The legacy of raw milk storage temperature is associated with cheese microbiome composition, notwithstanding pasteurization and starter addition

Using DNA metabarcoding, we assessed the relative impact of two variables: (a) raw milk storage temperature and (b) cheese maturation duration, on a semi-fresh cheese bacteriome composition under authentic factory-scale industrial conditions. The study is compared to a prior literature report run at a high-quality milk facility, whilst in the present case, milk from an average-quality farm, better reflecting typical local standards, was used. We tested three milk storage temperatures (4°C, 7°C, 9°C) and sampled cheese at six maturation stages (0, 10, 25, 30, 45, and 60 days). Results showed that raw milk storage temperature was the variable most strongly associated with microbial community composition across the sampled stages, exceeding the variation associated with maturation time. Even the pasteurization step and the addition of a Streptococcus thermophilus starter culture did not erase the microbial ‘memory’ of initial milk conditions. Interestingly, the cheese bacterial community shaping associated with different milk tank temperatures was moreover compositionally uncoupled from the dominant taxonomical pattern of the starting milk. Additionally, the study provided insights into balancing milk quality and storage temperatures to prevent spoilage by psychrotrophic pseudomonads. Under the conditions tested here, the findings suggest that the 4°C storage benchmark may warrant re-evaluation.