Foods that are fermented have a crucial role in global diets, these foods benefit from the process of fermentation, which enhances nutrition, flavor, and safety through the use of probiotics, anti-aging compounds, and antibiotics. Traditional fermentation is based on the spontaneous activity of microorganisms, while modern methods utilize defined cultures for consistency. The microorganisms in cheese are important for the flavor and texture of the product. These microorganisms are either non-starter or starter bacteria, yeast, and mold. The advances in sequencing technology have facilitated an increase in our understanding of these communities and their contribution to the quality and safety of cheese. Despite the health benefits of fermented dairy products, such as yogurt, they can pose a risk of contamination with pathogens. New methods of management and sequencing are crucial to ensuring the safety and quality of fermented foods, combining traditional methods with modern advances.

This article discusses advances in molecular technologies for detecting foodborne pathogens, specifically Listeria monocytogenes and Salmonella. Although traditional detection methods are reliable, they are time- and labor-intensive. On the other hand, molecular methods include polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), and next-generation sequencing (NGS), which enable rapid, specific, and sensitive detection of pathogens. The introduction of such procedures has significantly improved food safety testing and monitoring. Although challenges such as accessibility and cost remain, future developments in molecular diagnostics will lead to greater implementation in improving pathogen management throughout the food supply chain.