Background <p>Fluoride mouthwashes are commonly used for prevention of dental caries. The most common forms of fluoride are stannous fluoride (SnF₂), amine fluoride (AmF) and sodium fluoride (NaF), each with differing activities against oral bacteria. Since the microbiome has been linked to interindividual differences in responses to treatment, the phenotype of the microbiome may provide information on potential treatment responses. Flow cytometry successfully tracks microbial phenotypic heterogeneity and may prove useful for capturing interindividual treatment responses.</p> Methods <p>We compared the effect of fluoride-containing mouthwashes, Elmex Anti Caries (AmF/NaF), Listerine Anti Caries (NaF) and Meridol (AmF/SnF₂) on the salivary microbiome in vitro. We determined the effect on the microbial community structure using 16&#xa0;S rRNA gene amplicon sequencing, assessed the acidogenic potential by measuring organic acids after incubation, and constructed flow cytometric fingerprints of the microbial community to evaluate if it could be used to capture the response to treatment and to assess if it has potential for precision medicine.</p> Results <p>We observed mouthwash- and donor-dependent changes in the salivary microbiome composition and acidogenic potential. Meridol affected more bacterial taxa and showed the strongest reduction in organic acids, followed by Elmex. The response to treatment could be captured in the flow cytometric fingerprint of the initial intact salivary microbiota and a random forest classifier predicting the optimal mouthwash for each donor was successfully trained (MCC = 0.95).</p> Conclusions <p>Treatment with fluoride mouthwashes induces a shift in the salivary microbiome in vitro and alter its potential to produce organic acids, contributing to the prevention of dental caries. Moreover, flow cytometry shows promise for tailoring treatments to patients.</p>