Recent Advances in Microbial Community Composition of Fermented Soy Whey and Its Mechanism for Biotransformation of Soybean Isoflavones

Fermented soy whey (FSW), a traditional natural tofu coagulant, harbors complex microbial communities that drive soy‐protein coagulation via organic‐acid secretion and enhance the bioavailability of soybean isoflavones, conferring desirable flavor characteristics and health‐beneficial bioactivities. However, several critical knowledge gaps restrict its scaled‐up industrial deployment. The dynamic regulatory connections between microbial community temporal succession and metabolite biosynthesis during spontaneous FSW fermentation have not been fully deciphered. Interspecies interactions inside highly heterogeneous microbial consortia remain ambiguous, and the whole‐fermentation system is exceptionally sensitive to fluctuating environmental conditions. This review synthesizes prior literature together with cutting‐edge multi‐omics datasets to systematically dissect the temporal dynamics of FSW microbial ecosystems. Enzymatic mechanistic analysis delineates key catalytic and metabolic pathways responsible for transforming soy isoflavone glucosides into aglycones and subsequent bioactive derivatives. We critically evaluate promising technical strategies, covering targeted synthetic‐biology modification, integrated intelligent control systems, artificial intelligence, and digital‐twin modeling, to advance the transition from experience‐driven spontaneous fermentation to precision manufacturing. Selective manipulation of functional microbes or rate‐limiting catalytic enzymes enables directional enrichment of high‐activity isoflavone metabolites. This framework mitigates bioavailability drawbacks of native isoflavones and builds solid scientific foundations for zero‐waste valorization of soy‐processing by‐products, circular food manufacturing, and innovative high‐value‐added functional‐food development.