The effect of solid‐state fermentation on the bioaccessibility and in vitro gut microbiota modulation of soybean isoflavones

Abstract Background Soybean isoflavones mainly exist as isoflavone glycosides with poor bioaccessibility, which limits their functional application. Bioprocessing is commonly used as an effective strategy to enhance the nutritional quality of plant‐based foods. However, previous studies have largely focused on the physicochemical changes of isoflavones during fermentation, while the modulatory effects of isoflavones on gut microbiota remain insufficiently explored. To address this research gap, the present work further investigated the influence of isoflavones by solid‐state fermentation (SSF) with Rhizopus oligosporus RT‐3 on gut microbiota modulation. Results During SSF, β ‐glucosidase activity gradually increased, while the mycelial biomass showed a trend of first increasing and then decreasing. At 36 h of fermentation, the total isoflavone glycosides decreased from 466.25 to 95.47 μg g −1 d.w., while isoflavone aglycones increased to 1.93‐fold, from 130.70 to 252.88 μg g −1 d.w. Tempeh isoflavone aglycones exhibited better thermal stability than soybean isoflavone aglycones. The thermal degradation rate of total isoflavone aglycones in tempeh (11.93%) was 2.51 percentage points lower than that in soybean (14.44%) at 30 min. After SSF, daidzein content increased 2.73‐fold at 0.5 h of simulated in vitro digestion. Using fecal samples from four healthy donors, in vitro fecal fermentation indicated that tempeh isoflavones enhanced microbial diversity, enriching beneficial genera such as Bifidobacterium . Conclusion These findings demonstrate that SSF is a promising bioprocessing strategy for developing functional foods with microbiota modulation potential, supporting microbiota‐targeted nutrition and the industrial development of soybean products. © 2026 Society of Chemical Industry.