Characterization of chilled spoilage in pasteurized goat milk using an integrated microbiome-metabolomics analysis

Pasteurized goat milk is mainly spoiled through the activity of various microorganisms. Microorganisms with protein-hydrolyzing and lipid-degrading activities can act on proteins and lipids, ultimately resulting in the release of undesired metabolites. Characterizing the corresponding microbiota and metabolite profiles and clarifying their relationships will enhance our understanding of the mechanisms underlying the spoilage of pasteurized goat milk during chilled storage. In this study, 16S rRNA sequencing was employed for microbiome profiling, and ultra-performance liquid chromatography and tandem mass spectrometry was used for metabolome profiling. Weighted gene correlation network analysis and Spearman's correlation analysis were both used to investigate correlations between the microbiomes and metabolomes of pasteurized goat milk samples. The results showed significant changes in microbial diversity throughout the spoilage process. The Proteobacteria phylum and Pseudomonas genus were identified as dominant microorganisms involved in the spoilage process. Bacteria may contribute to spoilage through metabolic pathways such as glycerophospholipid metabolism and purine metabolism. In addition, significant correlations were observed between key bacteria taxa and important metabolites. Stenotrophomonas was identified as the primary spoilage bacterium, the relative abundance of which increased significantly (by 3.84%) during chilled storage, and it may serve as a biomarker for goat milk spoilage. Taking all this information into consideration, the present study proposes an integrated microbiome and metabolomics approach to investigate the spoilage mechanisms of pasteurized goat milk caused by microbial activity. These findings provide comprehensive insights into the microbial and metabolic profiles associated with spoilage during chilled storage. Our study can assist the dairy industry in understanding issues that may arise during the preservation of goat milk, thereby enhancing product quality and shelf life.