Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases

Abstract

We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we identified the most discriminative species between healthy and diseased subjects at baseline, evaluated their change over time, and provided evidence that clinical treatment had a positive effect on plaque microbiome composition in patients affected by mucositis and peri-implantitis.

Fig. 1. The plaque microbiome in peri-implantitis sites shifts toward a healthier microbiome after intervention.

a Species-level microbiome composition was different at T0 among study conditions (P < 0.001, PERMANOVA). Arrows indicate trajectories of peri-implantitis samples from T0 to T2. Two patients that showed initial microbiome improvement at T1 and later bounced back at T2 are highlighted with a different color (light green or yellow). We assessed proximity to the healthy implant microbiome composition by considering probability density functions (PDFs). Such PDFs were computed on diseased samples and normalized on the healthy ones for both b taxonomic and c functional data (“Methods”; P values computed using Wilcoxon–Mann–Whitney test). Variations in such PDF ratios showed a post-treatment shift of the microbiome initially associated with disease to the configuration of the microbiome in healthy implants.

Fig. 2. The plaque microbiome changed in peri-implantitis sites after the intervention.

We report changes in relative abundances as the (base 2 logarithm) ratio of the abundances at T2 and T0. This logRatio is reported for (a, c) case and (b, d) contralateral samples and stratified by study condition. Contralateral samples were grouped according to the diagnosis of the respective case implant. We report the top-10 SGBs identified as the ones most enriched in (a, b) health and (c, d) peri-implantitis through LEfSe (“Methods”). P value: *<0.1; **<0.05; ***<0.01. Whiskers are ±SD.