Transcriptomic analysis of peptide production from solid-state fermented soybean meal by Bacillus subtilis SBM_1

Microbially fermented feeds enriched with peptides possess high nutritional value and offer potential for antibiotic-free feed development. Understanding the mechanisms of peptide generation during solid-state fermentation (SSF) is essential for process optimization. This study investigated transcriptional changes in Bacillus subtilis SBM_1 during SSF to explore the mechanisms underlying peptide production.

Differentially expressed genes (DEGs) were primarily enriched in pathways associated with metabolism, ABC transporters, amino acid biosynthesis, and biosynthesis of other secondary metabolites. Genes involved in extracellular protease synthesis and secretion were up-regulated, including those encoding proteases, chaperones, signal peptides, signal peptidases, and translocases. Bacillus subtilis SBM_1 also demonstrated the capacity to synthesize and secrete both ribosomally synthesized and post-translationally modified peptides (RiPPs) and non-ribosomal peptides (NRPs), as reflected by significant up-regulation of the amylocyclicin-encoding Acc cluster (1.44-1.59-fold) and the subtilin-related Spa cluster (8.37-17.95-fold). Gene clusters involved in the synthesis and transport of surfactin, bacitracin, and bacillaene, including Srf, Bac, Pks, and Acp, exhibited varying degrees of up-regulation. Gene clusters associated with intracellular peptide transmembrane transport (App, Opp, and Dpp) were also substantially up-regulated (4.02-20.79-fold) during fermentation.

These results indicate that during SSF, B. subtilis SBM_1 can synthesize peptides and secrete extracellular proteases to hydrolyze soybean proteins for peptide production. The synthesized peptides are subsequently exported via the ABC transporter pathway, collectively contributing to the accumulation of peptides in the fermentation system. © 2026 Society of Chemical Industry.