Investigating microbial and metabolic dynamics in bovine and goat milk during refrigerated storage for 5 days

Raw milk is commonly stored at 4 °C prior to processing, a practice that can facilitate psychrotrophic proliferation, and milk physicochemical alterations and quality deterioration. This study aimed to elucidate the dynamic changes and interrelationships among microbiota, physicochemical parameters, and metabolite profiles in raw bovine and goat milk during refrigerated storage at 4 °C over a 5-day period. The results showed that both bovine and goat milk exhibited significant increases in bacterial counts, titratable acidity, zeta potential, and protein particle size, alongside decreases in pH and lipid particle size, as well as changes in color during refrigerated storage at 4 °C. Significant differences were detected between bovine and goat milk in terms of bacterial counts, protein and fat particle size (P < 0.001). Microbial diversity analyses revealed dominant taxa transitioned from Pseudomonas fluorescens (33.0 %) and Lactococcus raffinolactis to Pseudomonas fluorescens (46.0 %) and Flavobacterium frigidarium (23.4 %) in bovine milk. In goat milk, dominant taxa shifted from Psychrobacter aquimaris (45.6 %) and Pseudomonas fluorescens (20.5 %) to Pseudomonas fluorescens (54.7 %) and Serratia proteamaculans (21.5 %). These microbial successions were concomitant with significant metabolite fluctuations. Specifically, metabolites such as cystargolides A, and N-acetylneuraminic acid abundances increased, whereas d-glucose 6-phosphate and adenosine 3′,5′-cyclic monophosphate decreased in bovine milk. In goat milk, gaburedin F and 1-methyl-pseudouridine levels increased, while diprotin B and Met-Pro declined. Notably, cystargolides A (log₂|FC| = 6.04) and N-acetylneuraminic acid (log₂|FC| = 1.80) in bovine milk, along with gaburedin F (log₂|FC| = 1.99) in goat milk suggest their potential as biomarkers for detection milk spoilage. The observed microbial shifts and corresponding metabolite changes highlight the intricate interplay between microbial communities and milk composition, providing valuable insights for optimizing strategies to manage milk quality and safety during storage.