Genome-resolved insights into the ecology, metabolic potential, salt-stress adaptation, and safety of Staphylococcus in traditional Korean soybean fermentation

Staphylococcus species are frequently detected during traditional Korean soybean fermentations, yet their ecological roles, metabolic functions, and safety characteristics remain poorly defined. In this study, we conducted an integrated genome-resolved and phenotypic analysis of Staphylococcus strains associated with traditional Korean soybean fermentation to clarify their functional significance and safety relevance. Using 23 controlled fermentation batches prepared with region-specific raw materials, we isolated 66 Staphylococcus strains and generated 47 non-redundant representative genomes. Species-level community analysis identified eight Staphylococcus species, with S. xylosus, S. shinii, S. equorum, and S. nepalensis representing the major taxa during fermentation. Genome-based metabolic reconstruction, enzymatic assays, and carbohydrate utilization tests revealed pronounced species- and strain-level heterogeneity. Although protease and amylase activities were generally limited, lipase and β-glucosidase activities were relatively high and highly variable, indicating potential functional roles in soybean fermentation. The strains encoded diverse carbon metabolic pathways and conserved biosynthetic and transport systems for the compatible solutes glycine betaine and proline, supporting adaptation to high-salinity fermentation environments. Safety assessment integrating antimicrobial susceptibility testing with genome-based analyses showed that most strains were coagulase-negative, non-hemolytic, and susceptible to clinically important antibiotics. However, the identification of S. saprophyticus, a known pathogen, harboring mobile resistance elements, including SCCmec-associated genes, underscores the need for strain-level safety evaluation despite overall low phenotypic resistance rates. Overall, this study provides a comprehensive genome-resolved and strain-level evaluation of Staphylococcus associated with traditional Korean soybean fermentation.