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Abstract
Understanding the food microbiome is crucial for identifying microorganisms that impact food quality and safety. My studies aimed to contribute further research in this field. Specifically, one of my research objectives was to investigate the microbial content of eight edible insect product types using traditional microbiological methods and whole genome sequencing. Results showed that insect product type significantly influenced total viable counts, bacterial spore counts, and lactic acid bacteria counts (P = 0.00391, P = 0.0065, and P < 0.001), with counts ranging from <1.70 to 6.01, <1.70 to 5.25, and <1.70 to 4.86 Log10 CFU/g, respectively. Whole genome sequencing revealed the presence of 12 different bacterial genera among the analyzed isolates, with a majority belonging to the Bacillus genus. Some isolates from the Bacillus cereus group were identified as biovar Emeticus. My second research initiative explored the microbiome of various retail food products, including fresh produce, deli meats, and cheese, using a 16S rRNA sequencing approach. We observed that alpha diversity (Shannon and Simpson indices) was significantly higher (P < 0.001 for both) in fresh produce (2.4 to 4.1, 0.82 to 0.95, respectively) compared to other products. Beta diversity analyses showed distinct microbial community compositions across product types. Cheese, hard salami, and turkey breast were dominated by fermentation-associated genera such as Lacticaseibacillus, Latilactobacillus, and Pediococcus, while fresh produce harbored genera commonly associated with food spoilage or plant diseases, such as Pseudomonas, Pantoea, Psychrobacter, and Serratia. My final research objective was to investigate how the retail environment's microbiome interacts with foodborne pathogens within biofilms. This study examined biofilm formation, structural variability, and susceptibility to quaternary ammonium compounds (QUATs) in various biofilm structures involving retail-derived bacteria (Serratia liquefaciens and Pseudomonas simiae) and foodborne pathogens (Salmonella Typhimurium and Listeria monocytogenes). In mono-species biofilms, S. liquefaciens exhibited the highest biofilm-forming ability, while L. monocytogenes was the most susceptible to QUATs, with a mean log reduction of 3.83. In binary biofilms, L. monocytogenes demonstrated reduced sanitizer susceptibility. Overall, my research has provided important insights into microbial communities in food products and their implications for food safety.