Shift in the cow milk microbiota during alpine pasture as analyzed by culture dependent and high-throughput sequencing techniques

In the present study, two groups of cows from a permanent lowland farm (PF) were divided during summer and reared in the PF or in a temporary alpine farm (ALP), respectively. Microbiological analyses were performed with the objective to investigate the microbial evolution of milk before, during, and after summer transhumance comparing, in particular, the two groups of cows to determine whether the alpine pasture could directly influence the milk microbiota. A significant increase of all microbial groups was registered in milk samples collected in the ALP. Interestingly, many strains belonging to species with well reported technological and probiotic activities were isolated from Alpine milk (20% Lactococcus lactis subsp. lactis/cremoris, 18% Lactobacillus paracasei, 14% Bifidobacterium crudilactis and 18% Propionibacterium sp.), whereas only 16% of strains isolated from the permanent farm milk belonged to the species Lactococcus lactis subsp. lactis/cremoris, 6% to Lactobacillus paracasei, 2% to Bifidobacterium crudilactis and 5% to Propionibacterium sp. The MiSeq Illumina data showed that Alpine milk presented a significant reduction of Pseudomonas and an increase of Lactococcus, Bifidobacterium and Lactobacillus genera. These data confirmed the practice of Alpine pasture as one of the main drivers affecting the milk microbiota. All the microbial changes disappeared when cows were delivered back from Alpine pasture to the indoor farm.