Postgraduate research project

Roles of the genetic ‘dark matter’ in environmental and antimicrobial resistance of bacteria

Fully funded (UK and international)
Type of degree
Doctor of Philosophy
Entry requirements
2:1 honours degree
View full entry requirements
Faculty graduate school
Faculty of Environmental and Life Sciences
Closing date

About the project

Bacteria have been (in)famous for their remarkable ability to handle sudden, often unfavorable environmental changes, and to successfully occupy new habitats. This project will investigate genetic elements that control cellular processes enabling bacteria to withstand ever-changing conditions. These include temperature fluctuations and antibiotic exposure, by utilizing bacteriology, single-cell and computational approaches.

What gives a bacterium such flexibility to live just about anywhere, and adjust its behavior depending on what is happening in its environment?

In this project, you will explore the flexibility of these resilient bacteria that is encoded in their so-called 'accessory' genome. 

Despite our advances in DNA sequencing technology, accessory elements still form the genetic ‘dark matter’ in bacteria. We know little about the functions of the genes they encode, making it difficult to develop control strategies against disease-causing bacteria. 

This project will investigate: 

  • how accessory systems work
  • how they re-route bacterial core regulatory networks enabling bacteria to survive in harsh conditions
  • endure antimicrobial treatments

You will have the opportunity to employ: 

  • microbiology 
  • molecular biology 
  • time-lapse microscopy 
  • microfluidics 
  • flow cytometry 
  • bioinformatics 
  • genome analysis tools

The roles of accessory systems will be studied in a set of Escherichia coli commensal and antibiotic-resistant pathogenic strains. The research will address specific questions. They will range from ‘How do accessory genetic systems help bacteria to respond so quickly to environmental changes?’ to ‘How do accessory systems control the development of stress-tolerant 3D-structures called biofilms?’. 

The results of this project will not only help us better understand how to successfully combat bacterial diseases but will also give us insights of how accessory elements supercharge bacteria to adapt to new environments. This is an increasingly important topic in light of the evolutionary pressure posed by pollution and climate change.