Bacterial competition within the nasopharyngeal microbiome

8 September 2025 to 2 December 2025
Project No: D26001
DPhil Project 2026
Infectious Disease Epidemiology Unit

Background

The paediatric nasopharyngeal microbiome is a community of microbes that are harmless commensals and potentially pathogenic. Bacteriocins (antimicrobial peptides produced by bacteria to inhibit other bacteria) drive competition and the structuring of bacterial species in the nasopharynx.

Prof Brueggemann’s research group has characterised in detail a large collection of S pneumoniae, H influenzae, M catarrhalis and S aureus (5,400 genomes in total) recovered from the nasopharynx of an intensively sampled subset of children from the Drakenstein Child Health Study in South Africa, in collaboration with Prof Mark Nicol (now based in Australia).

In collaboration with Prof Voysey at Oxford, preliminary statistical analyses were performed to identify changes in the presence of bacteriocins among these four bacterial species over time, and by serotype. Further statistical analyses will be required to investigate the observed patterns of colonisation and predict the likelihood that these bacterial species will co-colonise. The findings will have implications for understanding the healthy paediatric nasopharyngeal microbiome, especially when the microbiome is disrupted by vaccination and/or antimicrobial treatment.

research experience, research methods and skills training

This project is data-intensive and will be statistically demanding. It will require a candidate with a creative and thoughtful approach to the analyses and interpretation of the findings. This project will also be highly rewarding, will very likely lead to several conference presentations and publications during the DPhil period, and will allow the candidate to investigate a uniquely rich dataset.

The candidate will broaden his/her statistical skills and will develop a solid understanding of the biology that underpins the observed findings. The candidate will work closely with both supervisors, each of whom bring different and complementary skills to this project.

FIELD WORK, SECONDMENTS, INDUSTRY PLACEMENTS AND TRAINING

There might be options for visiting collaborators in Australia if funding can be secured.

PROSPECTIVE STUDENT

The ideal candidate will have a Bachelor’s or Master’s degree in statistics and/or epidemiology and prior experience with a major role in analytical projects. The ideal candidate will also be an excellent writer and communicator.