PhD position on Metabolic Interactions in the Urinary Tract Microbiome (1.0 FTE)

Urinary tract infections (UTIs) are very common in women, with high recurrence rates even after antibiotic treatment. We have indications that a healthy urinary tract microbiome may protect against the development of UTIs, but these preliminary observations require quantification and a solid understanding of the mechanisms. You, as a PhD student, will use the computational tools to analyse and interpret the functioning and dynamics of the urinary tract microbiome. You will apply metagenomics to determine the composition of the urobiome in women with UTIs and healthy controls, annotate the microbial genomes to elucidate their functions, and predict ecological interactions. Based on these data and supported by direct metabolome measurements, you will develop and analyse community models to map metabolite usage, exchange, and trophic dependencies between different microbes in the urobiome. The ultimate goal is to identify potential metabolic intervention points in UTI-associated urobiome. In this project, you will collaborate closely with the University Medical Centre Utrecht (UMCU) and support them in recruiting the cohort of UTI patients.
The position is embedded in a multi-disciplinary research consortium that aims to identify the evolutionary strategies of microbes and to investigate how and why the urinary microbiome goes ‘off balance’ into a diseased state. You will be joining the Theoretical Biology & Bioinformatics division at Utrecht University. 

We are looking for an enthusiastic new colleague with a strong interest in microbial communities and metagenomics. You have the personal drive to contribute to address a major disease with significant clinical relevance. We would also like you to bring:

• An MSc in Bioinformatics, Computational Microbiology, or another relevant field;
• Experience with metagenomics (16S/whole-genome metagenomics) and genome-scale metabolic modelling;
• Interest and inter-personal skills to support University Medical Centre Utrecht in recruiting the cohort of UTI patient;
• Experience with bash, Python and/or R is essential, experience with Snakemake and/or Nextflow is beneficial;
• Strong motivation, demonstrable organisation skills and ability to contribute to a friendly and collaborative working environment in a cross-disciplinary scientific research team;
• You can express yourself well in English, both spoken and written .

• A position for 4 years;
• A full-time gross salary ranging from €2,541 to 3,247 in scale P;
• 8% holiday bonus and 8.3% end-of-year bonus;
• A pension scheme, partially paid parental leave, and flexible employment conditions based on the Collective Labour Agreement Dutch Universities.

In addition to the employment conditions from the CAO for Dutch Universities, Utrecht University has a number of its own arrangements. These include agreements on professional development , leave arrangements and sports. We also give you the opportunity to expand your terms of employment through the Employment Conditions Selection Model. This is how we encourage you to grow.
For more information, please visit working at Utrecht University .

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 at Working at the Faculty of Science of Utrecht University .
Your research will be performed in the Microbial Genome Evolution team headed by Dr. Michael Seidl. The team analyses large-scale (meta-) genomics data with innovative computational methods to discover fundamental processes of microbial adaptation on short and long evolutionary timescales. This project is in collaboration with the Metagenomics Group (MGX) headed by Prof. Dr. Bas E. Dutilh (Utrecht University and University of Jena, Germany) that studies microbial and viral ecology, as well as with Prof. Dr. Janneke van de Wijgert (Utrecht Medical Centre, translational infectious disease research).
The Microbial Genome Evolution and MGX Groups are part of the Theoretical Biology & Bioinformatics division at Utrecht University and the Utrecht Bioinformatics Center .

If you have any questions that you’d like us to answer, please contact Dr. Michael Seidl at [email protected] . 
Do you have a question about the application procedure? Please send an email to [email protected] .
Please note that international candidates that need a visa/work permit for the Netherlands require at least four months processing time after selection and acceptance. Our International Service Desk  (ISD) can answer your questions about living in the Netherlands as international staff . Finding appropriate housing in or near Utrecht is your own responsibility, but the ISD may be able to advise you therewith. In case of general questions about working and living in The Netherlands, please consult the Dutch Mobility Portal.

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, just apply via the "Apply" button. Please enclose:

• your letter of motivation;
• your curriculum vitae;

If this specific opportunity isn’t for you, but you know someone else who may be interested, please forward this vacancy to them.
Some connections are fundamental – Be one of them