Exploiting bacterial species interactions for antibiotic discovery.

Location: European Centre for Environment and Human Health, University of Exeter Medical School, Knowledge Spa, Royal Cornwall Hospital, Truro, Cornwall, TR1 3HD

Academic Supervisors:
Dr. Michiel Vos (University of Exeter Medical School)
Dr. Paolina Garbeva (Netherland Institute of Ecology, Wageningen, The Netherlands)

Project Description:
The increasing prevalence of antibiotic resistance in pathogenic bacteria is a global problem and there is an urgent need for the discovery of novel compounds to treat infections. Current drug discovery paradigms based on high-throughput synthetic library screening and genomics approaches have largely failed to deliver, having prompted a renaissance in natural product discovery. Most antibiotics have been derived from micro-organisms, and although many species are left to be screened for antibiotic production, returns are diminishing.

It has recently been shown that bacteria can upregulate antibiotic production against target species when in the presence of a third species (Tyc etal 2014, Abruzan etal 2015). Screening for antibiotic production in a community context has the potential to uncover many novel antibiotic compounds that would otherwise remain ‘silent’.

In this project, you will isolate bacterial communities from different environments and use high throughput assays to test for interaction-induced activity against the most problematic, multidrug resistant pathogens (including ESKAPE pathogens resistant to the latest generation of clinical antibiotics). Producers will be characterized using whole-genome sequencing and chemical structures of antimicrobial compounds will be elucidated in collaboration with Dr. Paolina Garbeva at the Netherlands Institute of Ecology in Wageningen, The Netherlands. We will combine systematic sampling and ecological theory to elucidate the relative benefits of constitutive antimicrobial activity versus induced activity to optimize discovery strategies. A specific novel focus will be the interactions between soluble compounds and much less well-known volatile compounds (Tyc etal 2017).

The student will develop expertise at the interface of microbiology, genomics, biochemistry, ecology and evolution. The student will be embedded within a multi-disciplinary research group situated within the Medical School laboratory based in the Environment and Sustainability Institute at the Exeter Cornwall Campus and encouraged to participate in the wide range of professional development opportunities available at the University of Exeter.Project description:

For more information about the project and informal enquiries, please contact the primary supervisor Dr. Michiel Vos http://www.ecehh.org/people/dr-michiel-vos/


Entry requirements:
You should have or expect to achieve at least a 2:1 Honours degree from a UK university, or equivalent.
If English is not your first language you will need to meet the English language requirements and provide proof of proficiency