PN_LVX+_T0
DNA libraries were prepared using the QIAseq FX DNA library kit (Qiagen, Hilden, Germany) according to the manufacturers instructions. Briefly, the microbial DNA was quantified with a Qubit fluorometer (Invitrogen, Waltham, MA, USA), and 100 ng of each sample was fragmented to a 450-bp size, end-repaired, and A-tailed using the FX enzyme mix with the following thermal cycle: 4C for 1 min, 32C for 8 min, and 65C for 30 min. Illumina adapter barcodes were attached through a 15-min incubation at 20C in presence of the DNA ligase enzyme. Libraries were then purified twice with AMPure XP magnetic beads (Beckman Coulter, Brea, CA, USA), and a 10-cycle PCR amplification was performed. After a further purification step as described above, the final library was obtained by pooling all samples at 4 nM equimolar concentration. Thereafter, sequencing was performed on an Illumina NextSeq platform using a 2150-bp paired-end protocol as per manufacturers instructions (Illumina, San Diego, CA, USA).