods to assess lactic acid bacteria diversity and compatibility in food

“…The Rep-PCR method is used to differentiate -at species, subspecies and potentially strain level -a wide range of LAB isolated from dairy products (FEUTRY et al, 2012) or fermented sausages (KESMEN et al, 2012). Pyrosequencing, an automated high-throughput sequencing technique that involves the synthesis of single-stranded deoxyribonucleic acid and the detection of the light generated by pyrophosphate released in a coupled reaction with luciferase, was recently proposed to study food fermentations (JUNG et al, 2011). This technique allows the rapid and accurate sequencing of nucleotide sequences that can then be used to analyse the population structure, gene content and metabolic potential of the microbial communities in an ecosystem.…”