Defatted Soybean Meal-Based Koji Promotes Flavor Development in Deyang Baiwo Soy Sauce: A Comparative Multi-Omics Study

Although the influence of raw material composition on soy sauce koji fermentation is well recognized, the differences in microbial succession and metabolic pathways between whole soybean koji (WSK) and defatted soybean–wheat bran koji (DSK) remain unclear. In this study, a multi-omics approach integrating absolute quantitative PCR and physicochemical analyses was employed to elucidate the mechanisms by which DSK enhances the quality of Deyang Baiwo soy sauce. Compared with WSK, DSK exhibited lower moisture content but higher total acidity, amino nitrogen, and reducing sugar levels, indicating its suitability for high-quality soy sauce production. Volatile analysis revealed greater accumulation of key aroma compounds such as 2-methoxy-4-vinylphenol and 4-vinylguaiacol in DSK, contributing characteristic smoky flavors. At the microbial community level, Aspergillus, Weissella, Enterobacter, and Bacillus were enriched in DSK, promoting the accumulation of flavor and aroma compounds in alignment with industrial koji production objectives. Metabolic pathway analysis indicated that Weissella in DSK was primarily responsible for lactic acid accumulation, whereas Aspergillus dominated early-stage substrate degradation and played a key role in the enrichment of 1-octen-3-ol in WSK. This study provides insights into the “substrate–microbiota–metabolite” regulatory network and offers a theoretical basis for optimizing the use of defatted soybean in traditional soy sauce fermentation.