Saliva and biofilm sampling Saliva and tooth biofilm samples were obtained immediately before (baseline) and after 4, 8, and 12 weeks of L. reuteri supplementation (Figure S1). Follow-up samples were collected 1 and 6 months after supplementation was terminated. Furthermore, whole stimulated saliva (~5 mL) was generated by chewing 1 g of paraffin and collected into ice-chilled sterile test tubes. One milliliter of saliva was used for cultural analysis, and the remaining saliva was centrifuged at 3,500 × g for 10 min at 4°C. The pellets were stored at −80°C until DNA extraction for strain-specific PCR reactions. For the pyrosequencing analysis, pooled supragingival plaque was collected with sterilized toothpicks and transferred to Eppendorf tubes (Sarstedt, Nümbrecht, Germany) containing 200 µL of TE-buffer (10 mM Tris, 1 mM EDTA, pH 7.6). The samples were stored at −80°C until DNA extraction.