Exploring the microbiota of raw and pasteurized milk and the bacterial link to slits in commercial Cheddar cheese

Milk and cheese are microbial ecosystems that can harbor diverse bacterial communities and therefore are vulnerable to spoilage and other defects. Cheese defects constitute a considerable burden to the dairy industry, among which slits are one of the most common concerns for Cheddar cheese. To advance the goal of producing cheese free of slit defects, we employed high-throughput DNA sequencing targeting 16S rRNA genes to understand how bacterial communities of raw and pasteurized milk affect the cheese quality. Included in our DNA sequencing approach is the capacity to distinguish between living and total bacteria by the application of propidium monoazide (PMA). Examination of Cheddar cheese samples showed a steady decline in alpha diversity of non-starter bacteria during the 120-day aging period. Compositional changes were also observed such that Streptococcus and Pseudomonas proportions decreased and Lactobacillus and Bacillus increased towards the end of aging. Comparisons between matched milk and cheese samples indicated cheese defects could be associated with the bacterial communities in pasteurized milk. Cheese that contained slits was made from milk harboring fewer contaminating bacterial cells but a larger number of species compared to milk that resulted in high-quality cheese. The presence of Bacillus, Brevibacillus, Corynebacterium, Lactobacillus and Turicibacter in pasteurized milk were also correlated with slits in cheese. The abundance of these genera were also highly dependent on equipment-cleaning schedules and their proportions decreased over 3-fold immediately after cleaning. Overall, our findings show that the slit defects might be due to a subpopulation of bacterial strains that survive milk pasteurization (HTST) in low abundance but persist and remain metabolically active during cheese fermentation. This work contributes to our understanding of bacterial population dynamics in dairy processing facilities and provides opportunities to modify cleaning and processing protocols to ensure the consistent production of high-quality dairy products.