Omics techniques in investigating the mechanism of novel technologies on microorganisms: an update review

As global food consumption rises, microbial inactivation technologies face dual challenges: ensuring safety while preserving quality. Although transcriptomics, proteomics, and metabolomics have advanced mechanistic studies of novel technologies (NTs), existing reviews often lack a systematic integration of these Omics approaches to address microbial adaptive responses. Additionally, when exposed to NTs, pathogens deploy sophisticated countermeasures that may compromise both food quality and consumer health. Therefore, understanding how different NTs affect specific bacteria is crucial in mitigating these risks. This review also discusses the challenges and future trends for NTs and Omics in food safety. Many NTs fail to balance antimicrobial efficacy with food integrity, indicating that future approaches may involve combining different NTs together or with chemical agents (e.g. disinfectants and antimicrobials) to achieve synergistic antimicrobial effects. Compared to single-Omics analyses, multi-Omics approaches provide deeper insights into microbial response mechanisms and enable more precise identification of NTs’ key targets. We also critically evaluate why current analytical bottlenecks, such as instrument sensitivity limitations and data interoperability barriers- constrain the applications of Omics in industrial settings. Ultimately, the analysis highlights that the integrated Omics frameworks, rather than incremental improvements to NTs alone, will drive next-generation solutions for food safety.