Microbial diversity and peptide dynamics during the spontaneous fermentation of whey from the Yunnan ethnic cheese...

Rushan whey (RW) is a byproduct of Rushan cheese production, yet its potential as a source of bioactive peptides remains unexplored. Here, microbial dynamics and peptide profiles were monitored throughout spontaneous RW fermentation. Bacterial diversity declined drastically within the first week, by the end of which Lactobacillus (specifically L. delbrueckii and L. helveticus), dominated the community, followed by Acetobacter (specifically A. fabarum and A. pasteurianus). Fungi, particularly Saccharomyces cerevisiae and Pichia kudriavzevii, appeared only on day 14. Peptide diversity decreased over time, while β-casein-derived peptides consistently dominated the peptidome. Abundances of total and putative bioactive peptides peaked on days 11 and 7, respectively, before declining markedly thereafter. Variations in total, casein-fraction-derived, and putative bioactive peptides were correlated with specific bacterial taxa. This study is the first to apply peptidomics to elucidate peptide generation dynamics during RW fermentation, providing a scientific basis for RW valorization through targeted, microbe-driven bioactive peptide enrichment.