Our group aims to combine theoretical & experimental approaches to understand major problems in the ecology and evolution of microbes. We often compare well-mixed systems such as chemostats with spatially structured systems such as biofilms to work out the effect of spatial structure.
Current research in the group is focussed on the population dynamics of resistance plasmids in spatially structured systems such as biofilms and modelling the fate of antimicrobial resistance in environments such as dairy farms and urban water systems (ie sewage and sewage treatment). We study the fascinating bacterium Bdellovibrio bacteriovorus, a predator of other Gram-negative bacteria, as an alternative to the use of antibiotics. A related interest are the microbial communities living in human and animal guts (upstream of sewage). In order to study these systems, we are keen to develop microfluidics systems to study single cells and use mathematical models to predict community dynamics from these single cell level observations.
As a basis for such studies, we have been developing individual-based modelling software such as iDynoMiCS (individual-based Dynamics of Microbial Communities Simulator) and eGUT (electronic gut):
Past interests have been the evolution of metabolic division of labour, cell-cell communication and aging (damage segregation) versus damage repair in single celled organisms.
I am seeking a motivated PhD student who shares our vision that the future of biology lies in close integration of mathematical and experimental approaches since this will allow us to understand how the behaviour of complex systems emerges from the multitude of interactions of its parts.
If you are fascinated by the diversity and complexity of life, would like to work on important problems and could contribute either mathematical or experimental expertise (or of course preferably both) to strengthen a growing team of mostly friendly people based at the Centre for Computational Biology and the Institute of Microbiology and Infection at the University of Birmingham – please do apply. Your project can involve any of the above mentioned or related areas and can be tailored to your interests and experience.
Please see http://www.biosciences-labs.bham.ac.uk/kreftlab/jobs.html
for current studentship and postdoc projects.
Please see http://www.biosciences-labs.bham.ac.uk/kreftlab/index.html
for further information on our group and research interests (somewhat out of date).
Please see my Google Scholar page for an up to date publication list: https://scholar.google.co.uk/citations?user=hLRsYpsAAAAJ&hl=en&oi=ao
When contacting me (j.kreft at bham.ac.uk), please explain your motivation and research interest and whether you have mathematical and/or experimental expertise.
The School of Biosciences offers a number of highly competitive UK Research Council (e.g. BBSRC, NERC, MRC) PhD studentships each year. Fully funded research council studentships are normally only available to UK nationals (or EU nationals resident in the UK) but part-funded studentships may be available to EU applicants resident outside of the UK. The deadline for applications for many research council studentships is 31 January each year but some deadlines may be earlier.
Each year we also have a few fully funded Darwin Trust Scholarships. These are provided by the Darwin Trust of Edinburgh and are for non-UK students wishing to undertake a PhD in the general area of Molecular Microbiology. The deadline for this highly competitive scheme is also 31 January each year.
For further funding details, please see the ‘Funding’ section.
Kreft JU, Booth G, Wimpenny JWT (1998).
BacSim, a simulator for individual-based modelling of bacterial colony growth.
Microbiology 144: 3275-3287
Kreft JU, Picioreanu C, Wimpenny JWT, van Loosdrecht MCM (2001).
Individual-based modelling of biofilms.
Microbiology 147: 2897-2912
Kreft JU (2004).
Biofilms promote altruism.
Microbiology 150: 2751-2760
Costa E, Perez J, Kreft JU (2006).
Why is metabolic labour divided in nitrification?
Trends in Microbiology 14: 213-219
Hense BA, Kuttler C, Müller J, Rothballer M, Hartmann A, Kreft JU (2007).
Does efficiency sensing unify quorum and diffusion sensing?
Nature Reviews Microbiology 5: 230-239
Clegg RJ, Dyson RJ, Kreft JU (2014).
Repair rather than segregation of damage is the optimal unicellular aging strategy.
BMC Biology 12: 52
Hellweger FL, Clegg RJ, Clark J, Plugge CM, Kreft JU (2016).
Advancing microbial sciences by individual-based modelling.
Nature Reviews Microbiology 14: 461-471
Clegg RJ, Kreft JU (2017).
Reducing discrepancies between 3D and 2D simulations due to cell packing density.
Journal of Theoretical Biology 423: 26–30