Comparative analysis of fungal microbiomes in Korean and Chinese chili pepper powders

Chili pepper powder plays a crucial role in kimchi fermentation; however, its use may result in fungal contamination. Therefore, analyzing its mycobiome is vital to maintain quality control standards. In this study, we used internal transcribed spacer (ITS)2 amplicon sequencing to compare fungal communities in commercially available Korean and Chinese chili pepper powders widely used in Korea (n = 9 per group).

Ascomycota was the predominant phylum in the Chinese and Korean chili pepper powders. Chinese powder samples exhibited higher genus-level diversity and were notably enriched in Vishniacozyma, whereas Korean powders showed relative enrichment in Fusarium and Issatchenkia. Species richness tended to be higher in Chinese than Korean samples (2.20 ± 0.42 vs. 1.82 ± 0.39). Beta diversity analysis revealed a distinct compositional separation between samples based on origin (permutational multivariate analysis of variance, P < 0.01). The distribution of potentially toxin-related genera also varied by origin: Aspergillus and Penicillium were more abundant in Chinese powders, whereas Fusarium predominated in Korean powders. Although detection at the genus level does not directly indicate mycotoxin contamination, origin-specific enrichment patterns suggest distinct toxin risk profiles warranting additional investigation.

These findings underscore the importance of systematically monitoring fungal and mycotoxin-producing communities in chili pepper powders and evaluating the impact of kimchi fermentation on mycotoxin persistence and mitigation. Such measures are essential for improving food safety and traceability. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.