DNA-Seq of Escherichia coli
Pure bacterial colonies were grown on MacConkey agar plates and then genomic DNA from all the strains was extracted using the QIAmp DNA Mini kit (Qiagen, Hilden, Germany), by following manufacturer's instructions. DNA was subsequently quantified using the Qubit fluorometer 2.0 (Invitrogen, Carlsbad, CA, USA) with the Qubit dsDNA Broad Range assay kit. DNA library preparation was performed using the Illumina DNA Prep kit (Illumina, San Diego, CA, USA) according to the manufacturers instructions. Nextera DNA CD Indexes (96 Indexes-96 Samples, Illumina, San Diego, CA, USA) were ligated after the amplification. DNA libraries were evaluated on the Agilent 4200 TapeStation System (Agilent Technologies Ltd, USA), while libraries concentration was checked using the Qubit fluorometer 2.0 (Invitrogen, MA, USA