Development and genome-level microevolution of peri-implant microbiome during surface colonization

The peri-implant microbiome is closely associated with dental implant health and disease, yet its development and genome-level dynamics remain insufficiently understood. In this longitudinal cohort, we performed shotgun metagenomics on 95 subgingival plaque samples from 19 participants, including peri-implant sites at weeks 1-4 after crown placement and adjacent teeth at week 1 as controls. Peri-implant and periodontal microbiomes showed distinct taxonomic and functional profiles, while shared taxa exhibited niche-related functional potentials, supporting selective assembly rather than fully passive translocation from adjacent sites. Longitudinal analysis identified microbiome development associated with three microbial modules, with distinct abundance and functional trajectories. Co-occurrence networks and generalized Lotka–Volterra simulations suggested that community context influenced attachment probabilities for specific taxa. At strain level, different microbial modules exhibited distinct extents of accumulative mutation, strain heterogeneity, and microevolutionary change. These findings provide a longitudinal framework of peri-implant microbiome succession and microevolution during early surface colonization.