Pediococcus inopinatus with a well-developed CRISPR-Cas system dominates in long-term fermented kimchi, Mukeunji.

Kimchi is produced through a low-temperature fermentation without pre-sterilization, resulting in a heterogeneous microbial community. As fermentation progresses, dominant lactic acid bacteria (LAB) species emerge and undergo a transition process. In this study, LAB were isolated from Mukeunji, a long-term fermented kimchi that is in the final stage of kimchi fermentation process. It was confirmed, through culture-dependent and independent analysis, as well as metagenome analysis, that Pediococcus inopinatus are generally dominant in long-term fermented kimchi. Comparative analysis of the de novo assembled whole genome of P. inopinatus with other kimchi LAB revealed that this species has a well-developed clustered regularly interspaced short palindromic repeats (CRISPR) system. The CRISPR system of P. inopinatus has an additional copy of the csa3 gene, a transcription factor for cas genes. Indeed, this species not only highly expresses cas1 and cas2, which induce spacer acquisition, but also has many diverse spacers that are actively expressed. These findings indicate that the well-developed CRISPR-Cas system is enabling P. inopinatus to dominate in long-fermented kimchi. Overall, this study revealed that LAB with a robust defense system dominate in the final stage of kimchi fermentation and presented a model for the succession mechanism of kimchi LAB.