DNA extraction, 16S rRNA gene sequencing and bioinformatic analyses
DENTAL PLAQUE
Genomic DNA from samples of the subgingival dental plaque collected before (initial inocula, t0) and 1 and 2 months after antibiotic treatment (t1 and t2, respectively), and the corresponding biofilms grown in xCELLigence impedance system for eight hours (alone and in combination with antibiotics) was isolated using MagNA Pure LC DNA Isolation Kit III for Bacteria and Fungi (Roche Diagnostics) according to manufacturer’s instructions. The 16S rRNA gene V3-V5 regions were amplified as previously described (The obtained reads were analyzed as previously described using dada2 v1.16 (R programming language was used to compare statistically the proportion of bacteria between groups (Based on the results from previous microbial-based studies, we grouped bacterial species considered periodontal pathogens into “disease-associated”, whereas those that are known to be more abundant in healthy individuals were computed as “health-associated”, following Perez-Chaparro et al. (