The Effects of Sampling Sites, Collection Time, and Refrigerated Storage Duration on Microbiota of Raw Milk From a Chinese Dairy Farm: An Exploratory Study

Raw milk is the primary material for all dairy products, making it imperative to characterize and monitor its microbial composition to ensure product quality. To investigate microbial contamination from pasture to processing facilities and establish microbial traceability systems, eighty-seven raw milk samples were collected from a dairy farm in Shijiazhuang of China in August. The raw milk samples were categorized into three experimental groups based on: sampling sites along the production chain (manual milking, buffer tank, filter, refrigeration tank, milk truck, and plant factory), sampling time (before dawn, morning, noon, and afternoon), and refrigeration storage (0-72 h at 12 h intervals). The microbiota were evaluated by 16S rRNA sequencing. The results identified Pseudomonas, Lactobacillus, and Prevotella as the predominant bacterial genera across all sampling conditions. The α-diversity (Shannon and Chao1) and β-diversity analysis jointly revealed significant differences in microbial communities of raw milk samples. Specifically, raw milk collected from milk truck showed distinct bacterial communities compared with upstream collecting points, while morning-collected samples showed marked compositional differences from other time points. These findings were consistently supported by cluster heatmap analysis. In addition, the relative abundance of Pseudomonas in raw milk decreased but Lactococcus and Serratia increased with refrigerated time (P < 0.05). This inverse relationship was further evidenced in cooccurrence network showing a strong negative correlation between Lactococcus, Serratia, and Pseudomonas. These results indicated where and when (after being transported to milk truck and in the morning) we need to alert owing to potential contamination in raw milk. Our results also suggested that psychrotrophic bacteria in raw milk should be paid attention, especially Pseudomonas during early refrigerated storage and Serratia during late refrigerated storage.