EastBio: From microbial cargo to host immunity: decoding bacterial extracellular vesicle-mediated signalling in the human gut

 Dr Indrani Mukhopadhya,  Dr Wael Houssen,  Dr T Vogwill

Application Deadline: 16 November 2026

Details

This fully funded, 4-year PhD project is part of a competition funded by the BBSRC EASTBIO Doctoral Training Partnership.

The human gut microbiota plays a fundamental role in shaping immune homeostasis, yet how strictly anaerobic commensal bacteria communicate molecular information to host cells remains poorly understood. Bacterial extracellular vesicles (BEVs) are nanoscale particles that transport proteins, lipids, metabolites and nucleic acids beyond the microbial cell, providing a potentially important mechanism of microbiota-host communication. Emerging evidence indicates that BEVs can modulate host immunity, but why vesicles from different gut commensals elicit distinct immune responses, how these properties vary within and between bacterial species, and which components of their molecular cargo determine these effects remain important unanswered questions. This PhD will investigate how variation within and between selected gut commensal species translates into compositionally and functionally distinct BEVs that programme divergent host immune responses.

Using a unique collection of cultured human gut anaerobes, the student will isolate and characterise BEVs from selected phylogenetically and functionally contrasting bacteria, including multiple strains where appropriate. Comparative genomic analyses will determine the scale of microbial variation underlying differences in BEV properties, from strain-level variation within species to differences between species. The immunomodulatory effects of selected BEVs will then be characterised using intestinal epithelial and innate immune-cell models, combining multiparameter flow cytometry with cytokine, signalling and functional assays to identify contrasting homeostatic and inflammatory responses.

Molecular profiling and bioactivity-guided approaches will identify proteins, peptides, lipids and metabolites associated with contrasting BEV phenotypes. Genomic, vesicular and quantitative host-response data will subsequently be integrated to identify candidate microbial and molecular determinants of immunomodulatory activity. Selected bioactive cargo and host-signalling pathways will be experimentally interrogated to establish causal mechanisms. Integrating these findings will connect microbial variation, vesicular cargo and experimentally defined immune function, moving beyond descriptive profiling towards mechanistic understanding.

The project brings together Dr Indrani Mukhopadhya’s expertise in gut microbiology and host-microbe interactions, Dr Wael Houssen’s expertise in chemical biology, and Dr Thomas Vogwill’s expertise in microbial evolution and comparative genomics. The project will be best suited to an individual with a background in microbiology, immunology, or similar biomedical degree. Working across the Institute of Medical Sciences and the School of Biological Sciences at the University of Aberdeen, the student will receive interdisciplinary training in anaerobic microbiology, extracellular-vesicle biology, chemical biology, cellular immunology, advanced flow cytometry, comparative genomics and bioinformatics. By integrating experimental and computational approaches, this training will equip the student to connect microbial diversity and vesicular composition with host immune function.

It may be possible to undertake this project part-time.

Interested applicants should contact the lead supervisor to discuss the project prior to applying. You can do this by selecting the first listed name at the top of this advert and sending your enquiry. Alternatively, you can search for the supervisor through the University of Aberdeen staff directory and email them directly.

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ELIGIBILITY:

Applicants should hold a minimum of a 2:1 UK Honours degree (or international equivalent) in a relevant subject. Those with a 2:2 UK Honours degree (or international equivalent) may be considered, provided they have (or are expected to achieve) a Distinction or Commendation at master’s level.

We encourage applications from all backgrounds and communities, and are committed to having a diverse, inclusive team.

All students must meet the eligibility criteria as outlined in the UKRI guidance on funding for postgraduate training and development. This guidance should be read in conjunction with the Terms and conditions for training funding – UKRI.

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APPLICATION PROCEDURE

For full details and to download the application form, visit: https://biology.ed.ac.uk/eastbio/how-to-apply

Please note that you may only apply for one EASTBIO project.

1. Application submission

Submit your complete application by 23:59 GMT on 16th November 2026 to smmsn-pgrenquiries@abdn.ac.uk.

Send your application as a single email with the subject line: “EASTBIO Application – [Your Name]”

2. Required documents

Your application email must include the following:

• Completed EASTBIO application form
• Academic certificates and transcripts
• Two references (one reference may be non-academic)

3. References

All references must be provided using the official EASTBIO reference form (available here).

References can be either:

• Included with your application, or
• Sent directly by referees to smmsn-pgrenquiries@abdn.ac.uk with the subject line: “EASTBIO Reference – [Your Name]”

All references must be received by 23:59 GMT on 16th November 2026.

It is the applicant’s responsibility to ensure both references are submitted by the deadline, as we cannot request them on your behalf.

Important notes

• No research proposal is required.
• Do not include any additional documents (for example, school certificates, conference papers, or dissertations).
• Incomplete applications or those including unnecessary materials will not be considered.
• Due to workload constraints, we are unable to follow up on missing documents or process incomplete applications.
• All candidates will be notified of the outcome of their application.
• We will confirm receipt of your applications upon processing. Due to the high volume of applications, this may not be until after the deadline. We ask that you please refrain from contacting us regarding updates or to see if your application has been received.

For any questions or assistance with the application process, please contact smmsn-pgrenquiries@abdn.ac.uk.

Funding Notes

This fully funded, four-year PhD project is offered as part of a competition within the EASTBIO BBSRC Doctoral Training Partnership. The opportunity is open to both UK and international applicants, although the proportion of international students recruited through the EASTBIO DTP is capped at 30% by UKRI BBSRC.

EASTBIO studentships provide a tax-free UKRI doctoral stipend (estimated at £22,437 for the 2027/28 academic year), a training grant of £5,000 per year for the first three years (and £1,500 in the fourth year), and a travel and conference allowance of £230 per year.

Please note that EASTBIO is unable to fund visa costs or associated healthcare surcharges for international students.