Impact of Antibiotics on the Subgingival Microbiome in Advanced Periodontitis: Secondary Analysis of a Randomized Controlled Trial

<b>Background/Objectives</b>: This study aimed to evaluate longitudinal changes in the subgingival microbiome over 12 months following non-surgical periodontal treatment, with or without adjunctive systemic antibiotics, in patients with stage III/IV periodontitis and peripheral artery disease. <b>Materials</b>: After randomizing patients to full-mouth mechanical debridement with/without adjunctive systemic antibiotics (PT1/PT2 group) or no subgingival debridement (control group), periodontal probing depths were measured, scores for 'periodontal inflamed surface area' (PISA) obtained, and subgingival plaque samples collected at baseline and during the 3-month and 12-month follow-up visits. Next-generation 16S DNA sequencing was used to characterize the microbiota of the samples for alpha/beta diversity and differentially abundant taxa. <b>Results</b>: Complete data was available for 76 patients. At 3 months, shallow (≤3.4 mm) or advanced (≥5.5 mm) pockets were significantly more, or less, prevalent in the PT1 than in the control group (<i>p</i> = 0.013/0.004). Microbiologically, the PT1 group was even more distinct, being associated with statistically significant changes over time (in alpha/beta diversity and differential taxa abundances) not seen in the PT2 and control groups. <b>Conclusions</b>: Although non-surgical treatment can reduce periodontal inflammation with or without antibiotics, subgingival microbial diversity can only be sustainably affected, and periodontitis-associated microbiota reduced, in the presence of adjunctive systemic antibiotics.