Nd 1000 spectrophotometer

Phage DNA was purified using a rapid method adapted from [22] (link), as described in [14] (link). Briefly, phages were amplified on fresh LB agar plates for 8 h at 37°C, then 5 ml of SM buffer were added to the plate, followed by overnight incubation at 4°C. The buffer was transferred to a tube, and bacterial debris were pelleted by centrifugation at 2,500×g for 10 min at 4°C. A mixture of 0.2 ml 2 M Tris-HCl pH 7.5, 0.4 ml 0.5 M EDTA, 0.2 ml 10% SDS and 10 μl diethylpyrocarbonate was added to 4 ml of supernatant. Following incubation at 65°C for 30 min, the tube was cooled on ice, and 1 ml of 5 M KOH was added. After 1 h incubation on ice, centrifugation was performed at 25,000×g for 20 min at 4°C. DNA contained in the supernatant was precipitated with 2 vol of absolute ethanol, pelleted by centrifugation, washed twice with 70% ethanol, dried and dissolved in 0.4 ml of TE buffer (10 mM Tris-HCl pH 7.5, 1 mM EDTA). Bacterial DNA was purified using the classical CTAB (cetyl-trimethylammonium bromide)-phenol extraction method as described [19] (link). Purified DNA was resuspended in TE buffer. The quality and concentration of DNA was measured using a ND-1000 Spectrophotometer (NanoDrop®, Labtech, Palaiseau, France).

For identification of all cultured bacterial isolates a DNA extraction of bacterial suspensions was performed using the Sigma Aldrich GenElute bacterial DNA extraction kit. All procedures followed the manufacturer’s instructions and reactions were carried out in 2 ml micro-centrifuge tubes at 16,000 rpm. DNA was eluted in 50 μ l SDW, quantified using a Nanodrop (ND-1000 Spectrophotometer, Labtech) and stored at − 20 °C. Extracted DNA was subjected to high throughput amplicon sequencing of a fragment of the 16S rRNA gene. Paired-end sequencing was performed on an Illumina MiSeq platform using the bacterial/archaeal forward primer 515F (GTGCCAGCMGCCGCGGTAA) and reverse primer 806R (GGACTACHVGGGTWTCTAAT). After removal of primer sequences 252 bp fragments were analysed using a 16S rRNA gene profiling analysis pipeline developed in Qiime57 (link). The amplicons were filtered for quality, singletons were removed, chimeras were screened and removed and taxonomy was assigned at the species and genus level.