Metagenomic WGS of oral subgingival plaque
Each library was generated from 20ng of genomic DNA, in accordance with procedures described in the NEBNext Ultra II DNA Library Prep Kit for Illumina protocol (New England Biolabs). NEBNext Multiplex Oligos for Illumina (Dual Index Primers set 1) were used to produce the individual libraries and label them with specific molecular barcodes. Then, Agencourt AMPure XP beads (Beckman Coulter) were used for library purification. Finally, libraries were quantified by using the High Sensitivity DNA Kit (Agilent Technologies, Santa Clara, CA, USA) on the Bioanalyzer instrument (Agilent), diluted and pooled together in equimolar amounts. Samples were sequenced with an Illumina NextSeq 500 sequencer with 2150-bp read, using NextSeq 500/550 Mid Output Kit v2.