Beyond the Oral Microbiome: Investigating the Oral Ecosystem and Disease Development

Background A diverse range of organisms form communities within the oral cavity, composing the oral microbiome. This is becoming increasingly associated with oral and systemic disease development. Current understanding of oral and oropharyngeal ecology is majorly based on traditional methods that rely on culturability or are limited to identifying known bacterial species (16S rRNA sequencing). The shotgun metagenomics (SM) approach gives a more representative snapshot of microbiome composition by identifying often overlooked fungal, viral, and novel populations. Aim Creating and utilising existing databases and clinical datasets to develop a reproducible toolkit that can be used to investigate the roles of oral microbiome components in health and disease. Methodology Public genomic and transcriptomic datasets related to oral health and microbiome will be interrogated further. Intuitive analysis pipelines and standard protocols will be developed for and validated by the investigation of oral cavity and oropharyngeal samples (e.g., ongoing tonsillitis study). This bioinformatic toolkit will be employed to study the role of oral microbiome members in the development of oral and systemic disease in current and future research. This study will contribute to the vast 16S rRNA data generated by the Oral Sciences Research Group and an ongoing Haleon project. Expected Results By employing SM and the toolkit, the inter-species dynamics present in oral microbiomes can be studied to help identify diagnostic and prognostic predictors of oral/systemic health and disease. SM could also elucidate factors beyond the microbiome, e.g., antimicrobial resistance genes, that influence disease pathology, potentially suggesting new therapeutic approaches.