Integrative Insights Into Bioactive Peptides in Milk Fermented With Autochthonous and Commercial Cultures Using High‐Throughput Peptidomics and Machine Learning

ABSTRACT Microbial fermentation represents an efficient strategy for the production of bioactive peptides (BPs) with numerous health‐promoting effects. This study addresses the lack of comparative data on how starter cultures influence the peptide content of fermented foods by analyzing three high‐quality milk drinks fermented with autochthonous (AC), commercial (CC), and combined starter cultures (CAC), using high‐throughput mass spectrometry‐based peptidome profiling. A total of 89 peptides were identified, 34 of which exhibit diverse bioactivities. Specifically, 75 peptides were detected in CC, 62 in AC, and only 36 in CAC drinks, including 32, 29, and 27 BPs, respectively. In silico screening of 55 peptides with previously unreported bioactivities filtered out peptides 42 KIAKYIPIQY 51 and 40 RINKKIEKF 48 as the most promising BP candidates, as they were predicted to be bioactive by five out of six machine learning models. These findings underscore the crucial role of starter culture selection in optimizing BP production in fermented dairy drinks.