Bovine milk microbiota: comparison among three different DNA extraction protocols to identify a better approach for bacterial analysis

Generating high-quality bacterial DNA for metagenomics characterization via shotgun or barcoded amplicons could be critical when starting from a matrix like milk, a complex biological fluid with high fat, protein, and calcium content. Here, bacterial DNA from one ultra-high temperature (UHT) commercial milk sample artificially spiked by a mock community (ZymoBIOMICS Microbial Community Standard) with a predetermined composition and from three bulk tank milk (raw milk) samples was isolated by three different protocols to evaluate the effect of the extraction procedures on milk microbiota composition and to identify the best approach for its characterization.For each extraction procedure, we performed at least 5 replicate experiments, in order to compensate for eventual one-time extraction differences. The performance and reproducibility of these protocols were assessed based on the quality and quantity of the DNA extracted, and bacterial community composition.