Effects of different stages of lactation on the microbial evolution during cheese fermentation: from milk to DPO Fontina Cheese by 454 -pyrosequencing

The bacterial populations of raw milk and Fontina cheeses produced in two cheese factories were investigated by 454 - high-throughput sequencing. Total microbial DNA was isolated from milk and cheeses sampled at 24h and after 7, 28 and 84 day of ripening. In each cheese factory nine cheese-making days were followed in a four months long period: three in the first 40 days after partum (S1), three in the following 40 days when the cows had their estrus cycle (S2) and three in the last 40 days (P3) when cows were pregnant. DNA was used as template in Polymerase Chain Reaction (PCR) to study the hypervariable V1, V2 and V3 regions of the bacterial 16S rRNA gene and analysed by 454-pyrosequencing. A total of 2,518,829 sequence reads were generated by the pyrosequencing of 18 milk and 72 cheese samples