The Microbial Diversity of Non-Korean Kimchi as Revealed by Viable Counting and Metataxonomic Sequencing

Abstract

Kimchi is recognized worldwide as the flagship food of Korea. To date, most of the currently available microbiological studies on kimchi deal with Korean manufactures. Moreover, there is a lack of knowledge on the occurrence of eumycetes in kimchi. Given these premises, the present study was aimed at investigating the bacterial and fungal dynamics occurring during the natural fermentation of an artisan non-Korean kimchi manufacture. Lactic acid bacteria were dominant, while Enterobacteriaceae, Pseudomonadaceae, and yeasts progressively decreased during fermentation. Erwinia spp., Pseudomonasveronii, Pseudomonasviridiflava, Rahnellaaquatilis, and Sphingomonas spp. were detected during the first 15 days of fermentation, whereas the last fermentation phase was dominated by Leuconostoc kimchi, together with Weissellasoli. For the mycobiota at the beginning of the fermentation process, Rhizoplaca and Pichia orientalis were the dominant Operational Taxonomic Units (OTUs) in batch 1, whereas in batch 2 Protomyces inundatus prevailed. In the last stage of fermentation, Saccharomyces cerevisiae, Candida sake,Penicillium, and Malassezia were the most abundant taxa in both analyzed batches. The knowledge gained in the present study represents a step forward in the description of the microbial dynamics of kimchi produced outside the region of origin using local ingredients. It will also serve as a starting point for further isolation of kimchi-adapted microorganisms to be assayed as potential starters for the manufacturing of novel vegetable preserves with high quality and functional traits.

Keywords: Candida sake; Leuconostoc kimchii; Weissella soli; fermented vegetables; microbial diversity.

Figure 1

Ready-to-eat cabbage-origin kimchi.

Figure 2

Results of pH measurements of two kimchi manufactures (batch 1 and batch 2) during fermentation. Values are expressed as means ± standard deviation. For each sampling time, means with different letters are significantly different (p < 0.05).

Figure 3

Principal Component Analysis (PCA) based on Operational Taxonomic Units (OTUs) relative abundance of kimchi samples for bacteria (panel A) and fungi (panel B) grouped according to the batch, or according to: (i) the fermentation period; (ii) beginning of fermentation: t0, t2, t5, t15; (iii) end of fermentation: t36, t43, t50, t57, for bacteria (panel C) and fungi (panel D).

Figure 4

Relative abundance of bacterial Operational Taxonomic Units (OTUs) detected by sequencing in the analyzed kimchi batches. Samples are grouped according to batch (1 and 2) and labeled according to fermentation time.

Figure 5

Relative abundance of lactic acid bacteria Operational Taxonomic Units (OTUs) detected by sequencing in the analyzed kimchi batches. Samples are grouped according to batch (1 and 2) and labeled according to fermentation time.

Figure 6

Boxplots showing the relative abundance of bacterial Operational Taxonomic Units (OTUs) between the beginning of fermentation: t0, t2, t5, t15, and the end of fermentation: t36, t43, t50, t57. Boxes represent the interquartile range (IQR) between the first and third quartiles, and the line inside represents the median (2nd quartile).

Figure 7

Relative abundance of fungal Operational Taxonomic Units (OTUs) detected by sequencing in the analyzed kimchi batches. Samples are grouped according to batch (1 and 2) and labeled according to fermentation time.

Figure 8

Boxplots showing the relative abundance of fungal Operational Taxonomic Units (OTUs) between the beginning of fermentation: t0, t2, t5, t15, and the end of fermentation: t36, t43, t50, t57. Boxes represent the interquartile range (IQR) between the first and third quartiles, and the line inside represents the median (2nd quartile).