Identifying the antibiotics and antibiotic resistance genes that shape a microbiome


Identifying the antibiotics and antibiotic resistance genes that shape a microbiome


Project Description


Prof Matt Hutchings (John Innes Centre) – Contact me

Prof Barrie Wilkinson, JIC

Prof Doug Yu, UEA


Project 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:

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


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 or masters in biology or chemistry.


  • Worsley SF, Innocent TM, Holmes NA, Wilkinson B, Murrell JC, Boomsma JJ, Yu DW and Hutchings MI (2021). Competition-based screening secures the evolutionary stability of a defensive microbiome. BMC Biology 19:205.
  • Heine D, Holmes NA, Worsley SF, Alve dos Santos AC, Innocent TM, Scherlach K, Patrick E, Yu DW, Murrell JC, Boomsma JJ, Hertweck C, Hutchings MI* and Wilkinson B* (2018). Chemical warfare between leafcutter ant symbionts and a co-evolved pathogen. Nature Comms. 9:2208.
  • Holmes N, Innocent T, Heine D, Worsley S, Findlay K, Murrell J.C., Wilkinson B*, Boomsma JJ* and Hutchings MI* (2016). Genome analysis of two Pseudonocardia phylotypes associated with Acromyrmex leafcutter ants reveals their biosynthetic potential. Front Microbiol. 7:2073
  • Batey SFD, Greco C, Hutchings MI and Wilkinson B (2020). Chemical warfare between fungus growing ants and their pathogens. Curr Op Chem Biol 59:172-181
  • Barke, J., Seipke, R.F., Gruschow, S., Heavens, D., Drou, N., Bibb, M.J., Goss, R.J.M., Yu, D.W. and Hutchings, M. I. (2010). A mixed community of actinomycetes produce multiple antibiotics for the fungus farming ant Acromyrmex octospinosus. BMC Biology 8:109

Key Information

  • This project has been shortlisted for funding by the ARIES NERC DTP and will start on 1st October 2023. The closing date for applications is 23:59 on 19th May 2023.
  • Successful candidates who meet UKRI’s eligibility criteria will be awarded a NERC studentship, which covers fees, stipend (£18,622 p.a. for 2023/24) and research 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,
  • ARIES students benefit from bespoke graduate training and ARIES provides £2,500 to every student for access to external training, travel and conferences, on top of all Research Costs associated with the project. Excellent applicants from quantitative disciplines with limited experience in environmental sciences may be considered for an additional 3-month stipend to take advanced-level courses.
  • ARIES is committed to equality, diversity, widening participation and inclusion in all areas of its operation. We encourage enquiries and applications from all sections of the community regardless of gender, ethnicity, disability, age, sexual orientation and transgender status. Academic qualifications are considered alongside non-academic experience, and our recruitment process considers potential with the same weighting as past experience.
  • All ARIES studentships may be undertaken on a part-time or full-time basis, visa requirements notwithstanding
  • For further information, please contact the supervisor. To apply for this Studentship follow the instructions at the bottom of the page or click the 'apply now' link.
  • ARIES is required by our funders to collect Equality and Diversity Information from all of our applicants. The information you provide will be used solely for monitoring and statistical purposes; it will remain confidential, and will be stored on the UEA sharepoint server. Data will not be shared with those involved in making decisions on the award of Studentships, and will have no influence on the success of your application. It will only be shared outside of this group in an anonymised and aggregated form. You will be ask to complete the form by the University to which you apply.

Applications are open

Apply now