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Oral subgingival plaque and saliva samples were obtained from five human subjects with periodontal disease under an IRB-approved clinical protocol. An unstimulated saliva sample (about 1 ml) was obtained by collection into a sterile 15-ml falcon tube following a 2-min water rinse. Samples were collected at a consistent time of day to avoid diurnal effects and were kept cold during and following collection. After collection was complete, the cap of the tube was tightly screwed and transferred to −80°C.

Two subgingival plaque samples per site were collected from periodontal sites of four periodontal teeth with ≥6 mm pocket depth using Endodontic absorbent paper points (size, 40). The sampling sites were gently air-dried and isolated with cotton pellets to avoid saliva contamination. The paper points were inserted in the pockets for 30 s until resistance was felt. Paper points were held with pliers, removed from the site, and placed into prelabeled 1.5-ml microcentrifuge tubes. Samples were eluted from the paper points by placing them in 100 μl of B-PER lysis buffer in a low-bind 1.5-ml tube, flicking the tube at one flick per second for 30 s, discarding the paper point, and snap-freezing the samples in liquid nitrogen. Each plaque sample was processed in this manner separately but combined for analysis. Twenty microliters of the eluate was used for COR553 probe labeling, 5 μl was used for BCA protein determination, and 2 μl was used for qPCR.

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