A novel antimicrobial peptide NDYT-8 with broad-spectrum activity from Bacillus subtilis natto: Antibacterial mechanism and sequence simplification

Abstract

The discovery of antimicrobial peptides (AMPs) holds critical significance in combating antibiotic resistance. In this study, a novel efficient antimicrobial peptide NDYT-8 with broad-spectrum activity was isolated and identified from Bacillus subtilis natto. Whole-genome sequencing revealed that NDYT-8 potentially derived from the minimal domain of 6-phosphogluconate dehydrogenase, exhibited broad-spectrum antibacterial activity against common foodborne pathogens, particularly Escherichia coli and Salmonella enterica, with a minimum inhibitory concentration (MIC) value of 16 μg/mL. Mechanistic investigations demonstrated that NDYT-8 exerted its antibacterial effects through increasing membrane permeability, as evidenced by the leakage of lactic dehydrogenase, intracellular proteins, and nucleic acids from the indicator strain cells. Furthermore, application of NDYT-8 in a tofu preservation model demonstrated significant short-term antibacterial efficacy, which achieved an 87.0 % reduction in bacterial count within 2 h and sustained this antibacterial effect for up to 10 h at a concentration of 20 mg/mL. Finally, the structure-activity relationship of NDYT-8 revealed that the number of positive charges or alkaline amino acids was the decisive factor in determining its antibacterial efficacy. RKILLMVK, a shorter peptide designed by deleting two amino acids, maintained its antibacterial activity against Escherichia coli similar to NDYT-8. These findings highlight the potential of NDYT-8 and its variants as a promising natural preservative in the food industry.