PhD Studentship: Identifying the Antibiotics and Antibiotic Resistance Genes that Shape a Microbiome

; University of East Anglia, United Kingdom

Updated: 12 months ago
Location: Norwich, ENGLAND
Job Type: FullTime
Deadline: 19 May 2023

Scientific background 

Microbiomes offer great benefits to their hosts, including nutrient acquisition, growth promotion, immunity, and defence against disease but they are complex and difficult to study. As a result, insects have emerged as simple, experimentally tractable models with which to study microbiomes. 

Our model is the leafcutter ant Acromyrmex echinatior, which has a simple cuticular microbiome dominated by antibiotic-producing bacteria that protect the ants against disease. The question in this project is how do the ants recruit antibiotic-producing (useful) bacteria while keeping out all other (cheater) bacteria? 

Hypothesis

We know the ants pass a single strain of antibiotic-producing Pseudonocardia bacteria from generation to generation. Preliminary data suggest these are bacteriocin-type antibiotics. We have shown in vitro that this vertically transmitted strain could result in selective acquisition of antibiotic-producing Streptomyces bacteria, resulting in a defensive microbiome producing multiple types of antibiotics that is robust to the evolution of resistance by pathogens. Antibiotic-producing bacteria are necessarily themselves antibiotic resistant, and are pre-adapted to the Pseudonocardia-toxin-infused ant cuticle, allowing them to consume nutrients provided by the ants to their cuticular microbiome. 

Research methodology 

The student will test the prediction that only antibiotic-producing bacteria that are resistant to Pseudonocardia antibiotics can colonise the ant cuticle, and this is why the ants are able to selectively recruit a microbiome dominated by Pseudonocardia and Streptomyces bacteria. This will involve:

  • Identifying the antibiotics made by the Pseudonocardia bacteria.
  • Testing them for activity against a range of different bacteria.
  • Determining their mode(s) of action.
  • Identifying the antibiotic resistance genes (ARGs) that make Streptomyces bacteria resistant.

    • Training 

    The student will be based at JIC where Hutchings and Wilkinson share laboratory space equipped for molecular microbiology and natural products chemistry. They will receive full training in microbiology, bioinformatics, antibiotic bioassays, purification of natural products and mass spectrometry. 

    Training will be provided by the supervisors and their groups, including core funded RAs. Support will also be provided by senior support scientists running bioinformatics, chemistry, metabolomics, and proteomics science platforms at JIC.

    Person specification  

    The student should have a first degree and/or Masters in biology or chemistry.

    Primary supervisor: Prof Matt Hutchings

    Start date: October 2023

    For more information on this project, please visit www.uea.ac.uk

    Funding

    This project has been shortlisted for funding by the ARIES NERC DTP. Successful candidates will be awarded a NERC studentship, which covers fees, stipend (£17,668 for 2022/23) and funding to support the doctoral research. Excellent applicants from quantitative disciplines may be considered for an additional three months’ studentship funding.

    Please note that all international awards have been made for our programme for 2023 so we will not be accepting applications from international candidates, as defined by UKRI’s guidance on International Eligibility criteria for UKRI funded studentships.

    Unfortunately, no additional funding is available to assist with relocation or visa costs.

    ARIES encourages applications from all, regardless of gender, ethnicity, disability, age, or sexual orientation. Academic qualifications are considered alongside relevant non-academic experience.

    For further information, please visit www.aries-dtp.ac.uk