Is pink discolouration defect in Pecorino cheese due to Thermus thermophilus presence?

Pink discolouration defect can be observed in different varieties of ripened cheese and can lead to economic losses for the producers due to the impossibility to sell the defected cheese. Little knowledge is available on the causes of this defect; however, Thermus thermophilus has been recently identified as a possible responsible. Further understanding of the factors involved in the development of pink discolouration in cheese can give economic benefits. The goal of this study was to characterise the microbial community in Pecorino cheese with pink discolouration defect. DNA was extracted from cheese samples from two different lots (lot1, with not defected cheeses – 4 samples from 2 cheese units – CU; lot2 with both defected – 8 samples from 2 CU – and not defected cheeses – 4 samples from 2 CU). The V5-V6 hypervariable regions of the bacterial 16S rRNA gene were PCR amplified. Amplicons were sequenced by Illumina MiSeq. Bioinformatic elaborations were performed by DADA2. Forward and reverse reads were truncated at 200 and 160 bases, respectively. Primers’ sequences were removed and low-quality reads (i.e. reads with expected errors higher than 0.5 and with Ns) were discarded. Error rates were estimated and used to infer the Amplicon Sequence Variants. The taxonomic classification was performed using the RDP database (confidence 80%). The most abundant bacteria belonged to the genera that were found into the starter culture (i.e. Lactobacillus ranged from Σ2% to Σ10%, Lactococcus ranged from Σ2% to Σ7%, Streptococcus ranged from Σ77% to Σ91%). No sequences belonging to the genus Thermus were detected. A permutational multivariate analysis of variance (PERMANOVA) based on Hellinger transformed genus relative abundance data showed that the microbial communities in the cheeses from lot1 and lot2 were different (p=.001). A Kruskal–Wallis test was performed to identify the genera with a different relative abundance in lot1 and lot2. The relative abundance of the genus Streptococcus was higher in the cheeses from lot1, while the relative abundance of the genera Escherichia/Shigella, Lactobacillus and Propionibacterium was higher in the cheeses from lot2 (p<.05). The presence of T. thermophiles was not observed suggesting that this bacterium was not responsible for the pink discolouration defect. Further analyses are needed to verify the potential correlation between the detected populations and the pink discolouration of Pecorino cheese.