A comprehensive oral examination was performed at each visit by one of two calibrated dentists in a dedicated examination room at the URMC, using standard dental examination equipment, materials, and supplies. Caries were scored using DMFT (decayed, missing, and filled teeth) and the International Caries Detection and Assessment System (ICDAS) [19 (link)]. Bleeding on probing (BOP) was used to assess the gingival inflammation. Supragingival plaque was assessed using the Plaque Index (PI) described by Löe [20 (link)]. Inter- and intra-examiner agreement for the evaluated criteria was calculated by Kappa statistics and exceeded 90% at the calibration.
Saliva/plaque sample collection was detailed previously [3 (link)]. The study participants spit approximately 2 ml of whole non-stimulated saliva into a sterile 50 ml centrifuge tube. Study subjects were instructed not to eat, drink or brush their teeth 2 h before oral sample collection prior to their study visit. Supragingival plaques from the whole dentition were collected using a sterilized periodontal scaler. The plaque samples were resuspended in 1 ml of a 0.9% sodium chloride solution in a sterilized Eppendorf tube. All samples were transported to the lab within 2 h of collection and stored in a – 80 °C freezer.