Nucleic acid-based approaches are used to investigate microbial-related cheese quality defects. Microorganisms can cause defects such as off-flavors, biogenic amine formation, gas production, and mineral deposition. These defects are influenced by factors like milk quality, processing parameters, and non-starter microorganisms. Traditional methods are biased and slow, while molecular techniques offer rapid and accurate detection of spoilage microbes and metabolic pathways. DNA-based methods, including PCR, qRT-PCR, DGGE, TTGE, SSCP, and T-RFLP, are used to detect spoilage bacteria and monitor microbial communities in cheese. These methods help improve cheese quality and reduce economic losses. Molecular techniques allow for early detection of microbial populations and metabolic pathways, enabling timely interventions. qRT-PCR is particularly effective for quantifying specific microorganisms and their gene expression. DGGE and TTGE are used to profile microbial communities, while SSCP and FISH allow for the identification of specific microbial species. ARDRA and RISA are used to analyze genetic diversity. These techniques are essential for monitoring and controlling microbial-related cheese defects.Nucleic acid-based approaches are used to investigate microbial-related cheese quality defects. Microorganisms can cause defects such as off-flavors, biogenic amine formation, gas production, and mineral deposition. These defects are influenced by factors like milk quality, processing parameters, and non-starter microorganisms. Traditional methods are biased and slow, while molecular techniques offer rapid and accurate detection of spoilage microbes and metabolic pathways. DNA-based methods, including PCR, qRT-PCR, DGGE, TTGE, SSCP, and T-RFLP, are used to detect spoilage bacteria and monitor microbial communities in cheese. These methods help improve cheese quality and reduce economic losses. Molecular techniques allow for early detection of microbial populations and metabolic pathways, enabling timely interventions. qRT-PCR is particularly effective for quantifying specific microorganisms and their gene expression. DGGE and TTGE are used to profile microbial communities, while SSCP and FISH allow for the identification of specific microbial species. ARDRA and RISA are used to analyze genetic diversity. These techniques are essential for monitoring and controlling microbial-related cheese defects.