shotgun sequencing of cheese production facility and associated samples

The microbial consortia present in food production environments can become part of the microbial composition of the final food products. Microorganisms which colonise food production facilities are thus an important consideration for food producers from both a spoilage and food safety perspective. Here, shotgun metagenomic sequencing was used to characterise the microbiome of a cheese production facility before and after the production of a continental style cheese. By adopting this approach, we were able to detect bacteria and phage present in substrates, production facility surfaces and in the cheese itself. Taxonomic analysis demonstrated that the production plant surfaces harboured lactic acid bacteria (LAB) prior to cheese production, but that the identity of the LAB present on these surfaces changed after the cheese production to be dominated by the specific strains used in continental cheese production. Pathogenic bacteria were detected in substrate samples on production plant surfaces but, importantly, not in cheese samples. Notably, brine and process water samples were found to harbour lactococcal phage, a major cause of starter culture failure in the cheese industry. These results demonstrate that shotgun metagenomic sequencing has the potential to become a valuable tool for monitoring the microbiology of food production facilities.