DNA metabarcoding for the identification and relative abundance assessment of general and potentially pathogenic bacteria in Sardinian sheep cheese processing environments

In dairy processing facilities, microbial contamination poses significant challenges to food safety and quality, even under rigorous hygiene protocols as those implemented in sheep milk processing in Sardinia. Specific niches within factories facilitate the persistence of spoilage and pathogenic microorganisms, including Listeria monocytogenes, Salmonella spp., Bacillus cereus, and Pseudomonas spp. Hereby, 16S rRNA-based bacterial metabarcoding was applied to assess bacterial populations in Sardinian cheese processing environments. The scope was to acquire taxonomical information on the total microbiota, including the presence of taxa known to feature also potentially pathogenic strains. Samples were collected from 14 dairy plants distributed throughout Sardinia, analyzing nine areas of the cheese processing line and their workflow pieces, distinguishing food-contact from non-food-contact surfaces, for a total of 253 samples. Five sequencing runs yielded 51,114,952 quality-filtered reads, resulting, upon bioinformatic processing, in 4426 annotated taxonomic lineages. A clear community partition driver within the technical workflow, was identified upon grouping the areas of washing-processing apart from those of salting-aging-shelving. Notably, the genus Halomonas and the family Halomonadaceae dominated and differentiated the microbial composition across samples. Sequences which belong to potential pathogens were instead prevailingly in the opposite sites when compared to salt-adapted biota.