Developing microbiological ammunition for robust decolonization of antibiotic resistant bacteria. PhD in Biosciences (BBSRC SWBio DTP) Ref: 4279
About the award
Dr Ben Raymond - College of Life and Environmental Sciences, University of Exeter.
Dr Lauren Cowley - Department of Biology & Biochemistry, University of Bath.
Location: Penryn Campus, University of Exeter, Falmouth, Cornwall
The BBSRC-funded South West Biosciences Doctoral Training Partnership (SWBio DTP) is led by the University of Bristol, together with the Universities of Bath, Cardiff and Exeter, alongside Rothamsted Research. This partnership also includes the following associate partners; Marine Biological Association (MBA), Plymouth Marine Laboratory (PML), SETsquared Bristol, Swansea University, UCB Pharma, and University of the West of England (UWE).
These institutions represent a distinctive group of bioscience research staff and students, with established international, national and regional networks, and widely recognised research excellence. As research leaders, we have a strong track record in advancing knowledge through high-quality research and teaching, in partnership with industry and the government.
The aim of this DTP is to produce highly motivated and excellently trained postgraduates in the BBSRC priority areas of Advancing the frontiers of biosciences discovery, Biosciences for sustainable agriculture and food and Biosciences for an integrated understanding of health. These are growth areas of the biosciences and for which there will be considerable future demand.
This project is one of a number that are in competition for funding from the South West Biosciences Doctoral Training Partnership (SWBio DTP).
Taking antibiotics is not risk free. For a year after completing a course, there is an increased risk of complex infection from antimicrobial-resistant microbes, and individuals colonized with resistant microbes can transmit them freely to others for extended periods.
These resistant bacteria are likely to be gut-dwelling commensals. Commensal bacteria make up most of the highly problematic multi-drug resistant microbes, and tackling the persistence of resistant commensals will be a key part of future antimicrobial stewardship and overall reduction in drug-resistant infections 1.
This project will explore how we might efficiently replace resistant Escherichia coli in the gut with harmless commensals by exploiting selective bacteriophage as phage therapy. Using novel experimental models, such as gut organoids, we aim to optimize these ‘decolonization’ strategies and develop approaches that are resilient to the evolution of phage resistance. Escherichia coli is a good target for this decolonization since one lineage (the ST 131 clonal complex) is responsible for a large proportion of multi-drug resistant infections, including life-threatening bacteraemia. The supervisors have already developed an efficient pipeline for isolating lineage specific phage as well as techniques (increasing within-species competition) that can make decolonization more effective.
Using this pipeline and an existing phage collection the student will develop diverse phage cocktails with the aim of displacing bacteria without producing widespread phage resistance in target E. coli genotypes. In addition, the student will isolate and sequence phage resistant E. coli in order to better understand the genetic basis of phage resistance to major phage families and test the efficacy of decolonization in simple in vivo models (insects, organoids). We also predict that broad-spectrum phage resistance might have severe fitness consequences for E. coli, especially in complex communities or under the harsher conditions in the gut, so the fitness consequences of phage resistance will also be explored in simple and diverse communities.
This is a multi-disciplinary project providing training in microbiology, evolutionary biology and bioinformatics with significant impacts on how we manage drug resistant and life-threatening infections. A successful student will gain important laboratory and analytical skills with infection models and microbial bioinformatics.
The team have expertise in bioinformatics, phage resistance and displacement of antibiotic resistant bacteria 2,3,4 and have a wide range of experience that could match the interests of diverse applicants.
(1) Raymond (2019) Evol Appl https://doi.org/10.1111/eva.12808 (2) Watson et al (2021) Cell Host Microbe https://doi.org/10.1016/j.chom.2021.03.018. (3) Mikonranta et al. (2019) Biol Lett https://doi.org/10.1098/rsbl.2018.0895 (4) Cowley et al. (2019) Front Genetics https://doi.org/10.3389/fgene.2019.00763
To be eligible for a fully-funded studentship, you must meet both the academic and residence criteria.
A fully-funded four year SWBio DTP studentship will cover
• a stipend* at the standard Research Council UK rate; currently £15,609 per annum for 2022-23
• research and training costs
• tuition fees (at the standard Research Councils UK rate)
• additional funds to support fieldwork, conferences and a 3-month internship
Please refer to the regulations or Annex 1 of the Research Council Training Grant Guide to confirm that you meet the residence criteria for a fully-funded studentship. Any further queries in relation to residency must be directed to the institution that you are applying to.
* An enhanced stipend is available for students with a recognised veterinary degree qualification (£24,090 per annum for 2022-2023). There may also be enhanced stipends associated with projects that have a CASE partner (CASE projects are highlighted as *CASE in the project lists).
UKRI have recently updated their policy for funded studentships which starts from the 2022/2023 academic year.
IMPORTANT: Please refer to the UKRI Full Eligibility Criteria alongside the information provided below.
Fully-funded studentships are available for Home students. To be classed as a Home student, candidates must meet the following criteria:
• Be a UK National (meeting residency requirements), or
• Have settled status, or
• Have pre-settled status (meeting residency requirement) or,
• Have indefinite leave to remain or enter
If you do not meet the above criteria, you will be classed as an International student.
A limited number (up to 30%) of UKRI fully-funded studentships are available through the SWBio DTP, that applicants who would be classed as an International student are eligible for. Please apply through the application route below for funding.
Applicants should 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. Applicants with a Lower Second Class degree will be considered if they also have Masters degree or have significant relevant non-academic experience.
In addition, due to the strong mathematical component of the taught course in the first year and the quantitative emphasis in our projects, a minimum of a grade B in A-level Maths or an equivalent qualification or experience is required.
- Physics A-level (grade B and above)
- Undertaking units as part of your degree that have a significant mathematical component*
*Significant mathematical component examples include; maths, statistics, bioinformatics.
Applicants must ensure they highlight their Maths background within their application and to upload any supporting evidence.
If English is not your first language you will need to have achieved at least 6.5 in IELTS and no less than 6.5 in any section by the start of the project. Alternative tests may be acceptable, please see http://www.bristol.ac.uk/study/language-requirements/profile-c/.
How to apply
Please be aware you will be asked to upload the following documents:
- Letter of application outlining your academic interests, prior research experience and reasons for wishing to undertake the project. Please indicate your preferred project choice if applying for multiple BBSRC SWBio DTP projects.
- Transcript(s) giving full details of subjects studied and grades/marks obtained. This should be an interim transcript if you are still studying.
- Two academic referees - see information below about references.
- If you are not a national of a majority English-speaking country you will need to submit evidence of your proficiency in English (see entry requirements above)
The closing date for applications is midnight on Monday, 6 December 2021. Interviews will be held at the University of Exeter between Monday 24th January – Friday 4th February 2022. (Exact dates to be confirmed shortly)
You will be asked to submit two references as part of the application process. If you are not able to upload your reference documents with your application please ensure you provide details of your referees. If you provide contact details of referees only, we will not expect receipt of references until after the shortlisting stage. Your referees should not be from the prospective supervisory team.
If you are shortlisted for interview, please ensure that your two academic referees email their references to email@example.com, 7 days prior to the interview dates. Please note that we will not be contacting referees to request references, you must arrange for them to be submitted to us by the deadline.
References should be submitted by your referees to us directly in the form of a letter. Referees must email their references to us from their institutional email accounts. We cannot accept references from personal/private email accounts, unless it is a scanned document on institutional headed paper and signed by the referee.
If you have any general enquiries about the application process please email firstname.lastname@example.org.
Project-specific queries should be directed to the primary supervisor.
Please note, the studentship selection process will take place in two stages:
1. The project supervisors will consider your application and may invite you to visit for an informal interview. You can apply for more than one BBSRC SWBio DTP project, although supervisors may take into account your interest and commitment to their particular project. If you apply for multiple projects, please indicate your preferred project choice in your letter of application. Each application for an individual project will be considered separately by the project supervisors.
2. After closure of applications, each supervisory team will then nominate their preferred applicant. A shortlist will be selected from these nominations and shortlisted applicants will be invited for interview on a selection day at the University of Exeter. Please note that nomination by a project supervisor therefore does not guarantee the award of a studentship.
During the application process, the University may need to make certain disclosures of your personal data to third parties to be able to administer your application, carry out interviews and select candidates. These are not limited to, but may include disclosures to:
the selection panel and/or management board or equivalent of the relevant programme, which is likely to include
staff from one or more other HEIs;
- administrative staff at one or more other HEIs participating in the relevant programme.
Such disclosures will always be kept to the minimum amount of personal data required for the specific purpose. Your sensitive personal data (relating to disability and race/ethnicity) will not be disclosed without your explicit consent.
|Application deadline:||6th December 2021|
|Value:||Tuition fees and an annual stipend allowance at Research Council rates, currently £15,609 per year for 2022-23|
|Duration of award:||per year|
|Contact: PGR Recruitment Officeemail@example.com|