Prior to DNA extraction, the aliquot of bacteriophage lysate was filter–sterilized using a 10 ml syringe barrel fitted with a 0.22 μm filter Millex® GV filter unit (Merck) and maintained at 4°C prior to analysis. Bacteriophage particles were concentrated and purified using the method reported previously [27 (link)].
For DNA extraction, Qiamp DNeasy Blood and Tissue kit (Qiagen) was used following manufacturers’ instructions. DNA extracts were tested and concentrations adjusted to 0.2 ng μl-1 using a Quantus fluorometer and Quantifluor dsDNA kit (Promega) following the manufacturer’s instructions. Agencourt®AMPure® magnetic beads (Beckman Coulter) and Nextra®XT Library Preparation (Illumina) kits were used following the manufacturer’s instructions. For tagmentation, 5 μl of diluted bacteriophage DNA was treated using the Nextra®XT Library Preparation (Illumina) kit following the manufacturer’s instructions. Next-generation sequencing (NGS) was performed using the MiSeq™ sequencer (Illumina) with v2 2 x 250 sequencing reagents (Illumina) following the manufacturer’s instructions for denaturation of a 2 nM library.
For DNA extraction, Qiamp DNeasy Blood and Tissue kit (Qiagen) was used following manufacturers’ instructions. DNA extracts were tested and concentrations adjusted to 0.2 ng μl-1 using a Quantus fluorometer and Quantifluor dsDNA kit (Promega) following the manufacturer’s instructions. Agencourt®AMPure® magnetic beads (Beckman Coulter) and Nextra®XT Library Preparation (Illumina) kits were used following the manufacturer’s instructions. For tagmentation, 5 μl of diluted bacteriophage DNA was treated using the Nextra®XT Library Preparation (Illumina) kit following the manufacturer’s instructions. Next-generation sequencing (NGS) was performed using the MiSeq™ sequencer (Illumina) with v2 2 x 250 sequencing reagents (Illumina) following the manufacturer’s instructions for denaturation of a 2 nM library.