With the increase of personal care products targeting the microbiome for cosmetic benefits, there is a need to ensure that perturbations of the microbiome do not have potential unwanted consequences on the health of consumers. Safety assessments of new technologies currently rely on monitoring changes of microbial taxa in clinical studies, but it would be desirable to characterise the protective functions of the microbiome.    The role of commensal bacteria against pathogens can be effectively studied using a combination of in vitro and in silico models in the context of dental caries. A continuous bioreactor-based in vitro model utilizing hydroxyapatite coupons as tooth enamel analogues was inoculated with four early colonizer commensals alongside the caries-associated Streptococcus mutans. Together with individual-based modelling of biofilm growth, this showed that S. mutans dominated at low pH. However, as bacterial metabolism was represented using stoichiometric equations for growth derived from literature, ongoing work aims to reconstruct genome-scale metabolic models for each species to enable more accurate community modelling. Additionally, the resilience of a healthy microbiome - a key indicator of oral health- can be investigated in vivo through experimental gingivitis models. A study was designed collecting samples including during the recovery phase for metagenomics and meta-transcriptomics samples alongside clinical indices. Shotgun sequencing facilitates the identification of functional genes and pathways, while meta-transcriptomics reveals their activity. Taken together, these examples demonstrate the value of integrating in vitro, in silico, and in vivo models to elucidate microbiome functions relevant to safety assessments.