Spoilage Indicators, Bacterial Dynamics, and Metabolomic Profiles of Chilled Yak Meat Under Tray, Vacuum, and Modified-Atmosphere Packaging: A Comparative Study with Integrated Multi-Omics Focused on Tray Versus MAP Conditions

Yak meat faces limitations in the packaging methods available to extend its shelf life and maintain quality. This study compared the effects of tray packaging (YM), vacuum packaging (YZ) and 70% O2/30% CO2 modified-atmosphere packaging (YP) on the extension efficiency of yak longissimus dorsi muscles stored at 4 °C. Physicochemical parameters and total viable counts (TVCs) were measured for all three groups, while 16S rRNA sequencing and untargeted metabolomics were performed only on YM and YP samples to explore the mechanisms underlying quality differences. YP treatment significantly delayed the pH increase and color deterioration compared with YM and YZ. Furthermore, YP samples exhibited lower increases in TVB-N, TVC, and drip loss than YZ and YM samples during storage. The genera Brochothrix, Macrococcus, Photobacterium, Delftia, Acinetobacter, Pseudomonas, and Lactococcus were considered predominant spoilage organisms of yak meat. Notably, Lactococcus and Pseudomonas showed a significantly decreased proportional representation in YP samples over the storage period. Through untargeted metabolomics, a total of 818 metabolites were identified. Several pathways, including 2-oxocarboxylic acid metabolism, histidine metabolism, biosynthesis of amino acids, and D-amino acid metabolism, were identified as the main pathways influencing the metabolic differences between the YP and YM samples near spoiled stages. Pearson correlation analysis showed that bacterial genera such as Macrococcus, Photobacterium, Pseudomonas, Lactococcus, and Enhydrobacter were significantly correlated with key differential metabolites. Furthermore, 1-methylhistidine, 3-methylhistidine, alpha-ketoglutaric acid, PC 34:2, ergothioneine, anserine, LPC 16:0, and L-methionine sulfone were positively correlated with predominant spoilage microorganisms. These findings enhance our understanding of the spoilage characteristics of yak meat stored under the most prevalent commercial option (tray packaging) and the most promising modified-atmosphere packaging alternative (70% O2/30% CO2 MAP).