Tracing the evolutionary relationships of the oral microbiome in genetically diverse populations

Lead Research Organisation: University of Leicester
Department Name: Genetics


The oral microbiome is acquired at birth, reaches its full diversity during childhood, and maintains itself relatively stable and resilient to stresses throughout the individual's adult life. The restricted mother-to-child vertical mode of transmission and the high genetic diversity observed in members of the oral community are critical properties in the development of biogeographic differences by their genomes across populations. In this sense, the study of the genomic variation of these commensals across human populations can shed light on the dynamics of the co-evolution between humans and of their commensals. In addition, some of these members are closely related with important human pathogens that show a very efficient and distinct person-to-person transmission. The study of the genetic and phenotypic variation of these oral commensals and of their evolutionary relationships with their pathogenic relatives may then provide important insights into the genetic determinants of different life strategies. The current feasibility in performing whole-genome sequencing of hundreds of bacterial genomes in a single reaction will allow to obtain a significant set of genomic variation for population and phylogenetic/evolutionary analyses at an affordable cost. The aim of this PhD project is to study the transmission, genomic variation and evolution of oral commensals and of their related pathogen species within and among major human populations. To this end, the work will combine microbiological techniques with novel genomics and computational approaches to investigate the patterns of oral bacterial evolution in cohorts from Africa, Europe and Asia.


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Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M01116X/1 01/10/2015 30/09/2023
1791005 Studentship BB/M01116X/1 03/10/2016 30/09/2020 Charlotte Davison
Description This project studied the oral commensal microbe, Streptococcus mitis which is a close relative of the pathogen Streptococcus pneumoniae which causes worldwide morbidity and mortality. Understanding genetic diversity in S. mitis is of critical importance as it acts as a genetic reservoir for the pneumococcus, facilitating in antibiotic resistance and immune evasion. We found S. mitis to have high genetic diversity, comparable with the highly diverse bacterium Helicobacter pylori. This diversity was not the result of a higher mutation or recombination rate in S. mitis than the pneumococcus but due to S. mitis being an ancient species with little constraint due its commensal lifestyle. Whilst pathogens undergo frequent bottlenecks, S. mitis has not and as a result the effective population size is very large, permitting high genetic diversity. This is an important finding because it aids in elucidating the indirect role commensal bacteria can play in pathogensis.
Exploitation Route These findings could be applied to other pathogen-commensal pairs with the aim of further understanding of how commensals contribute to pathogenic potential in a broader scale.
Sectors Healthcare,Pharmaceuticals and Medical Biotechnology

Description High Speed super-resolution confocal laser scanning microscope for sub-diffraction analysis at the multi-user Leicester Advanced Imaging Facility
Amount £283,824 (GBP)
Funding ID BB/S019510/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2019 
End 06/2020
Description London Institute of Medical Sciences Community days 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Organised events for the London Institute of Medical Sciences including the PhD outing to Kew Gardens and the launch of the institute at The Royal Society, which attracted prominent figures including Professor Sir Mark Walport and Emmanuelle Charpentier.
Year(s) Of Engagement Activity 2017
Description School Visit 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Schools
Results and Impact Local schools (12-15 years old) interacting with different research groups in an interactive manner
Year(s) Of Engagement Activity 2017