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The Hidden Life of Pathogens: Ecology and Evolution of Commensal Communities
Project Description
Many bacterial pathogens spend much of their life in a commensal state, persisting as members of their host’s microbiota without causing disease. This phase is difficult to detect, as it leaves little trace on host health and pathogens often exist only as minor components of a complex microbial community. Nevertheless, this hidden state is central to pathogen ecology and evolution. It is the source of onward transmission and future infections, and the setting in which pathogens interact with strictly commensal bacteria and the host environment, both competing for resources and exchanging genes. While cases of disease may emerge as side effects of traits shaped in this context, the commensal state remains one of the least understood aspects of pathogen biology.
This project will investigate how the commensal state shapes evolutionary outcomes, including pathogenicity and antimicrobial resistance. Key questions include:
- How do interactions with other microbes in the commensal state shape the persistence and adaptation of pathogens?
- Why do resistance and susceptibility to antimicrobial drugs coexist within microbial species and communities, and what determines the prevalence of resistance?
- How and why do lineages shift between more and less commensal ecologies, and how are these transitions shaped by host populations and broader environments?
Drawing on ecological and evolutionary theory and integrating genome sequence data from natural populations and experimental systems, this project will link fundamental questions in ecology and evolution to urgent global challenges, particularly how human-driven environmental change shapes the evolution and spread of antimicrobial resistant pathogens.
Research themes
Project Specific Training
The student will be trained in mathematical and statistical modelling, genome sequence analysis (including phylogenetics, population genetics, and comparative methods), bioinformatics and data science approaches applied to evolutionary biology and ecology. Training will be delivered through one-to-one supervision and peer-support, supported by expertise within the UCL Centre for Biodiversity and Environment Research, UCL Genetics Institute, and the RHUL Centre for Ecology, Evolution and Behaviour. In addition, opportunities for training across a range of disciplines and methodological approaches will be available through collaborations with external partners, providing the student with a broad, interdisciplinary skill set.
Potential Career Trajectory
The training provided by this project will support a wide range of career trajectories. Depending on their interests, the student will develop expertise in mathematical modelling, ecological and evolutionary theory, statistical analysis, and bioinformatics (including genome sequence analysis). These skills will equip them for further research in diverse fields including biology, conservation, public health, and data science. The project’s interdisciplinary nature will also allow the student to explore connections across scientific fields and across science, government and industry. Beyond academia, the skills gained, especially in quantitative analysis, computational methods and genomics, are highly transferable and valued across various sectors including public health, conservation, agriculture, government, charities, and industry.
Project supervisor/s
Gemma Murray
Genetics, Evolution and Environment
University College London
gemma.gr.murray@ucl.ac.uk
David Murrell
Genetics, Evolution and Environment
University College London
d.murrell@ucl.ac.uk