The Holistic Microbiome in Health and Disease: Linking the Oral, Gut and Respiratory Microbiomes

The human gut microbiome is recognised as a major determinant of health and disease. Studies to date, including those of the international Human Microbiome Project, have largely focused on individual body sites such as nose or mouth or faeces. Oral bacteria have recently been associated with several systemic conditions, suggesting a need to integrate microbiome science into a holistic model studying body sites contemporaneously so that we can understand these associations and ultimately explore novel therapeutic options.

The project focus is on recruiting new cohorts to study the microbiome contemporaneously across multiple body sites. Initially, 100 healthy volunteers (50 children and 50 adults) will be recruited from clinics at Dundee Dental Hospital & School to explore microbial colonisation of the respiratory tract (nose), mouth, and gut (faeces) to facilitate molecular microbiological assessment of 50 subjects, including 16S rRNA sequencing, and targeted microbial culture to recover Fusobacterium, Haemophilus and Campylobacter in 25 subjects. These organisms have been chosen as candidates of interest in oral, gut, liver, and respiratory diseases, but also to help develop the necessary techniques to target an organism and study isolates in detail.

Once techniques and methods are established, the student will expand to proof-of-principle pilot work in small cohorts (5 patients each) of four disease states: paediatric Crohn’s disease, chronic obstructive pulmonary disease, orofacial granulomatosis, and cirrhosis. The core sites will be sampled again alongside disease-relevant samples taken from elsewhere as convenient including endoscopic mucosal biopsies and sputum as available.

This PhD will be important in defining a local “healthy” microbiome for use in countless future studies as controls. It will also generate pilot data in disease as a springboard for future funding.

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