Scientific Publications
Microbial community succession and functional potential during processing and storage of cooked ham assessed by shotgun metagenomics
Food Microbiology
Wet-cured ham is a ready-to-eat meat product in which microbial communities contribute both to desirable product characteristics and to spoilage risk. Microorganisms are introduced early during the live brining of raw meat, influencing nitrate generation and other microbial processes. To support quality control and provide early indicators of spoilage, this study investigated taxonomic and functional changes in the microbiome across all stages of production, from brining and cooking through to cold storage, slicing, and packaging under modified atmosphere.
Using metagenomics, we characterised microbial community composition and functional profiles across 67 samples from raw ingredients, intermediate steps, and final products. Microbial communities differed significantly between stages, despite sharing a related taxonomic structure. Brining led to a marked reduction in diversity, and cooking further decreased richness and evenness. A set of 28 taxa was consistently detected across stages, though their relative abundance varied. Notably, Latilactobacillus curvatus was abundant prior to cooking but declined sharply afterward, while Arthrobacter rhombi, initially rare, became dominant in the cooked product. During chilled storage, microbial succession continued, with some taxa re-emerging after being nearly eliminated by cooking. Functional gene profiling revealed distinct metabolic pathway shifts across stages, particularly involving respiration, amino acid metabolism, and fermentation.
These findings provide a detailed baseline of microbial and functional dynamics in the production and storage of wet-cured ham. The results offer a foundation for spoilage risk assessment and contribute to the development of microbiological monitoring strategies to support product safety and shelf-life management.
Food Microbiology
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