Job description: Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). These rapid changes are promoted by mobile genetic elements (MGEs), entities that evolved to persist and replicate by moving DNA within and between microbial cells. MGEs are often considered to be on a continuum between parasitism and mutualism, sometimes benefitting their host, and sometimes merely replicating for their own gain.

The precise relationships between MGEs and their hosts are complex, ever-changing, and highly dependent upon ecological context. In our team, we build multi-level models of microbial evolution, for example to understand how MGEs co-evolve with microbial populations and how these interactions affect the health of plants, animals, and ecosystems.

For this PhD position, you will build and analyze computational models on the co-evolution between MGEs and their microbial hosts (supervised by co-promotor Dr. Bram van Dijk). The goal is to understand which types of MGEs are linked to the emergence of plant or animal pathogens, for example by carrying virulence factors as cargo, or by silencing genes that are recognized by the immune system.

For this, the first step will be to adopt existing in-house models of microbial evolution, and build-upon them by (i) including interactions with plant/animal hosts and (ii) incorporate MGEs that potentiate gene transfer of ecologically relevant genes. It will also be interesting to understand why other host-beneficial traits (such as antimicrobial resistance) are less often associated with those same mobile elements, which is likely related to their lifestyle (parasitic vs. mutualistic).

 Depending on your own interests, this position may involve additional approaches and research questions, collaborations with other research groups of Theoretical Biology and Bioinformatics, and collaborations with other researchers at Utrecht Science Park.

This PhD position in the area of multi-level modelling will grant you an appreciation and understanding of complex biological systems and biodiversity. You will get the opportunity to learn about both simple and complex biological models, computer programming, data visualization, and bioinformatic methods to cross-compare insights from your simulations with real-world data.

Additionally, this position will grant you opportunities to pick up on additional skills such as teaching and science communication, and enables you to build a strong scientific network. Finally, our goal is to help you pursue scientific ambitions while also maintaining a healthy work-life balance.

You will join a new research group headed by Dr. Bram van Dijk, which will be established 1 September 2023. The team will specialize on building multi-scale simulations of microbial ecosystems (“virtual laboratories”), and use these to unpack fundamental rules that govern microbial life. The group is embedded in the Theoretical Biology and Bioinformatics group within the department of Biology


We are looking for an enthusiastic colleague with a drive to tease apart the intricacies of the microbial world. To apply to this PhD position you need:

  • a completed, or almost completed, Master’s degree in biology, bioinformatics, or a related discipline;
  • a strong interest in the ecology and evolution of microbial ecosystems;
  • a good command of English, both oral and written.

It is considered a pro if you have:

  • a background in microbial biology, microbial ecology, and genome evolution;
  • experience with computer programming;
  • good communication skills.

Note: women, ethnic minorities, and people from any other minority group are especially encouraged to apply.

Please do not feel demotivated when you feel like you do not meet all the listed criteria. When in doubt, please reach out to us.


  • embedding in a great team of world-class scientists, where English is the main working language;
  • academic training within the Graduate School of Life Sciences;
  • a full time PhD position for 4 years;
  • a full-time gross salary starting at € 2.541 in year one, and increasing to €3.241 in year four (scale P Collective Labour Agreement Dutch Universities, CAO);
  • 8% holiday bonus and 8.3% end-of-year bonus; excellent secondary conditions, including an attractive retirement scheme, (partly paid) parental leave and flexible employment conditions (multiple choice model). For more information, please visit working at Utrecht University or working at the Faculty of Science.

Are you an international applicant? Find out more about what our International Service desk does and for more info about the what and how on living in the Netherlands.

About the organisation

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Sustainability.

At the Faculty of Science, there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences, and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing problems. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects. Find out more about us

The research will be performed at a new research group headed by Dr. Bram van Dijk, which will be established 1 September 2023. The team will specialise on building multi-scale simulations of microbial ecosystems (“virtual laboratories”), and use these to unpack fundamental rules that govern microbial life. Current interests are geared towards understanding why various vehicles of gene transfer (MGEs like phages, plasmids, and transposons) have different impacts on microbial evolution, for example by driving the horizontal transfer of different types of genes. However, many other interesting topics are ongoing, including:

  • the evolution of environmentally transmitted microbiomes;
  • the diversity of closed, open, and “leaky” microbial ecosystems;
  • black queen dynamics and natural selection for low growth rates;
  • the evolution of “chromids”; plasmids that became chromosomes;
  • gamification of plant-pathogen evolution in agriculture (outreach project).

which uses computational biology, bioinformatics, modelling, and big data to address both fundamental and applied questions in the life sciences. A selection of ongoing research lines includes the evolution of genomes, protein complexes, systems genetics, metagenomics, host-microbe interactions, and the basic principles of ecology and evolution. Together with more than 35 research groups distributed over five research and educational institutes, we form the Utrecht Bioinformatics Centre that combines world-class bioinformatics research and coordinates bioinformatics education at all levels at the Utrecht Science Park

Additional information

If you have any questions regarding the position, please contact Dr. Bram van Dijk via Do you have a question about the application procedure? Please send an email to


Everyone deserves to feel at home at our university. We welcome employees with a wide variety of backgrounds and perspectives. If you are enthusiastic about this position and have the expertise to excel in this role, simply respond via the “Apply now” button!

Please enclose:

  • your letter of motivation;
  • your curriculum vitae;
  • the names, telephone numbers, and email addresses of at least two references;
  • a copy of your MSc certificate or a letter from your university stating when your MSc studies will be completed.

Some connections are fundamental – Be one of them

The application deadline is 1 May 2023.


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