The oral microbiome is a highly diverse microbial community that varies greatly between individuals. It plays a central role in oral health, where it can protect the host from disease. However, under certain circumstances a healthy microbiome can get disturbed enough that it results in dysbiosis and possible onset of disease. The most prevalent oral diseases are dental caries and periodontal diseases. Both are associated with a state of dysbiosis of the oral microbiota. Periodontal diseases are commonly treated with antimicrobials, while antimicrobial formulations with fluoride are mostly used for the prevention of dental caries. Although antimicrobials are effective at alleviating clinical manifestations of these oral diseases, they can further unbalance the oral microbiome. Knowledge on how interindividual differences in the oral microbiome may influence the response to antimicrobial treatment is insufficient and requires further research. Apart from assessing the microbial community composition, it is also important to consider the phenotype of the community as it reflects its functionality and can provide clues on response to treatment. Flow cytometry is an excellent technique for studying phenotypic heterogeneity in microbial populations and has been applied to study the oral microbiome before. Therefore, it forms an interesting platform to explore for research in oral microbiology.