Longitudinal Changes in the Peri-Implant Microbiome Following Implant Placement: A 3-Year Follow-Up Study

To investigate longitudinal changes in the submucosal peri-implant microbiome during early healing and long-term maturation, and their association with clinical and radiographic outcomes.

This is the 3-year follow-up of a subset of individuals from a randomized controlled clinical trial. Marginal bone level changes (MBL) were measured at implant placement, loading, 12 months, and 3 years; clinical parameters were recorded at 12 months and 3 years. Submucosal plaque samples were collected at 1 week, 4 weeks, and 3 years post-implantation and analyzed by 16S rRNA gene sequencing. Microbial diversity, composition, and co-occurrence networks were evaluated.

Twenty-seven patients (64 implants) completed the 3-year visit. At 3 years, peri-implant clinical conditions and MBL remained stable across visits, although early supracrestal remodeling was observed. The incidence of peri-implant mucositis was 14.8% and peri-implantitis 11.1% at patient-level. Microbiome richness and phylogenetic diversity increased over time (p < 0.0001). Early biofilms were dominated by facultative anaerobes (e.g., Haemophilus parainfluenzae, Neisseria elongata), which declined at 3 years, when anaerobic/proteolytic taxa (e.g., Prevotella, Porphyromonas gingivalis, Fusobacterium nucleatum) became more prominent. Presence/absence analyses at 3 years showed persistence of early colonizers alongside the integration of later-arriving species. Lactococcus lactis and Enterococcus italicus increased in abundance and occupied more central positions in co-occurrence networks.

Over 3 years, the peri-implant microbiome matured into a more diverse and structured community, while MBL remained stable with physiological early supracrestal remodeling. These longitudinal findings suggest that early colonization and its subsequent evolution may influence long-term peri-implant health.