Non-starter bacterial communities in aged Cheddar cheese: Patterns on two timescales

Though it is well established that the food production environment can be a source of microbial contamination during food manufacturing, the stability of this contamination over time has not been thoroughly examined. The aim of this study was to investigate the temporal stability of microbial contamination during Cheddar cheese production by examining patterns of non-starter bacteria in aged Cheddar collected from the start and end of 30 production days over a 40-day sampling period. Further, we aimed to provide insight into the source of these temporal microbial variations by comparing microbial communities in the aged cheese to those on food contact surfaces from a piece of cheesemaking equipment previously identified as a major source of non-starter bacteria in the same processing environment. 16S rRNA metabarcoding and culture-based sequencing methods identified two Streptococcus sequence variants significantly associated with the end of the production day in both the aged cheese and the cheese processing environment. Closer inspection of these sequence variants in the aged cheese over the 40-day sampling period revealed sinusoidal-like fluctuations in their relative ratios, which appeared to coincide with the Lactococcus starter rotation schedule. These results demonstrate that the microbial composition of finished cheese can vary according to the timing of processing within a production day. Further, our results demonstrate that time-of-day microbial differences in cheese can result from bacterial growth on food contact surfaces and that the composition of these microbial differences is subject to change day-to-day and may be linked to routine changes in the Lactococcus starter culture.