Unlocking the Hidden Microbiome of Food: The Role of Metagenomics in Analyzing Fresh Produce, Poultry, and Meat
Teresa Margarita González Martínez, Bianca Rodríguez, Milagros Rodríguez-Montaño, Jessica Alfau, Claudia Reyes, Yumeris Fernandez, Rommel Thiago Jucá Ramos, Edian F. Franco, Luis Orlando Maroto-Martín
Abstract
The increasing complexity of food safety concerns, driven by the rising risks of contamination from pathogens, chemical hazards, and environmental influences, has highlighted the need for more effective detection and prevention strategies. Metagenomics, a powerful molecular tool, is transforming the food industry by providing a comprehensive understanding of the microbial communities in fresh produce, poultry, and meat. Advances in microbial detection techniques, such as shotgun sequencing, metabarcoding, and long-read sequencing technologies, have led to faster and more accurate pathogen detection, reducing the risk of outbreaks and ensuring public health protection. Despite its promise, several challenges remain in implementing metagenomics on a broader scale, including the high cost of sequencing technologies, the complexity of analyzing large datasets, and the lack of standardized procedures across platforms. These limitations hinder its adoption, particularly for smaller operations or in regions with fewer resources. This review examines the applications of metagenomics in food safety, focusing on its impact on meat, poultry, and fresh produce, while discussing the obstacles to its widespread use and potential solutions to overcome these barriers.