The potential of organic acids to inactivate foodborne pathogens in food industry has gained attention, while the sanitizing mechanism of acid stress has not been explained fully at metabolomics level. The aim of this study was to elucidate the antimicrobial mechanism of low-concentration organic acids (1.5% acetic acid, 1% citric acid, and 1.5% lactic acid) on Salmonella enterica strains (ATCC 6962, ATCC 13076, and ATCC 14028) inoculated on cucumber slices. Flow cytometry, nuclear magnetic resonance (NMR) combined with multivariate data analysis revealed that the population of S. enterica reduced 1.7–2.5 log CFU/g after different organic acid treatments. Bacterial membranes (2.37–19.00%) were destroyed and nucleic acid exposed, 40.27–85.33% of membranes was partially damaged, and 44 metabolites were identified from these three strains. The amino acids (Trp, Met, and Val) decreased significantly. Conversely, the intracellular organic acids and hydrocarbon grew obviously. The flux of marked metabolites showed that metabolisms of energy, amino acids, and carbohydrates pathways were disturbed which included TCA cycle, glycolysis, and biosynthesis of amino acids. The antibacterial mechanism on S. enterica provides clue to enhance the application of organic acids in controlling foodborne pathogens on fresh produce.
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