Effects of fermentation on protein digestion and peptide release in an in vitro adult digestion model

Fermented milk is considered a functional food, while how the fermentation influences the protein digestion and especially the peptide formation during digestion is not fully understood. Therefore, pasteurized whole milk (W) was compared with two fermented samples obtained by fermenting W with Lactobacillus bulgaricus in combination with Bifidobacterium animalis subsp. lactis (Y1) or with Lactobacillus bulgaricus alone (Y2). This study compared the digestion of yoghurt and whole milk, especially focusing on the peptides profile of gastric and intestinal digesta. Y1 and Y2 showed higher protein hydrolysis degree and higher intensity of overall peptides than W, both in gastric and intestinal digesta. PCA analysis of peptidomics data showed that fermentation altered the peptide profile of the gastric digesta but not that of the intestinal digesta. Further analysis of gastric digesta peptides showed that subgroup of peptides significantly more abundant and only present in fermented milk samples was generally longer than those more abundant in whole milk. The cleavage site patterns of these peptide subgroups also differed between fermented and unfermented samples. According to in silico analysis, the intensity and diversity of both bioactive peptides and epitopes were higher in the gastric digesta of fermented milk samples, consistent with the overall trend observed for total peptides. Whole milk digesta showed higher overall epitope intensity than fermented milk after intestinal digestion, suggesting a potentially lower allergenicity of fermented milk; however, further validation is required. This study provides insight into how milk fermentation influences protein digestion and peptide formation, with implications for the bioactivity and allergenic properties of fermented milk products.