The present disclosure describes methods and kits for selecting treatments for, and treating, an oral infection in a patient. Oral samples are collected from multiple locations of the patient's oral cavity and include saliva, tongue biofilm, and interproximal biofilm. The samples are analyzed to determine a pathogen profile of the oral cavity, using nucleic-acid based analysis. Based on the pathogen profile, an antibiotic rinse is selected as the treatment of the oral infection.
