PhD Studentship: Engineering Synthetic Microbial Ecosystems for Deployable Microbiome Modulation

Applications are invited for a fully funded four-year PhD studentship at the University of Birmingham exploring how engineered microbial ecosystems can be developed as next-generation microbiome modulation technologies.

The gut microbiome plays an important role in immunity, metabolism, and resilience to environmental stress. Disruption of this ecosystem can arise from infection, antibiotic exposure, and environmental pressures, reducing physiological resilience and performance. Current microbiome therapies, such as faecal microbiota transplantation (FMT), highlight the potential of microbiome modulation but remain limited by challenges in standardisation, deployment, scalability, and storage.

This project will develop novel bioengineered microbial ecosystems that capture the beneficial properties of complex gut microbiota while overcoming the limitations of donor-derived materials. These systems will be designed to be stable, reproducible, and deployable, creating new opportunities for microbiome-based biotechnology.

The studentship is delivered in collaboration with the UK Defence Science and Technology Laboratory (Dstl) and will include a research placement at Dstl, providing unique experience in applying microbiome science within a Defence context.

Research Project:

This interdisciplinary PhD will combine microbiology, biomaterials engineering, and bioreactor systems to develop a scalable platform for microbiome modulation.

The research will focus on two key areas:

1. Engineering synthetic microbial ecosystems
Advanced intestinal bioreactor systems will be developed to cultivate high-complexity microbial communities derived from healthy donor microbiota. The aim is to establish Engineered Synthetic Microbial Ecosystems (ESMEs) that maintain the diversity and function of natural microbiota while enabling reproducible and scalable production.

2. Developing deployable microbiome formulations
The project will explore formulation technologies to stabilise these microbial ecosystems. This will include optimisation of lyophilisation methods and biomaterial-based encapsulation strategies to improve microbial survival and long-term storage stability.

Training Environment

The student will join a vibrant interdisciplinary research environment and will receive training across multiple disciplines including:

• Microbiology and microbiome science
• Bioreactor engineering and microbial culture systems
• Biomaterials and formulation science
• Translational microbiome research

A research placement at Dstl will provide additional training and insight into how microbiome technologies can support national security and defence challenges.

Candidate Requirements

Applicants should have, or expect to obtain, a first or upper second-class degree (or equivalent) in a relevant discipline such as Microbiology, Biomedical Science, Biotechnology, Chemical Engineering, Biological Engineering, Biochemistry, or Materials Science.

A Master’s degree with a research component and prior experience working in a laboratory environment would be advantageous. Experience in microbiology, molecular biology, bioengineering, or biomaterials would also be beneficial but is not essential.

This interdisciplinary project sits at the interface of biology and engineering, and we welcome applicants from diverse subject backgrounds. Candidates with expertise in areas such as microbiology, molecular biology, or chemical/biochemical engineering (e.g. reactor or process engineering) are encouraged to apply. Training will be provided to develop skills across both areas.

The ideal candidate will have a strong interest in interdisciplinary research combining microbiology, biomaterials, and bioengineering, with curiosity about how microbial ecosystems can be engineered and stabilised for real-world applications.

Funding notes:

This studentship is funded through an EPSRC Industrial Doctoral Landscape Award (IDLA) and includes full UK tuition fees (4 years) and a stipend at the UKRI rate plus Dstl enhancement/top-up.

Due to the nature of the project and its collaboration with a UK government organisation, eligibility is restricted to UK nationals.

Informal enquiries are encouraged and should be directed to:

Dr Richard Horniblow, r.horniblow@bham.ac.uk

https://www.engineered-microbiome.co.uk/

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