Schematic diagram of the experimental design.

The BCMC was tested for the effects of variations in sample preparation, cell lysis, DNA purification and collection methods. Cells were lysed using a bead beater (B), vortex (V), or incubated for chemical lysis (C). Wash solution denotes the solutions included in DNA extraction kits used for purification. Wash step(s) were performed following manufacturer’s protocol. Underlined text indicates experiments performed with both BCMC1 and BCMC2. For all other experiments, BCMC2 was used. Filled boxes are methods used to test raw bulk milk samples.