Identification and validation of core microbes for isoflavone conversion and flavor formation in fermented sojae semen praeparatum

Sojae semen praeparatum (SSP), a fermented derivative of Glycine max (L.) Merr, is extensively utilized in the food industry due to its distinctive flavor profile. However, the core microbial community driving fermentation, its functional contributions to isoflavone conversion and flavor formation, and the underlying microbial interactions remain poorly understood. This study characterized the dominant microbial taxa in SSP fermentation, assessed their associations with isoflavone metabolism and flavor modulation, and validated their functional roles through single and co-culture fermentation models. Six bacterial and two fungal genera were identified as core constituents. Correlation analysis demonstrated that Aspergillus played a significant role in isoflavone transformation, while Bacillus contributed to the augmentation of key aroma compounds in SSP ( p < 0.01). Functional validation experiments confirmed that co-culture fermentation markedly intensified flavor complexity, particularly by amplifying fruity and mushroom-like aromatic notes. Moreover, co-cultivation facilitated the conversion of bound isoflavones into bioavailable aglycones, thereby enhancing antioxidant potential. These findings provide a framework for deciphering microbial interactions in SSP fermentation and offer insights for targeted modulation of the fermentation process, ultimately enabling the optimization of strategies to improve product consistency and quality. • Identified 409 VOCs in fermented sojae semen praeparatum via HS-SPME-GC-MS. • Six bacterial and two fungal genera were identified as core microbes. • Core microbes ( A.oryzae , B. subtilis ) drive flavor formation. • Co-fermentation enhanced conversion of bound isoflavones to bioactive aglycones.