Multidimensional omics evaluation of the feather hydrolysates produced by Bacillus subtilis natto as a safe and functional feed protein.
Feather keratin is an abundant but poorly utilized protein resource for animal nutrition due to its highly recalcitrant structure. Here, we investigated whether the food-grade probiotic Bacillus subtilis natto can directly hydrolyze intact chicken feathers and evaluated the resulting fermentation product as a safe and functional feed protein using multidimensional omics. B. subtilis natto efficiently degraded feathers in sterile tap water, accompanied by bacterial proliferation and increased extracellular proteolytic activity. Recombinant nattokinase was produced and purified to support mechanistic interpretation of keratinolysis. The hydrolysate comprised a soluble fraction enriched in free amino acids and short peptides, as well as an insoluble fraction containing keratin-derived nano/microparticles and bacterial cells. Bioinformatic annotation of hydrolysate peptides suggested potential roles in cell-cell junction organization, tight-junction regulation, and diverse transport and metabolic processes. In a 30-day mouse feeding trial, hydrolysate supplementation showed no adverse effects on growth, organ histology, or serum biochemical indices, while elevating IgA. Intestinal transcriptomic and proteomic profiling indicated enhanced mucosal immune programs and barrier-associated pathways. 16S rRNA sequencing further revealed a remodeled gut microbiota characterized by enrichment of multiple probiotic genera, accompanied by altered short-chain fatty acid profiles. Collectively, these data establish a simple probiotic fermentation strategy to valorize feather waste into a biosafe, omics-validated functional feed protein with potential benefits for gut homeostasis.