Methods and systems for treating and controlling oral periopathogens that have been found to be associated with systemic inflammation and/or disease in a periodontal pocket, inhibiting their entry into the host circulatory system, and decreasing the systemic effects. A bacterial community present in one or more oral treatment regions is determined. A periodontal medicament delivery tray is prepared for the patient with the delivery tray being configured with one or more application regions, each configured for applying a medicament to a different one of the oral treatment regions. The medicaments are applied to each oral treatment region, including placing each medicament into a different application region of the delivery tray. Each of the applied medicaments is applied as a function of a determined efficacy of the medicament against the bacterial community determined to be in the oral treatment region associated with the application region in which each medicament is applied.