Resolving coevolutionary dynamics within microbiomes using lineage tracking

Microbial communities, or microbiomes, are incredibly important in a variety of health-associated and environmental contexts.

 The gut microbiome plays an important role in critical aspects of human metabolism and immune health. Microbiomes are not static, species change in abundance but also evolve, both through point mutations and gene exchange. These are mediated by mobile genetic elements (MGEs), particularly plasmids, extra-chromosomal circular DNA that is transmissible between hosts.

This is an exciting studentship opportunity within a vibrant research group to contribute to our growing understanding of evolutionary dynamics within microbiomes. In this studentship you will develop novel molecular methods for genetic engineering of microbes, enabling barcoding of individual lineages within a microbial species. 

These engineered organisms will be introduced into natural communities in order to understand how within a community context the processes of evolution, random drift and immigration combine to structure diversity. This will then be combined with further methods for resolving host-plasmid associations to link genomic evolutionary change to plasmid tranmission. 

This will help us understand how important genes such as those for antimicrobial resistance can persist within the commensal gut microbiota.

This studentship will involve complex molecular biology and anaerobic microbiology. 

It will also generate considerable amounts of sequence data that you will be taught to process and interpret. It would therefore suit a biologist with a strong interest in quantitative analysis or someone from a more mathematical background willing to learn experimental biology.

Further Reading:

• Hildebrand, F., et al. Dispersal strategies shape persistence and evolution of human gut bacteria. Cell host & microbe, 29(7):1167–1176.e9, jul 2021.
• Jasinska, W., Manhart, M., Lerner, J. et al. Chromosomal barcoding of E. coli populations reveals lineage diversity dynamics at high resolution. Nature ecology & evolution, 4(3):437–452, mar 2020.
• Lee, K., Raguideau, S., Sirén, K. et al. Population-level impacts of antibiotic usage on the human gut microbiome. Nature Communications, 14(1):1191, 2023.
• Assembly line: making sense of metagenomics through MAGs

Further Information:

Application deadline: Monday 20 November 2023 (23:59 i.e.,midnight).

Shortlisted applicants will be interviewed on 23, 24 or 25 January 2024.

Visit the NRPDTP website for further information on eligibility and how to apply.

Our partners value diverse and inclusive work environments that are positive and supportive. Students are selected for admission without regard to gender, marital or civil partnership status, disability, race, nationality, ethnic origin, religion or belief, sexual orientation, age or social background.

This project is awarded with a 4-year Norwich Research Park Biosciences Doctoral Training Partnership (NRPDTP) PhD studentship.

The studentship includes payment of tuition fees (directly to the University), a stipend to cover living expenses (2023/4 stipend rate: £18,622), and a Research Training Support Grant of £5,000pa for each year of the studentship.

Entry requirements:
At least UK equivalence Bachelors (Honours) 2:1 or UK equivalence Master's degree. English Language requirement (Faculty of Science equivalent: IELTS 6.5 overall, 6 in each category).