Mass Spectrometry-Based Oral Meta-Omics Analysis-What We Know and What We Don't

According to the World Health Organization, dental caries and periodontal disease are the most prevalent oral health conditions worldwide, usually linked with oral microbiome dysbiosis. It is assumed that oral microbiota alterations are also associated with immune challenges, beyond the oral cavity, thus having implications in the progression of various systemic diseases, but the mechanism by which the plaque biofilm microbiota contributes to the development of such diseases is not entirely clear. In this context, metaproteomics and mass spectrometry-based metabolomics can reveal essential information about such correlations, particularly by integration with other -omics technologies. It can extend the molecular analytical repertoire and provide a deeper understanding of the molecular mechanism, delivering disease-specific biomarkers with great potential for clinical application, mainly considering the recent technological innovations in the field. Here, we address some of the latest findings exploiting mass spectrometry in the pathological context of dysregulated oral microbiome, by describing essential principles and methodologies in the field of mass spectrometry-based multi-omics analysis. We emphasize critical aspects related to sample collection, preparation and analysis using liquid chromatography coupled with mass spectrometry, with a focus on some controversial key aspects related to the analysis workflow.