DNA concentration was determined using the Life Technologies Qubit broad range and high sensitivity assay kits. A 1 μl aliquot of DNA was combined with 198 μl of the appropriate buffer and 1 μl of dye in a 0.5ml qubit tube, vortexed and left at room temperature for 2 min. DNA concentration was then measured on a Qubit 3 fluorometer. If DNA concentration between the high sense and broad range assays differed by more than 10%, then the extractions were repeated. DNA was then calculated by averaging the measurement from each assay.
To confirm molecule length extracted DNA was run on either the Agilent Tapestation or Agilent Femto Pulse. For the initial extractions, DNA was diluted, if required, to < 50ng/ μl and a 1 μl aliquot run on an Agilent Genomic Tape on a Tapestation instrument according to the manufacturer’s instructions. For the second set of extractions, DNA was diluted to 0.25ng/ μl and a 1 μl aliquot run on an Agilent Femto Pulse instrument according to the manufacturer’s instructions. Electropherograms for each bacterial species can be seen in Additional file2 : Figs. S1-S17.
To confirm molecule length extracted DNA was run on either the Agilent Tapestation or Agilent Femto Pulse. For the initial extractions, DNA was diluted, if required, to < 50ng/ μl and a 1 μl aliquot run on an Agilent Genomic Tape on a Tapestation instrument according to the manufacturer’s instructions. For the second set of extractions, DNA was diluted to 0.25ng/ μl and a 1 μl aliquot run on an Agilent Femto Pulse instrument according to the manufacturer’s instructions. Electropherograms for each bacterial species can be seen in Additional file