Unwanted microorganisms greatly affect the quality and safety of the final food products. For instance, besides foodborne pathogens, quality defects in Swiss cheese result in great economic loss annually to the industry. Ohio has the largest Swiss cheese industry in the U.S., and to reveal microbial causative agents in Swiss cheese with quality defects has become a critical need to solve the problem for the industry. While conventional approaches were insufficient to identify the risk factors promptly and accurately, recent advancements in molecular techniques enabled in-depth investigation of potential causative agents and the development of rapid detection method for safety and quality control.In Chapter 1, an extensive literature review was conducted in terms of cheese quality and safety issues. The Swiss cheese microbiota consist of starter cultures and environmental microorganisms. The major safety risk in cheese is the contamination of pathogenic bacteria from raw milk or post-pasteurization handling. Non-pathogenic bacteria usually cause quality issues in cheese.In Chapter 2, a rapid detection system for Propionibacterium in food matrices were successfully developed. One pair of genus-specific primers targeting the 16S ribosomal RNA of the genus Propionibacterium, and four pairs of species-specific primers targeting different protein coding genes of P. freudenreichii, P. acidipropionici, P. acnes, P. avidum, were designed and evaluated. This detection system showed no cross-reactivity with other dairy-related bacteria, indicating its utility in dairy industry.In Chapter 3, the starter cultures and non-starter microbiota from split Swiss cheese blocks made by two different factories were analyzed. Result showed the relative abundance of Enterobacteriaceae was significantly higher in split Swiss cheese than that of non-split samples, providing evidence that Enterobacteriaceae could be a microbial causing candidate for split defects. A comprehensive assessment of the bacterial profiles potentially associated with Swiss cheese quality made by one factory was conducted. The microbial profile of retail cheese with eyes, factory-made Swiss cheese, pasteurized milk, and starter cultures were extensively analyzed by 16S metagenomics. Using Principal Component Analysis and a heat map with dendrograms, it was demonstrated that the split areas in Swiss cheese were microbiologically different from eye areas, which could be due to inhomogeneous distribution of starter cultures.In Chapter 4, retail oysters as a potential channel disseminating antibiotic resistance was assessed. A total of nine oysters belong to three types were collected. High prevalence of culturable bacteria resistant to tetracycline, cefotaxime, lincomycin, gentamicin, ciprofloxacin and ceftazidime were investigated using Brain Heart Infusion, MacConkey and Phenylethyl Alcohol media. Shotgun metagenomics on oyster microbiota was conducted on genomic DNA with high throughput sequencing using Hiseq platform. The microbial profile, functional metabolic groups, and antibiotic resistome were analyzed from the sequencing data using MG-RAST. High prevalence of multidrug- and acriflavin-resistant genes were identified in oyster microbiota. Results of these studies contributed to a comprehensive understanding of the microbial cause of split defect in Swiss cheese, enabled culture-independent methods in microbial assessment for dairy products, and illustrated the power of metagenomics in improving fundamental understanding of the microbiology in Swiss cheese and oysters.