Bulk Tank Raw Milk Microbiota Differs Within and Between Farms

One of the main sources of microbial contaminations of raw milk occurs at farm. To acquire a deeper knowledge of the microbiota of farm tank milk, we studied milk from 45 farms situated in 2 geographical areas in Norway. Each farm was visited every two or three weeks on three different occasions. We combined both bacterial cell counts and a sequence variant inference method of the amplicon-based high throughput sequencing to achieve a high-resolution overview of the microbiota in each sample. The farm milk microbiota was subjected to compositional variation between the areas, between the farms and between the sampling times. Despite the near constant level of bacteria enumerated in the milk from most of the farms, the dominant microbiota differed significantly between the samplings at individual farms. Pseudomonas, Lactococcus, Bacillus and Streptococcus were the dominant genera. Analysis of the identified sequence variants within the same genus, showed that the milk populations of Pseudomonas and Lactococcus were similar between the farms but that Bacillus and in particular Streptococcus populations were highly diverse both within the same farm samples and between farms and also geographical areas. Further, the presence of Bacillus was inversely correlated to the level of Paenibacillus detected in the 2 geographical areas. The results presented here provide new insight into the farm milk microbiota and show that this microbiota is a dynamic community highly subjected to variation in composition.