A total of 29 partially or fully edentulous patients were consecutively recruited from the Department of Oral Surgery, Heinrich Heine University, Düsseldorf, Germany, between April 2013 and July 2014. Nineteen patients (7 men and 13 women; mean age 58.8 ± 12.6 years) suffered from initial to moderate or advanced peri-implantitis, while ten patients (6 men and 4 women; mean age 55.2 ± 11.3 years) revealed clinically healthy implant sites. Prior to participation, each patient was given a detailed description of the procedure and was required to sign informed consent forms. The study was in accordance with the Helsinki Declaration of 2008 and the study protocol was approved by the ethics committee of the Heinrich Heine University.

For patient selection, the following inclusion criteria were defined: 1) partially or fully edentulous, 2) presence of one screw-type titanium implant either exhibiting healthy (absence of bleeding on probing (BOP), probing depth (PD) <4 mm) or established peri-implantitis (i.e., bleeding on probing with or without suppuration/pus, pocketing, and radiographic bone loss - initial to moderate: <50%/advanced: >50% of the implant length relative to baseline) [11], 3) presence of a sufficiently dimensioned (>2 mm) keratinized mucosa, 4) no implant mobility, 5) no systemic antibiotic medication within the last 3 months, 6) no history of malignancy, radiotherapy, chemotherapy, or immunodeficiency within the last 4 years, 7) proper recall/periodontal maintenance care, 8) non-smoker or light smoking status in smokers (<10 cigarettes per day).

After a gentle supramucosal cleaning, submucosal plaque samples and peri-implant sulcus fluid were collected at the deepest aspect of each implant site by means of sterile paper points (i.e., each was left in place for 30 s). The paper point was transferred into 200 μl G2 buffer of the EZ1 DNA Tissue Kit (Qiagen, Hilden, Germany) and stored at −20°C until transportation to the Institute of Medical Microbiology and Hospital Hygiene at the Heinrich Heine University for analysis.