Jan-Ulrich Kreft

Colleges, School and Institutes

Research interests

My research interests revolve around the interactions between microbes and microbes and macrobes. I aim to study these interactions on the single organism level, using individual-based modelling and single-cell experiments using microfluidics. For comparison, I also employ other mathematical models such as ordinary differential equation or partial differential equation models and experiments on the population level.

One very important factor in determining interactions is spatial structure of the environment and the population; to learn about the effect of the structure on interactions, I compare the spatially mixed chemostat with the spatially structured biofilm.

Interactions cover plasmid transfer, transmission and selection of antimicrobial resistance, predator prey dynamics, competition, cooperation, communication and metabolic division of labour.

In order to investigate these interactions, we have been developing open source software for individual-based modelling that we make available for other groups, such as iDynoMiCS. We are currently working on developing a software platform to simulate animal and human guts, called eGUT for electronic gut.


I studied Biology in Germany from 1985 to 1991, first at the University of Konstanz and then at the University of Tübingen, finishing with a “Diplom” which is roughly equivalent to a combined BSc and MSc as it included a decent amount of chemistry, physics and mathematics as well as biology in the first two years known as the “Grundstudium” and specialisation in four areas of biology during the two years of the “Hauptstudium” in Tübingen, finishing with a one year laboratory project (total of 5 years nominal study time that due to unavoidable waiting times took 6 years).

After that, I did my PhD (Dr. rer. nat.) at the University of Konstanz with Professor Bernhard Schink from 1991 to 1995 working on the biochemistry and physiology of an anaerobic bacterium that degrades methylated phenolic compounds produced by plants.

For my postdoc at Cardiff University with Professor Julian Wimpenny, I decided to switch completely and use mathematical modelling to better understand the big questions in biology. I was able to obtain a DFG fellowship to spend 1.5 years in Cardiff, during which time I wrote the first paper using individual-based modelling to understand bacterial interactions. On the basis of that publication we obtained further funding from the BBSRC so I stayed in Cardiff another 3 years.

From Cardiff I moved to the University of Bonn in Germany to become a “Wissenschaftlicher Assistent" with Professor Wolfgang Alt, which is the traditional German career path to become a full professor, now mostly replaced by the “Junior Professor”. At Bonn, I broadened my research and improved my skills base.

In 2007, I joined the University of Birmingham as a Lecturer in Computational Biology.

Education/Academic qualification

  • Doctor rerum naturalium, University of Konstanz

    The methyl ether cleaving enzyme system of the anaerobic bacterium Holophaga foetida

    1 Sep 1991 - 9 Jun 1995
  • Master of Biology, Eberhard-Karls-Universität Tübingen

    Diplom Biologie

    1 Oct 1987 - 16 Aug 1991

Professional Qualifications

  • Medici Enterprise Training,

    2013 -
  • Associate Fellow of the Higher Education Academy, AFHEA

    1 Sep 2011 -

Willingness to take PhD students


PhD projects

Dr Kreft's current research includes:

Interactions between microorganisms and microorganisms and hosts, such as:
Dynamics of the spread of resistance plasmids in chemostats and biofilms
Dynamics of AMR in wastewaters and farm manure/slurry
Bacterial predator prey dynamics (Bdellovibrio)
Evolution of cooperation in biofilms
Cell-cell communication
Twitching motility and biofilm structure
One-step nitrification

Developing mathematical models such as individual-based models:
Models for chemostats, biofilms, the animal and human gut