Abstract
Bacillus velezensis, a key microorganism in traditional Korean soybean-fermented foods such as Meju, contributes to flavor and food safety. In this study, B. velezensis strains were isolated from Meju, and their morphological characteristics and biosynthetic gene clusters were analyzed using whole-genome sequencing. Pangenome analysis identified core and accessory genes, with MJ06 showing the highest number of genes associated with secondary metabolite biosynthesis, transport, and catabolism. Antimicrobial assays against six foodborne pathogenic bacteria and six fungi revealed MJ06 had the strongest antimicrobial activity, correlating with its enriched secondary metabolite biosynthetic gene clusters. Active antimicrobial compounds were extracted using C18 cartridges and anion exchange chromatography, and liquid chromatography-mass spectrometry analysis identified surfactin and bacillomycin D as major bioactive metabolites. This study highlights the power of comparative genomics in linking genetic potential to functional antimicrobial traits, facilitating the targeted selection of industrially valuable strains for food safety applications. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10068-025-01901-3.