Targeting the Biofilm for Drug Design: Modelling the roles and impacts of extracellular matrix composition in a mixed species bacterial biofilm.

Bacterial biofilms are an evolved strategy used by bacteria to protect themselves in large colonies. The biofilm, which is composed of an extracellular mixture of sugars, proteins, DNA, ions and lipids, acts as a sophisticated barrier, preventing therapeutic molecules, such as antibiotics, from reaching the bacterial cells. The major components of most bacterial biofilms are polysaccharides (sugars), and each bacterial species has a different type or range of polysaccharides that it employs for this purpose. In this project we will look at the polysaccharide extracellular matrices (glycocalyx) of multi-species biofilms, for example Pseudomonas aeruginosa and Staphylococcus aureus, which are two dangerous pathogens linked to poor human health and the rapid development of antimicrobial resistance (AMR). Previous work has revealed an ambiguity with these two bacteria, showing both that they work cooperatively and, alternatively, antagonistically.<br /> <br /> For this PhD we will model the polysaccharide structures of the multi-species biofilm, exploring the interactions and partitioning behaviour of the biofilm components. We will also examine how quorum sensing (the messages sent between bacteria to ensure positive collective behaviour) and nutrient components move through this overlapping matrix; for example, can the quorum sensing molecules of one species navigate their way through the extracellular matrix of the other? This knowledge will then inform the rational design and modification of antibiotics, targeted against extracellular enzymes that maintain the glycocalyx.<br /> <br /> The project, based at the University of Leeds, will be entirely computational in nature, using computer-aided drug design and working on the University of Leeds’ new High-Performance Computer, Aire. It would suit a student with a chemistry, physics, materials or maths background, or equally someone with a background in biology or microbiology who is also interested in exploring computational methods.<br />

<p paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{113}" paraid="1539768372"><strong>You must contact the proposed supervisor for this project before you make a formal application. </strong></p> <p paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{119}" paraid="1895649428">A formal application for research degree study should then be made online through the <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees" rel="noreferrer noopener" target="_blank">University's website</a>. You will need to create a login ID with a username and PIN: </p> <ul> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{125}" paraid="1717955186">For ‘Application type’ please select ‘Research Degrees – Research Postgraduate’. </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{131}" paraid="1941411394">The admission year for this project is 2026/27 Academic Year.   </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{137}" paraid="1823221166">You will need to select your ‘Planned Course of Study’ from a drop-down menu. For this project, scroll down and select ‘PhD Food Science and Nutrition Full-time’.   </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{143}" paraid="754352421">The project start date for this project is October 2026, please use this as your Proposed Start Date of Research. </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{149}" paraid="202248598">Please state clearly in the research information section that the research degree you wish to be considered for is ‘Targeting the Biofilm for Drug Design: Modelling the roles and impacts of extracellular matrix composition in a mixed species bacterial biofilm’ as well as <a href="https://environment.leeds.ac.uk/food-nutrition/staff/7163/dr-james-smith">Dr James Smith</a> as your proposed supervisor. </li> </ul> <p paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{155}" paraid="812110430">If English is not your first language, you must provide evidence that you meet the University's minimum English language requirements (below). </p> <p paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{161}" paraid="1891516213">More information on how to apply is available on our website <a href="https://www.leeds.ac.uk/research-applying/doc/applying-research-degrees" rel="noreferrer noopener" target="_blank">here</a>. You will need to provide copies of the following documents: </p> <ul> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{172}" paraid="1858125611">a research proposal for this project</li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{178}" paraid="877561217">your CV </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{184}" paraid="1448270499">certificates and transcripts of all academic qualifications </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{190}" paraid="932080590">English language qualification certificates </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{196}" paraid="1315959137">visa and immigration documents, if applicable </li> <li paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{202}" paraid="226045984">funding information – sources of funding that you are applying for (e.g. government scholarship), or if you are able to pay your own fees and maintenance  </li> </ul> <p paraeid="{cc558561-e300-45f5-a898-3bd20c9a5968}{208}" paraid="1308150127"><em>As an international research-intensive university, we welcome students from all walks of life and from across the world. We foster an inclusive environment where all can flourish and prosper, and we are proud of our strong commitment to student education. Across all Faculties we are dedicated to diversifying our community and we welcome the unique contributions that individuals can bring, and particularly encourage applications from, but not limited to Black, Asian, people who belong to a minority ethnic community, people who identify as LGBT+ and people with disabilities. Applicants will always be selected based on merit and ability. </em></p>

Applicants to research degree programmes should normally have at least a first class or an upper second class British Bachelors Honours degree (or equivalent) in an appropriate discipline.

For start dates from September 2026, the minimum English language entry requirement for research postgraduate research study in the School of Food Science and Nutrition is an IELTS of 6.0 overall with at least 5.5 in each component (reading, writing, listening and speaking) or equivalent. The test must be dated within two years of the start date of the course in order to be valid.

<p paraeid="{3d04e34c-3522-40f3-8630-c6f14cbc41d0}{143}" paraid="557166827"><strong>This is not a funded project, but you can apply for funding separately. Self-funding students are also welcome to apply. </strong></p> <p paraeid="{3d04e34c-3522-40f3-8630-c6f14cbc41d0}{149}" paraid="1936376053"><strong>Please note that in addition to the <a href="https://www.leeds.ac.uk/research-fees/doc/research-degrees-fees" rel="noreferrer noopener" target="_blank">tuition fee</a> for the programme there will also be a <a href="https://www.leeds.ac.uk/research-fees/doc/postgraduate-research-bench-policy" rel="noreferrer noopener" target="_blank">bench fee</a> of £3,000 per year for this project.   </strong></p> <p paraeid="{3d04e34c-3522-40f3-8630-c6f14cbc41d0}{171}" paraid="1993701339">Funding opportunities for Home students – The <a href="https://phd.leeds.ac.uk/funding/209-leeds-doctoral-scholarships-2026" rel="noreferrer noopener" target="_blank">Leeds Doctoral Scholarship</a> and <a href="https://phd.leeds.ac.uk/funding/234-leeds-opportunity-research-scholarship-2026" rel="noreferrer noopener" target="_blank">Leeds Opportunity Research Scholarship</a> are available to UK applicants.  <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary" rel="noreferrer noopener" target="_blank">Alumni Bursary</a> is available to graduates of the University of Leeds. </p> <p paraeid="{3d04e34c-3522-40f3-8630-c6f14cbc41d0}{194}" paraid="629442306">Funding opportunities for International students –The <a href="https://phd.leeds.ac.uk/funding/48-china-scholarship-council-university-of-leeds-scholarships-2021" rel="noreferrer noopener" target="_blank">China Scholarship Council - University of Leeds Scholarship</a> is available to nationals of China. <a href="https://phd.leeds.ac.uk/funding/60-alumni-bursary" rel="noreferrer noopener" target="_blank">Alumni Bursary</a> is available to graduates of the University of Leeds. </p>

<p>For further information regarding the project, please contact Dr James Smith by email (<a href="mailto:j.smith252@leeds.ac.uk">j.smith252@leeds.ac.uk</a>). You must contact James before making a formal application.</p> <p> </p>