Exploring microbial dynamics and metabolomic profiling of isoflavone transformation in black and yellow soybean tempe for sustainable functional foods

Tempe, a traditional Indonesian fermented food, is rich in bioactive isoflavones and peptides, offering significant health benefits. This study explores how fermentation methods and soybean varieties shape isoflavone profiles and microbial communities. Two fermentation approaches were compared: Raprima™ starter culture and a co-culture of <i>Rhizopus oligosporus</i> and <i>R. stolonifer</i>. Metabolomic analysis showed that co-culture fermentation significantly increased genistein levels and enhanced isoflavone bioavailability. Proteobacteria (78 %) and Firmicutes (18 %) dominated bacterial communities, with yellow soybeans containing more Enterobacteriaceae. Co-culture fermentation enriched <i>Stenotrophomonas</i>, while Raprima™ favored <i>Acinetobacter</i>. The fungal community, primarily Mucoromycota (92 %), exhibited significant correlations with isoflavone transformation. Co-culture fermentation improved microbial synergy and metabolic efficiency, boosting isoflavone aglycone production. While yellow soybeans had higher isoflavone content, black soybeans, with elevated genistein, present a promising alternative. These findings emphasize fermentation's role in enhancing tempe's functionality for sustainable, nutritionally rich food development.