Mapping bacterial microbiota variations in raw milk: geographic and type-specific insights

ABSTRACT Milk harbors a diverse array of microorganisms; however, the current understanding of the microbial diversity in raw milk from specific geographical origins and milk types remains unclear. To address this knowledge gap, this study employed single-molecule real-time sequencing to analyze the differences in microbial communities across various farms and milk types from different regions, specifically by examining the microbial diversity in Holstein cow milk samples from farms situated in both adjacent and distant regions, and comparing the microbial diversity between Holstein cow milk and non-bovine milk from farms in adjacent regions. The results demonstrated that several genera, such as Lactiplantibacillus , Pseudomonas , Acinetobacter , and Chryseobacterium , exhibited significant differences in Holstein cow milk from adjacent regions. Additionally, genera like Lactiplantibacillus and Chryseobacterium consistently showed substantial variation in Holstein cow milk across distant regions. At the species level, Lactiplantibacillus plantarum , Pseudomonas lurida , and Haloanella gallinarum displayed significant variations in Holstein cow milk from adjacent regions, while Lactiplantibacillus plantarum and Chryseobacterium carnipullorum were significantly more prevalent in distant regions. The bacterial diversity does not have a clear relationship with the geographic proximity of farms, a finding that is consistent with the results of the principal coordinates analysis. Moreover, milk type had a pronounced impact on microbial diversity, with species such as Acinetobacter johnsonii , Pseudomonas fragi , Enterobacter ludwigii , Achromobacter arsenitoxydans , and Leuconostoc mesenteroides exhibiting substantial variations across different milk types. Furthermore, 22 species of lactic acid bacteria were identified in the studied milk samples. Notably, Holstein, donkey, and camel milk exhibited higher lactic acid bacteria diversity compared to buffalo and horse milk. Among these, Lactiplantibacillus plantarum was significantly more abundant in Holstein cow milk, while Lactobacillus helveticus and Leuconostoc mesenteroides were the predominant beneficial species in donkey and camel milk. IMPORTANCE The data generated through this research present invaluable insights into the intricate microbial ecosystems inhabiting both Holstein and non-bovine milk varieties. These novel findings significantly advance our knowledge and approach toward understanding and managing microorganisms within milk, thereby bolstering their efficient utilization and facilitating the design of enhanced strategies for their prevention and control. This research not only sheds light on the diversity and dynamics of microbial communities in different milk types but also paves the way for more targeted interventions to ensure milk safety and quality across different production systems.