RAHMAN, ASIM UR (2026) Microbiome Mapping in Meat Food Chain from Farm-to-Fork. [Tesi di dottorato]

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Abstract

Meat-processing environments harbour complex microbial ecosystems that influence product quality and safety. However, the combined effects of season, sanitation procedures, and bacteriophage activity on these ecosystems remain unclear. To address this, we conducted a longitudinal farm-to-fork investigation across four beef processing facilities over two seasons using shotgun metagenomics. A total of 712 samples were collected during the production and post-cleaning stages, followed by industrial wet-aging (2-77 days) and the retail shelf-life period (0-24 days). This approach has revealed distinct ecological patterns. Indeed, long-term maturation was dominated by Carnobacterium, whereas Lactococcus species dominated during the retail period. Furthermore, environmental microbiomes exhibited broad metabolic potential, in contrast to the specialized, low-diversity profiles of mature meat. Routine sanitation failed to eliminate the resident microbial communities, although it exerted selective pressure, reducing spoilage taxa while enriching biofilm-forming genes by up to 3.2-fold in post-cleaning samples. Additionally, bacteriophages showed a positive overall association with their bacterial hosts; however, niche-specific analyses revealed strong antagonistic effects against Listeria monocytogenes and Salmonella enterica. Collectively, these findings demonstrate that beef processing microbiomes are structured by the interaction of multiple ecological forces rather than by sanitation alone. Understanding these interactions provides a comprehensive framework for ecology-based strategies to improve meat quality, safety, and shelf life.

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