Time-Resolved Regulation of Soymilk Matrices by Seed Germination: Linking Gastrointestinal Fate to Controlled Enhancement and Overprocessing-Induced Loss

Germination alters the nutrient matrix of soymilk, yet its digestion-related impacts remain unclear. Here, soymilk prepared from soybean seeds germinated for 0, 1, 2, and 3 days was heated and evaluated using a dynamic in vitro gastrointestinal model combined with rheology, particle/interaction analysis, and LC-MS/MS peptidomics. Increasing the level of germination strengthened the matrix, reduced the protein solubility, and enlarged particles, creating a more viscous system. During digestion, moderate germination (1-2 days) accelerated early proteolysis and enhanced intestinal peptide release and the diversity/abundance of several bioactive peptides, whereas extensive germination (3 days) produced excessive viscosity, delayed gastric protein breakdown, caused burst-type intestinal peptide release, and reduced detectable peptides. Peptidomics further identified the β-conglycinin α-subunit as the most digestion-variable protein, whose cleavage shifted from loops/terminal helices (1-2 days) to depletion of resistant β-strands at 3 days. These findings define a practical germination time for optimizing the soymilk matrix and functional outcomes.