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Help from the past: exploring the genomic architecture of a historical collection of Vibriobacteria in the hunt for novel antimicrobials, [Microbiology/Bioinformatics)] – PhD (Funded)


   College of Life and Environmental Sciences

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  Dr S Michell  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

Location:

Biosciences, Streatham Campus, Exeter

The Centre for Environment, Fisheries & Aquaculture Science (Cefas) and the University of Exeter have a Strategic Alliance that aims to combine the complementary capabilities and perspectives of both organisations.

This Alliance was further strengthened in 2018 via establishment of the Centre for Sustainable Aquaculture Futures (see: https://www.exeter.ac.uk/research/saf/).

A major component of the Alliance is to support joint PhD studentships. In accordance, we are pleased to announce the intention to fund one new PhD projects to start 26th September 2022 or 9th January 2023. This project is one of two projects that are in competition for funding from the University of Exeter and Cefas.

For eligible students the studentship will cover Home or international tuition fees plus an annual tax-free stipend of at least £16,062 for 3.5 years full-time, or pro rata for part-time study. The student would be based in Biosciences at the Streatham Campus in Exeter.

Project Description:

Antimicrobial resistance (AMR) is one of the biggest global challenges of our time. AMR is a complex problem that requires a united multisectoral approach1. Fortunately, over the last decade research has identified a new and novel class of antimicrobials produced by environmental bacteria4. These are effector molecules produced by bacterial secretion systems which kill neighbouring non-kin microbes. The Gram-negative bacterium Vibrio parahaemolyticus (Vp), present in marine and estuarine habitats, is an important human and animal pathogen that directly impacts the safety and trade of shellfish species as well as the global aquaculture sector. Recent genome sequencing has identified a vast array of antimicrobial effector genes linked to T6SSS within the genome of this species.

This PhD will study a unique strain collection of global Vp isolates. Specifically, the student will de novo whole-genome sequence strains from this collection, assemble the microbial genomes against known reference genomes and identify all antimicrobial effectors in silico.

This is a truly collaborative and interdisciplinary project and the student will work between Cefas and the UoE where they will characterise, in the laboratory, the effectiveness of the newly identified antimicrobials from the genome sequencing effort described above. This will be achieved by creating mutant strains that will have had the genes for the effectors removed, with subsequent study of the effector mutant strains in competition assays. The collaborative group at Exeter have state of the art fluorescence reporter strains of numerous clinical bacterial pathogens that can be utilised to investigate the effectiveness of the novel antimicrobials.

These strains are currently being utilised for such studies both in vitro and in vivo in the wax moth larvae model. The outputs from this project will provide a data-driven and translational approach to tackling the pressing global issue of AMR in addition to contributing to the Exeter/Cefas alliance’s goal of sustainable, healthy seafood.

1 Advancing the One Health response to Antimicrobial Resistance (AMR) (unep.org),

This award provides annual funding to cover Home or International tuition fees and a tax-free stipend of at least £16,062 per year tax-free stipend. .

International applicants need to be aware that you will have to cover the cost of your student visa, healthcare surcharge and other costs of moving to the UK to do a PhD.

Entry requirements

Applicants for this studentship must have obtained, or be about to obtain, a First or Upper Second Class UK Honours degree, or the equivalent qualifications gained outside the UK, in an appropriate area of science or technology. 

If English is not your first language you will need to have achieved at least 6.5 in IELTS and no less than 6.0 in any section by the start of the project. Alternative tests may be acceptable (see http://www.exeter.ac.uk/postgraduate/apply/english/).

How to apply

In the application process you will be asked to upload several documents. 

• CV

• Letter of application (outlining your academic interests, prior research experience and reasons for wishing to undertake the project).

• Transcript(s) giving full details of subjects studied and grades/marks obtained (this should be an interim transcript if you are still studying)

• Two references from referees familiar with your academic work. If your referees prefer, they can email the reference direct to [Email Address Removed] quoting the studentship reference number.

• Names of two referees familiar with your academic work. You are not required to obtain references yourself. We will request references directly from your referees if you are shortlisted.

• If you are not a national of a majority English-speaking country you will need to submit evidence of your proficiency in English.

The closing date for applications is midnight on 7th September 2022

If you have any general enquiries about the application process please email [Email Address Removed] or phone 0300 555 60 60 (UK callers) +44 (0) 1392 723044 (EU/International callers) 

Project-specific queries should be directed to the main supervisor.

For further information and to submit and application please visit - https://www.exeter.ac.uk/study/funding/award/?id=4377


Funding Notes

A major component of the Alliance is to support joint PhD studentships. In accordance, we are pleased to announce the intention to fund one new PhD projects to start 26th September 2022 or 9th January 2023. This project is one of two projects that are in competition for funding from the University of Exeter and Cefas.
For eligible students the studentship will cover Home or international tuition fees plus an annual tax-free stipend of at least £16,062 for 3.5 years full-time, or pro rata for part-time study. The student would be based in Biosciences at the Streatham Campus in Exeter.
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