Can metagenomic analyses be used effectively in safe food production?

Abstract

This review aims to bring together current research on the importance, recent applications, and possible impacts of metagenomic analysis and emphasize that metagenomic analyses, which provide direct analysis of the genomes of the food itself and all the microbiota in its environment, are revolutionary approach for effective management of food safety requirements. The increasing health problems in recent years and the related developments regarding nutritional awareness have led people to seek safe food consumption. In order to ensure the quality and safety of food products and protect the health consumers worldwide, necessary preventive measure should be taken by conducting innovative control methods. Numerous microbial hazards threaten food safety worldwide. In this respect, rapid and accurate detection of pathogens is critical. Although traditional culture-based methods continue to be widely used, they often fail to detect organisms that are viable but cannot be cultured. This limitation has led to the increasing adoption of metagenomic analyses, which allow direct genome-level detection and provide a more comprehensive view of microbial communities in food systems. In this context, metagenomic analyses within new-generation technology has been inspired, as it can be a powerful tool to ensure food safety. In this study, for this purpose, the keywords 'metagenomics and food' and the studies on metagenomics published in English, peer-reviewed journals, and available in the Web of Science and Scopus databases were investigated. The years 2020-2024 were taken as a basis for the studies with the keywords identified and studies on antibiotic resistance and unrelated foods were excluded from the review's scope. This review brings together current research on the significance of metagenomics analysis in food safety, its latest applications, and possible effects. The study is a reference source for potential studies to be carried out in this context.