Integrating genomic and molecular approaches to understand bacterial adaptation and competitive fitness.

• Funding – self-funded/externally sponsored applicants  (PhD Fees can be found here)
• Applications are accepted year round
• Standard Entry dates – January and September
• Applicants are expected to have a degree (equivalent of Honours or Masters) in a relevant discipline.

Opportunistic Gram-negative bacteria can adapt to thrive in multiple environmental niches, including clinically-significant and antibiotic-resistant human infections and agriculturally-relevant plant associations. Adaptations facilitating host colonisation and pathogenesis typically include the ability to survive in, and manipulate, the host environment. Recently, it has become clear that the ability to actively compete with other bacteria within polymicrobial communities in the environment and the host, for example by the injection of anti-bacterial toxins or production of antibiotics, is also critical to the success of opportunistic bacterial pathogens. However, the genetic and molecular basis of ‘real life’ bacterial adaptation in relation to selection from inter-bacterial competition remains poorly understood. Large-scale genomics approaches can provide broad-ranging and unbiased insight into bacterial evolution and adaptation, whilst molecular and cellular analysis of specific genes and proteins can provide detailed functional insight into key determinants of bacterial fitness and success. In this project, we will combine genomic and molecular approaches to identify and characterise genes and corresponding proteins required for the adaptation of key opportunistic bacterial pathogens to the clinical environment. We anticipate that this will provide broader, fundamental insight into how bacteria adapt to many other environments.

This project will involve close collaboration between the Coulthurst and Holden labs. We have already developed approaches to analyse large sets of bacterial whole genome sequences in order to identify the genes most subject to selection pressure in one particular environmental niche, such as the clinic, and gene clusters encoding variable determinants of inter-bacterial competition. These approaches will be applied to one or more clinically-important species of opportunistic pathogens, under the supervision of Prof. Holden, an expert in fundamental and applied bacterial genomics and the evolution of bacterial virulence and AMR. Once candidate genes of interest have been identified, the role and mechanism of action of the corresponding proteins will be investigated using an appropriate combination of microbial cell biology, molecular genetics and biochemical approaches, under the supervision of Prof. Coulthurst, an expert in molecular bacteriology and the interactions of bacteria with other organisms.

Ultimately, we hope that the findings of this project may contribute to the development of new anti-bacterial strategies of relevance to health and agriculture. The student will gain experience in state-of-the-art genomics and a range of genetic, cell biology and biochemical techniques, as well as a strong grounding in microbiology and opportunities to engage with the international research community and the general public.

Our research community thrives on the diversity of students and staff which helps to make the University of Dundee a UK university of choice for postgraduate research.  We welcome applications from all talented individuals and are committed to widening access to those who have the ability and potential to benefit from higher education.

2nd Supervisor:  Prof. Matt Holden (St. Andrews University)