Longitudinal microbial community analysis of a food processing environment reveals dynamic interactions of commensal in-house microbiota and potential pathogens

Food-borne disease outbreaks are often associated with pathogenic bacteria contaminating ready-to-eat foods during primary processing. One major issue is the formation of biofilms on processing equipment, which can lead to continuous dispersal of microorganisms on the product. Biofilms are complex microbial ecosystems that usually occur as mixed-species consortia consisting of multiple species interacting with each other. Despite the complexity and strong persistence of biofilms in the food industry, most of our knowledge about the microbial assemblage of biofilms is based on in vitro experiments, but direct investigations of them in the environment remain limited. Here, we analysed the microbial community structure throughout a meat processing facility using high-throughput full-length 16S rRNA gene sequencing. We took samples at different stages during processing as well as from multiple sites throughout the facility environment to capture the product and the surface-associated microbiota. Our findings contribute to our general understanding of the built environment microbiome in the food processing context. While the overall community structure clearly differs between product and environmental samples, we were able to discern correlation patterns regarding the presence/absence of Listeria monocytogenes in both sample groups. Specifically, our longitudinal analysis revealed association of L. monocytogenes with known biofilm-producing Pseudomonas, Acinetobacter, and Janthinobacterium species on the meat samples. Similar patterns were also observed on the surface, indicating dispersal of microorganisms from this multispecies biofilm. Our data provided a better understanding of the biofilm community structure and promoted more effective options for targeted disinfection in the analysed facility.