Longitudinal microbiome dynamics in peri-implantitis: From dysbiosis to recovery

Objectives: This study aimed to investigate the temporal dynamics of the peri-implant microbiome in patients with peri-implantitis, comparing microbial shifts before and after non-surgical therapy with those observed at healthy implant sites. Methods: Peri-implant sulcus fluid was collected from patients with peri-implantitis and healthy implant controls at baseline, 90 days, and 180 days. The peri-implantitis group received non-surgical periodontal treatment, including scaling, root planing, and local antimicrobial therapy, while the control group received no intervention. Microbial DNA was extracted, and the V3–V4 region of the 16S rRNA gene was sequenced. Bioinformatic analysis was performed using DADA2 for sequence processing, principal coordinates analysis (PCoA) and PERMANOVA for community comparison, and MaAsLin2 for differential abundance testing. Alpha and beta diversity metrics were also calculated to assess microbial composition changes over time. Results: At baseline, peri-implantitis sites showed significantly lower alpha diversity than healthy implant sites and were enriched with Prevotella, Fusobacterium, Treponema denticola , and Porphyromonas gingivalis , while healthy sites were dominated by Streptococcus and Neisseria . At 90 days post-treatment, Haemophilus abundance increased in both groups, more prominently in the peri-implantitis group. By 180 days, peri-implantitis sites exhibited a partial microbial shift toward a healthier profile, characterized by increased Streptococcus and reduced pathogenic taxa. However, full restoration to a healthy microbiome was not achieved. The control group maintained a stable community composition, dominated by Veillonella and Neisseria . Conclusions: Peri-implantitis is characterized by a dysbiotic microbial community that only partially recovers following six months of non-surgical therapy. Although treatment promotes a shift toward a healthier microbiome, persistent imbalances remain, underscoring the need for targeted microbiome-based therapeutic approaches and long-term follow-up studies to optimize peri-implantitis management outcomes.