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Developing and validating a computational model of the gut microbiota–mucosa interactions to replace and reduce animal experiments

School of Biosciences

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Dr J U Kreft , Dr T Iqbal No more applications being accepted

About the Project

An explosive growth of research on the gut microbiota, often using rodent models, has amply demonstrated the huge importance of the previously neglected microorganisms for our health. However, the complexity of the system poses a formidable challenge. Our central hypothesis is that mathematical modelling is required to understand and predict such a complex system. Our long-term goal is to replace & reduce animal experiments and improve our understanding by developing and utilizing a general mathematical modelling platform. The specific aim of the studentship is to develop a mathematical model of the gut mucosa as part of our eGUT (electronic gut) software and to validate the model with an in vitro microfluidic and an insect model as well as training the student in a range of alternatives to rodent models. This is timely as research in this area using animal experiments is growing exponentially. By improving the science, we can best realize the potential of eGUT to ultimately replace & reduce ~75,000 animals per year globally.

The project is supervised by Dr Jan-Ulrich Kreft, a computational biologist in the Centre for Computational Biology (CCB), and co-supervised by Prof Tariq Iqbal, a gastroenterologist at the University Hospital Birmingham.

We are looking for enthusiastic candidates who have a strong background in mathematical modelling and computer programming. Ideally, candidates should also have experience with laboratory experiments and knowledge of microbiology and human physiology.
The experiments to validate the model will be conducted at the University of Luxembourg in Prof Wilmes group (in vitro microfluidic model) and at the University of Valencia in Prof Moyes group (insect model). The candidate should therefore be happy to live in Luxembourg and Spain for about 6 months each.

For more information, visit the project description on the NC3Rs website and the description on the Kreft lab pages, where you can also find the grant proposal case for support, which has all the details.

This studentship is funded by the NC3Rs for 3 years. There is no first Masters like year as with other RCUK funded studentships, so you will be starting your PhD project straight away.

Like other Biosciences PhD students, you will need to undertake a limited amount of training throughout your PhD. In addition, you will take part in the NC3Rs summer school and other training events.

You will need to complete the standard University of Birmingham online application form (Biosciences PhD). In the funding section of the form, state that you wish to be considered for the NC3Rs studentship.


Funding Notes

The studentship will pay the full tuition fees for UK/EU students and a stipend in line with other RCUK studentships (currently at £14,553) and a generous Research Training Support Grant of £30k.

Unfortunately, RCUK eligibility criteria mean that EU students, unless they have been resident in the UK for more than 3 years, can only receive the tuition fees.

Start date: 1 Oct 2018 or earlier!

Please email j.kreft at if you have any questions.


Clegg RJ, Kreft JU (2017). Reducing discrepancies between 3D and 2D simulations due to cell packing density. Journal of Theoretical Biology 423: 26–30

Hellweger FL, Clegg RJ, Clark JR, Plugge CM, Kreft J-U. 2016. Advancing microbial sciences by individual-based modelling. Nature Reviews Microbiology 14: 461–471

Widder S, Allen RJ, Pfeiffer T, Curtis TP, Wiuf C, Sloan WT, Cordero OX, Brown SP, Momeni B, Shou W, Kettle H, Flint HJ, Haas AF, Laroche B, Kreft JU, Rainey PB, Freilich S, Schuster S, Milferstedt K, van der Meer JR, Großkopf T, Huisman J, Free A, Picioreanu C, Quince C, Klapper I, Labarthe S, Smets BF, Wang H, Isaac Newton Institute Fellows, Soyer OS (2016). Challenges in microbial ecology: building predictive understanding of community function and dynamics. ISME Journal 10: 2557–2568

Lardon LA, Merkey BV, Martins S, Dötsch A, Picioreanu C, Kreft JU, Smets BF (2011). iDynoMiCS: next-generation individual-based modelling of biofilms. Environmental Microbiology 13: 2416–2434
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