Long-read rRNA operon sequencing reveals bacterial community divergence between traditional and industrial soybean fermentations

Traditional and industrial soybean fermentations harbor distinct microbial communities that influence product quality and safety. In this study, long-read rRNA operon sequencing was applied to investigate the bacterial communities of traditional and commercial doenjang and cheonggukjang. The 16S-23S rRNA operon (∼4.2 kb) was amplified and sequenced using the Oxford Nanopore MinION platform to obtain high-resolution taxonomic profiles. Traditional doenjang and cheonggukjang exhibited greater microbial diversity than commercial products, as revealed by alpha and beta diversity analyses. Bacillus species, particularly B. velezensis and B. subtilis, were dominant across all samples, while Loigolactobacillus coryniformis, Caldifermentibacillus hisashii, and Tetragenococcus halophilus were more abundant in traditionally fermented samples. These genera are associated with proteolysis, amino acid metabolism, and flavor compound formation during fermentation. Overall, these findings provide insights into the microbial ecology of fermented soybean foods and suggest that non-starter lactic acid bacteria and thermophilic species may contribute to the unique sensory characteristics of traditionally fermented doenjang.