This systematic review of RCTs aimed to characterize short- and long-term changes in peri-implantitis-associated microbiota (total biofilm microbial load and predominant pathogens’ counts) following (any) peri-implantitis treatment in systemically healthy, non-smoking, partially/totally edentulous adults. The study protocol, compliant with the PRISMA statement, was registered on PROSPERO (CRD42024514521) before the literature search. Data from 11 RCTs, assessed through the ROBINS-2 tool, were qualitatively synthesized. No data were retrieved on total edentulism, healthy peri-implant/periodontal sites, treated mucositis, gingivitis, and periodontitis sites. Shortly after treatment, Prevotella intermedia, Fusobacterium nucleatum, and Peptostreptococcus micros prevailed, indicating early colonization, as after implant placement. After both surgical and non-surgical approaches, although not eradicated, the peri-implant total biofilm load, red- and orange-complex species, and Aggregatibacter actinomycetemcomitans counts generally decreased for up to about three months. However, one month after treatment, red-complex species and Prevotella intermedia increased, likely due to persistent tissue-invasive bacteria, unresolved pathological conditions (high probing depth values) favoring anaerobiosis and dysbiosis, and a qualitatively and quantitatively decreased biofilm community, competing and balancing the predominant pathogens (biofilm “competitive balancing” effect), thus allowing recolonization by more virulent bacteria. Red-complex bacteria gradually leveled off to baseline at the six- and twelve-month follow-ups. Fusobacterium nucleatum remained almost unchanged after treatment.
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