As a group of important bioactive compounds in soybeans, isoflavones are beneficial to human health, and aglycone isoflavones are more readily absorbed and utilized by the human body. Soymilk is a widely consumed soy-based beverage. The reduction in isoflavones content during soymilk production can lower its nutritional quality. This study aimed to increase the total isoflavones content and the proportion of aglycone isoflavones in soymilk through seeds germination and the followed soymilk incubation. In this study, changes in the isoflavone content and composition of soymilk made from germinated and raw soybeans were detected at different processing stages. Single-factor and response surface experiments were carried out to optimize the incubation conditions, aiming to enhance the content of aglycone isoflavones in soymilk made of germinated soybeans. The results showed that total isoflavones content increased from 3722.23 μg/g DW to 4337.93 μg/g DW in 2-day germinated soybeans, and incubation promoted the conversion of conjugated isoflavones to aglycone isoflavones in soymilk. Under the optimal incubation conditions (53.26 ± 1.0 °C for 56.64 ± 1.0 min), the content of aglycone isoflavones in soymilk significantly increased by 44.43% compared with the control, and the incubation with optimized conditions had little effect on its microbial safety, nutrients content and overall flavor, consequently leading to no significant deterioration in its quality after incubation. Therefore, the combination of germination and incubation is an efficient strategy to enhance the aglycone isoflavones content in soymilk, providing valuable information for enhancing the isoflavones bioactivity of soymilk during processing.
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