Characterization of chilled chicken spoilage using an integrated microbiome and metabolomics analysis

Spoilage of chilled chicken can occur as a result of microbial development and consumption of meat nutrients by spoilage bacteria, ultimately resulting in the release of undesired metabolites. Characterizing the profiles of the microbiota and metabolites and clarifying their relationships will contribute to an improved understanding of the mechanism underlying chilled chicken spoilage. In the present study, 16S rRNA gene sequencing and ultra-high-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS)-based untargeted metabolomics analyses were applied to determine the microbial and metabolic profiles in chicken during chilled storage. The microbial and metabolic datasets were subjected to combined analysis using weighted gene co-expression network analysis (WGCNA) and Spearman’s correlation analysis. Brochothrix, Carnobacterium, Photobacterium, Pseudomonas, Acinetobacter, Serratia, Kurthia, Shewanella, and Obesumbacterium genera were identified as the dominant spoilage bacteria in chilled chicken. Ten metabolic pathways, including histidine metabolism and purine metabolism, were identified as potential mechanisms underlying chilled chicken spoilage. Correlation analysis demonstrated that spoilage bacterial genera were highly correlated with spoilage-related metabolites. Taken together, the present study proposed an integrated microbiome and metabolomics approach to investigate the mechanism of chilled chicken spoilage caused by microbial activity. The results obtained by this approach provide a comprehensive insight into changes in the microbial and metabolic profiles of chilled chicken during spoilage.