Soybean whey, a nutrient-rich byproduct generated during the production of soybean protein isolate, can only be discharged after undergoing sewage treatment, which imposes a significant economic burden on enterprises. In this study, we investigated a Bacillus subtilis BSNK-5 fermentation soybean whey process that yielded high production of nattokinase (NK) and γ-polyglutamic acid (γ-PGA), along with the fabrication of an emulsion using fermentation soybean whey, to achieve high-value conversion of soybean whey. The results showed that soybean whey can be used as a nutrient-rich substrate to promote the efficient synthesis of NK and γ-PGA by BSNK-5, with the highest yields of 9 × 104 IU/mL and 250 g/L, respectively. Meanwhile, the synthesized γ-PGA can serve as a suitable biological macromolecule to form an emulsification system that protects NK. The encapsulation efficiency of NK was over 60%, and the release of encapsulated NK was delayed in vitro. Meanwhile, the nanoemulsions remained stable when exposed to 37 °C and 65 °C temperatures, salt concentrations ranging from 50 to 150 mM, and undergoing a single freeze-thaw cycle. The development of functional thrombolytic preparations by self-emulsification protection of NK by γ-PGA produced via BSNK-5 fermentation represents an effective way to achieve high value utilization of soybean whey.
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