Omics of saliva, GCF and plaque in periodontitis management

o Baseline and initial treatment visit (0-month; 1 hour duration) o Pre-operative periodontal charting recorded by registered periodontists (Ivanovaki, Lee, and otherrelevant staff) or DClinDent postgraduate registrars, with a periodontal UNC probe. All examiners will becalibrated. o This will allocate participants into the group categories: periodontal health, gingivitis and periodontitis (with and without systemic diseases) o Saliva, gingival crevicular fluid (GCF) and plaque samples will be collected from all Groups, - For saliva collection: participants will be asked to refrain from eating and drinking for at least one hourprior to saliva sample collection. At the appointment, participants will rinse their mouths with ~10 mL ofwater to remove the food debris. Unstimulated whole saliva through spitting (5mL ideally; minimum 1-1.5ml) will be collected. - GCF will be collected prior to commencing treatment to avoid contamination via blood. This willbe conducted using our established protocol (Han et al, 2023, PMID: 35771077) where paper strips (Oraflow)will be inserted into the deepest site of each quadrant (to reduce saliva contamination) and pooled. - For healthy patients: 6 paper strips will be collected each from 6 healthy sites (free of inflammation and BOP) from the same tooth and pooled. Up to 3 teeth will be collected - For gingivitis patients: 6 paper strips will be collected from 6 inflamed sites (or 2 sites from the same tooth) - For periodontitis patients: up to 6 paper strips will be collected each from 1 deepest site and 1 healthy site o Plaque, GCF and saliva samples will be placed in sterile glycerol (final concentrations: 15-30%), or stored immediately at -80 degrees at the Research Lab, Level 6, Oral Health Centre, until elution andextraction. Extracellular vesicles from those samples may be isolated and compared the omics between orginal oral samples and their derived EVs. Samples containing glycerol may be subjected to in vitro culturing for biofilm development prior to bacterial extracellular vesicles omics (proteome, methylome, microbiome, lipidome and metabolome or relevant omes), with saliva, GCF and plaque samples used as controls. Patients in the periodontitis group will be allocated the next available appointment for standard care,receiving supragingival and subgingival non-surgical debridement using hand scalers and ultrasonicinstruments over 2 appointments (60-90 mins duration per appointment). Routine surgical treatment may be performed if deemed necessary. Follow-up reviews (3-, 6-, 12- and 18-mo post-periodontal treatment; 1-1.5 hours duration) o Periodontitis patients will be recalled 3 mo following debridement to re-assessperiodontal parameters and recollect saliva and GCF (from the same sites as baseline appointment). o They will then receive the standard protocol of care, including oral hygiene instruction (OHI), non-surgicalre-instrumentation of persistent sites and supragingival maintenance of remaining sites. o Patients will then be recalled at the 3, 6 12, and 18 mo time points (since initial therapy) o Patient compliance with treatment reviews will be recorded using a clinic attendance checklist. Salivary omics (proteome, lipidome, metabolome), GCF cytokines and plaque bacterial load and omics (16S sequencing, metagenomic sequencing, and ITS sequencing) will be conducted for all samples.