Lactobacillus casei-Derived Postbiotics Elevate the Bioaccessibility of Proteins via Allosteric Regulation of Pepsin and Trypsin and Introduction of Endopeptidases

The potential of probiotics to benefit digestion has been widely reported, while its utilization in high-risk patients and potential adverse reactions have focused interest on postbiotics. A variable data-independent acquisition (vDIA)-based spatial-omics strategy integrated with unsupervised variational autoencoders was applied to profile the functional mechanism underlying the action of Lactobacillus casei-derived postbiotic supplementation in goat milk digestion in an infant digestive system, from a metabolomics–peptidomics–proteomics perspective. Amide and olefin derivatives were proved to elevate the activities of pepsin and trypsin through hydrogen bonding and hydrophobic forces based on allosteric effects, and recognition of nine endopeptidases and their cleavage to serine, proline, and aspartate were introduced by postbiotics, thereby promoting the generation of hydrophilic peptides and elevating the bioaccessibility of goat milk protein. The peptides originating from αs1-casein, β-casein, β-lactoglobulin, Ig-like domain-containing protein, κ-casein, and serum amyloid A protein, with multiple bioactivities including angiotensin I-converting enzyme (ACE)-inhibitory, osteoanabolic, dipeptidyl peptidase IV (DPP-IV) inhibitory, antimicrobial, bradykinin-potentiating, antioxidant, and anti-inflammatory activities, were significantly increased in the postbiotic supplementation group, which was also considered to potentially prevent necrotizing enterocolitis through inhibiting the multiplication of pathogenic bacteria and blocking signal transducer and activator of transcription 1 and nuclear factor kappa-light-chain-enhancer of activated B cells inflammatory pathways. This research deepened the understanding of the mechanism underlying the postbiotics affecting goat milk digestion, which established a critical groundwork for the clinical application of postbiotics in infant complementary foods.