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Developing delivery strategies for next generation probiotics and microbiome therapeutics

   School of Medicine, Medical Sciences & Nutrition

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  Dr Karen Scott, Dr A Walker, Dr S Duncan  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

The Rowett Institute has an international reputation for teaching and research in human nutrition and food science. As part of its funding through the Scottish government we are advertising a number of high-profile PhD studentships in nutrition, food science, microbiology and analytical chemistry.

The mammalian gut microbiota makes many important contributions to host health, including digesting dietary fibres and releasing health-associated metabolites, and providing protection against invading pathogens [1]. In many diseases, the microbiota is perturbed, which can exacerbate the condition. Thus, there is increasing interest in manipulating the gut microbiota of humans and animals in order to prevent or treat a range of diseases. However, delivery of microbiome-targeted therapeutics is complicated by the fact that many of the dominant and beneficial gut bacteria are strictly anaerobic, and therefore difficult to cultivate and package into easily consumed products. In this project we will study alternative mechanisms to deliver novel microbiome-based therapeutics, and assess which may be the most feasible for translation going forward.

In our previous research we have identified a number of anaerobic gut bacteria that actively inhibit the growth of several important enteric pathogens, including Clostridioides difficile, Salmonella enterica and Escherichia coli [2, 3]. These anaerobic gut bacteria therefore have potential for development as next generation probiotics for use in animal and human populations to prevent enteric disease.

A key requirement in progressing and fully translating this research is to develop novel ways of delivering the product to the recipient host. This project will address knowledge gaps by assessing three distinct delivery strategies for these strictly anaerobic next-generation probiotic candidates with inhibitory activity against pathogens.

First, the student will investigate the potential of freeze-drying, microencapsulation and the application of spores as methods to optimise delivery of the putatively beneficial gut anaerobes. Second, the student will assess the range of dietary substrates that specifically enhance the growth of individual candidate next-generation probiotics. This information will be used to select tailored substrates, including known prebiotics and other dietary fibres, that could support the establishment of the promising bacterial strains in the host gut. Finally, the student will explore the potential for isolating secreted compounds with direct antimicrobial activity against key enteric pathogens by identifying, cloning and expressing the genes that encode these antimicrobial compounds in more readily amenable bacterial host species [4].

This project is therefore an excellent opportunity for the student to progress innovative research, building on the Rowett Institute’s longstanding expertise in microbiome research, our exciting preliminary data, and utilising our specialist facilities. It is cutting edge, highly multi-disciplinary and translational, and will provide training in anaerobic microbiology, molecular biology, and bioinformatic analyses. The supervisory team has experience of all of the approaches outlined above, giving the student a fully supportive learning environment.

Essential background of student:

BSc Hons (1st class or upper second class degree) in Microbiology or equivalent.

Informal enquiries would be welcomed for a discussion, Please contact the lead supervisor, Dr Karen Scott ([Email Address Removed]) for more information.


This project will be based within the Rowett Institute, part of the School of Medicine, Medical Sciences and Nutrition, at the University of Aberdeen. The Rowett Institute is located on the Foresterhill Health Campus, one of the largest clinical complexes in Europe, which also includes the Institute of Applied Health Sciences, a large teaching hospital and the the Institute of Medical Sciences (IMS)



International applicants are eligible to apply for this studentship but will have to find additional funding to cover the difference between overseas and home fees (approximately £17,000 per annum)

  • Formal applications can be completed online:
  • You should apply for the Degree of Doctor of Philosophy in Medical Sciences to ensure your application is passed to the correct team
  • Please clearly note the name of the supervisor and exact project title on the application form. If you do not mention the project title and the supervisor on your application it will not be considered for the studentship.
  • Candidates should have (or expect to achieve) a minimum of a 2:1 Honours degree (or international equivalent).
  • General application enquiries can be made to [Email Address Removed]

Funding Notes

Project funded through the Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government.
Funding covers tuition fees at the UK/Home rate, bench fees, and a stipend at the UKRI rate.
This is a four-year project and the expected start date is October 2022.
Full funding is available to UK candidates only. International candidates can apply for this studentship but will have to find additional funding to cover the difference between overseas and home fees (approximately £17,000 per annum).


1. Flint HJ, Duncan SH, Scott KP, Louis, P (2014). Links between diet, gut microbiota composition and gut metabolism. Proceedings of the Nutrition Society 760.
2. Hatziionou D, Mayer MJ, Duncan SH, Flint HJ, Narbad A (2013). A representative of the dominant human colonic Firmicutes, Roseburia faecis M72/1, forms a novel bacteriocin-like substance. Anaerobe 23, 5-8.
3. Hatziioanou D, Gherghisan-Filip C, Saalbach G, Horn N, Wegmann U, Duncan SH, Flint HJ, Mayer MJ, Narbad A. (2017). Discovery of a novel lantibiotic from Blautia obeum A2-162 isolated from the human GI tract with a unique cluster composition and nisin-like structural peptides. Microbiology 163, 1292-1305.
4. Scott KP, Mercer DK, Richardson AJ, Melville CM, Glover LA, Flint HJ (2000). Chromosomal integration of the green fluorescent protein in lactic acid bacteria and the survival of introduced strains in human gut simulations. FEMS Microbiology Letters 182, 23-27.
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