Metataxonomic Longitudinal Study of Bacterial and Fungal Dynamics in Vacuum-Packed Beef

The microbial dynamics of vacuum-packed (VP) beef are shaped by intrinsic and extrinsic factors, as well as by complex interactions between bacterial and fungal communities, which influence spoilage progression, metabolite production, and overall meat quality during storage. While bacterial succession and interactions have been extensively studied, the role of fungi remains largely unexplored. In this study, we investigated bacterial and fungal communities in VP beef using spike-in, qPCR, 16S and 18S rRNA gene amplicon sequencing, culture-based approaches, whole genome sequencing, and co-culture experiments. Our results indicate that during an 85-day period Pseudomonas and Brochothrix initially dominate the microbial community but are progressively outcompeted by lactic acid bacteria (LAB), which establish themselves as the predominant bacterial group by day 15. The fungal community remains diverse throughout the examination period, with Kurtzmaniella, Barnettozyma, Debaryomyces, and Yarrowia as the dominant genera. Co-culture experiments revealed a “triangular interaction network” among LAB, yeasts, and Enterobacterales: Yeasts enhanced LAB growth, LAB inhibited Enterobacterales, and Enterobacterales negatively impacted yeasts. The mechanisms remains unclear, but whole-genome analysis indicated the potential for yeast-derived metabolites (e.g., amino acids and enzymes) enhancing LAB growth, LAB inhibiting Enterobacterales through organic acids and bacteriocins, and Enterobacterales producing fungal cell wall-degrading enzymes (e.g., chitinases and exo-1,3-ß-glucanases) that negatively impact yeasts. This dynamic interplay highlights the importance of microbial interactions in shaping community composition and function and also underscores the overlooked role of fungi in meat preservation. By elucidating these interactions, we provide a foundation for microbiome-informed strategies to enhance meat safety and shelf life through targeted modulation of microbial communities.