Antimicrobial activity enabled by chitosan-ε-polylysine-natamycin and its effect on microbial diversity of tomato scrambled egg paste

•Chitosan-ε-polylysine-natamycin exhibit an excellent antimicrobial effect.•Compound preservatives could destroy microbial cell wall/membrane.•Compound preservatives reduced tomato scrambled egg paste microbial diversity.•Compound preservatives reduced tomato scrambled egg paste microbial richness. For a long time, food spoilage posed a severe impairment on food safety and public health. Although chemical preservatives are commonly used to inhibit spoilage/ pathogenic microbial growth, the disadvantages of a single target, potential toxicity and high dose of use limit the better use of preservatives. In this research, the combination of natural preservatives: Natamycin (Nat), ε-polylysine (ε-PL), and Chitosan (CS) could achieve an excellent antimicrobial effect including bacteria and fungi, and reduce the usage of a single preservative. Compound preservatives could destroy microbial morphology and damage the integrity of the cell wall/membrane by leakage of protein and alkaline phosphatase (AKP). Besides, high-throughput sequencing revealed that compound preservatives could decrease microbial diversity and richness, especially, Pseudomonas, Acinetobacter, Fusarium, and Aspergillus. Therefore, the combination of 1/8 × MIC CS, 1/4 × MIC ε-PL, and 1/2 × MIC Nat can achieve an excellent antibacterial effect, providing new ideas for food preservation.