Fermentation by Bacillus siamensis BSJ-2 degrades Cruciferin to improve bioactive peptides and essential amino acids in rapeseed meal

Background Rapeseed meal is an economical agricultural by-product with a high protein content. The main storage protein Cruciferin accounts for about 60% crude protein, but is difficult to be digested. The nutritional value of rapeseed meal is constrained by the low digestibility of Cruciferin. Results We identified Bacillus siamensis BSJ-2 as a potent Cruciferin-degrading strain and demonstrated that fermentation with B. siamensis BSJ-2 substantially improved the protein quality and value of rapeseed meal. Peptidomic analysis revealed a marked increase in the abundance and diversity of total peptides following B. siamensis BSJ-2 fermentation. Notably, a series of newly identified Cruciferin-derived peptides containing the sequence motif SYDLPILRFLRL were specifically enriched in B. siamensis BSJ-2-fermented rapeseed meal and exhibited antioxidant activity. Furthermore, targeted metabolomic analysis demonstrated a pronounced increase in several essential amino acids after B. siamensis BSJ-2 fermentation. Conclusions Our findings demonstrate that fermentation with B. siamensis BSJ-2 can effectively remodel the protein-derived peptide and amino acid profiles of rapeseed meal, enhancing the generation of potential bioactive peptides and essential amino acids. This study provides new insights into the value-added bioconversion of rapeseed meal and establishes a promising microbial fermentation strategy for developing high-protein, nutritionally enhanced feed ingredients.