High-Resolution Characterization of the Bacterial Microbiome in Chili Pepper Powder Using SMRT Sequencing

Chili pepper powder is an essential ingredient of Korean cuisine and kimchi products. As such, ensuring its microbiological safety is crucial from a public health perspective. In this study, the bacterial microbiomes of Korean and Chinese chili pepper powder samples were compared using high-resolution single-molecule real-time sequencing. Nine samples each from Korea and China were analyzed, yielding high-quality sequencing data with N50 values exceeding 1,460 bp and quality scores greater than Q30. Based on alpha diversity analysis, Chinese samples exhibited higher microbial diversity, whereas Korean samples had a more selective and clustered microbial structure, composed predominantly of <i>Bacillus</i>. Taxonomically, Chinese samples contained a wider range of genera, including <i>Pantoea</i>, <i>Weissella</i>, and <i>Klebsiella</i>, in contrast, Korean samples were dominated by Firmicutes, primarily <i>Bacillus</i> species. Although <i>Salmonella enterica</i> was detected in some Korean samples, viability was not confirmed. This may have indicated residual DNA or viable but nonculturable cells due to the low water activity of chili powders. Beta diversity analysis indicated moderate separation between the two groups, with Korean samples showing tighter clustering and Chinese samples displaying greater variability. Linear discriminant analysis effect size identified <i>Bacillus altitudinis</i> and <i>Bacillus safensis</i> as biomarkers for Korean samples, and <i>Pantoea agglomerans</i> and <i>Weizmannia coagulans</i> as biomarkers for Chinese samples. Overall, despite slightly lower microbial diversity, Korean chili pepper powder samples exhibited a more stable microbial community structure. Selection of chili pepper powder characterized by a stable and controlled microbiome could play an essential role in promoting the hygienic production and microbial safety of kimchi.