This systematic review evaluated concomitant trends in microbial (total biofilm load and pre-dominant pathogens' counts) and clinical, radiographic, and crevicular variations following (any) peri-implantitis treatment in partially vs. totally edentulous, systemically healthy, non-smoking adults and compared them to peri-implant mucositis treated sites. The study protocol, compliant with the PRISMA statement, was registered on PROSPERO (CRD42024514521). Findings from six randomized controlled trials (RCTs), evaluated through the ROBINS-2 tool, were qualitatively synthesized. No data concerning total edentulism and treated peri-implant mucositis sites were retrieved from the included RCTs. Instead, as expected, in the partially edentulous subjects, peri-implantitis treatments effectively provided biofilm control, although Plaque Index (PI) tended to increase again over time. Notably, Bleeding on Probing (BoP) rose slightly after treatment but decreased markedly by three months, indicating, at least, a partial resolution of the infective-inflammatory process. Probing Depth (PD) showed a slower but consistent improvement throughout. Despite a return of PI levels by twelve months, BoP and PD continued to improve, underscoring the successful long-term outcomes of peri-implantitis treatment. Over time, variations in PI did not consistently reflect changes in predominant pathogenic species, especially at the 1-month follow-up; BoP aligned with predominant pathogens rather than total microbial biofilm load at the 1- and 3-month follow-ups, and PD did the same at the 3- and 6-month follow-ups, likely affecting peri-implantitis-associated microbiota. No data concerning crevicular parameters were retrieved in the included RCTs, and the extracted radiographic outcomes were not comparable. The impact of the microbial variations after peri-implantitis treatment on peri-implant clinical parameters highlight the critical role of dysbiosis, rather than total microbial load, in influencing inflammation and tissue destruction, emphasizing the need for targeted approaches to manage persistent pathogens and improve treatment efficacy.

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