16s compositional metagenomic data from raw milk and environmental samples

pasture-based systems, changes in dairy herd habitat due to seasonality results in the exposure of animals to different environmental niches. These niches contain distinct microbial communities that may be transferred to raw milk, with potentially important food quality and safety implications for milk producers. It is postulated that the extent to which these microorganisms are transferred could be limited by the inclusion of a teat preparation step prior to milking. Here high-throughput sequencing, of a variety of microbial niches on the farm, is employed to study the patterns of microbial movement through the dairy production chain and, in the process, investigate the impact of seasonal housing and inclusion/exclusion of teat preparation regime on the raw milk microbiota from the same herd over two sampling periods, i.e., indoor and outdoor.