Postdoc in microbiome metabolomics

Are you interested in combining mass spectrometry and computational metabolomics to map the role of microbiome products in urinary tract infections? Apply now

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. In this project we aim to develop (computational) metabolomics methods and apply tools to identify microbiome products in both patient samples and complex microbial communities.

As a postdoc, you will take responsibility for the design and the realisation of the project. You will develop both targeted and untargeted liquid chromatography - mass spectrometry (LC-MS/MS) methods to measure predicted and unknown microbiome products in urine and reconstituted microbial communities. Advanced data analysis will aid in understanding (metabolic) interactions in microbial communities. You will set up the computational workflows to mine spectra and identify novel microbiome products that could ultimately biomarkers for the detection of urinary tract infections. You will also supervise related research projects of Bachelor's and Master's students.

You will work both at the division Cell Biology, Metabolism and Cancer at Utrecht University and at the Bioinformatics Group at Wageningen University. At both universities there are plenty of opportunities to facilitate your professional and personal development. Throughout the project, you will develop core skills in LC-MS/MS and data analysis, microbiome metabolism, and computational metabolomics and gain insight into the role of the urinary microbiome in urinary tract infections.

The position is embedded in a multi-disciplinary research consortium of clinical microbiologists, infectious disease specialists, bioinformaticians, modellers, chemists, and eco-evolutionary biologists. This consortium aims to identify the evolutionary strategies of microbes and to investigate how and why the urinary microbiome goes ‘off balance’ into a diseased state. Throughout the project, you will attend consortium meetings and benefit from a close collaboration with the department of Biology at Utrecht University, the University Medical Center Utrecht and Groningen University.

We are looking for an enthusiastic new colleague with a strong interest in the microbiome, mass spectrometry, and computational metabolomics. You have the personal drive to contribute towards treatments of a major disease with significant clinical relevance. Furthermore:

• You hold a PhD degree, preferably in analytical chemistry, computational biology or another relevant field.
• You have experience with mass spectrometry, mass spectrometry data analysis and/or (computational) metabolomics and you are willing to learn technical and computational skills needed for the project. Experience with mass spectrometry instrumentation is essential, experience with computational mass spectrometry or metabolomics is very beneficial, experience with coding is beneficial, especially programming in Python.
• You are a team player and have a strong motivation, demonstrable organisation skills and the ability to contribute to a friendly and collaborative working environment in a cross-disciplinary scientific research team.
• You communicate clearly and effectively and have proven English skills in presenting and writing.
• You are willing to present research at (international) conferences and to stakeholders, and to supervise and educate (master)students on related projects.

We offer:

• a postdoc position for 30 months; 
• a working week of 36 hours and a gross monthly salary between €3,345 and €5,278 in the case of full-time employment (salary scale 10 under the Collective Labour Agreement for Dutch Universities (CAO NU)); 
• 8% holiday pay and 8.3% year-end bonus; 
• a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU. 

In addition to the terms of employment laid down in the CAO NU, Utrecht University has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. 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 Pathways to Sustainability. Sharing science, shaping tomorrow.

At the Faculty of Veterinary Medicine we train the veterinarians and researchers of the future, provide care for animals and conduct leading and societal relevant research. That is what we are good at. We see that the health and welfare of animals, humans and the environment are interconnected. By sharing our knowledge and working together, we make positive impact, both nationally and internationally. Our 1,500 students and 950 staff members inspire and strengthen each other. Our engagement connects us. The drive to, from an integral perspective, make the world a better place.

You will become part of the department of biomolecular Health Sciences (BHS), Division Cell Biology, Metabolism and Cancer (CMC) and your research will be performed mainly Cancer Metabolism research group of Berkers and Helms. BHS houses the central research core facilities for metabolomics and lipidomics analysis (CMC). Within the Cancer Metabolism group, ample expertise is available on mass spectrometry, intracellular metabolism and metabolic cross-talk as well as on metabolomics, lipidomics and fluxomics analyses in advanced model systems.

At Wageningen University, you will become part of the Bioinformatics Group that is housed within the Plant Sciences Group and your research will be mainly performed within the van der Hooft team. The Bioinformatics Group is a rapidly expanding research group that focuses on fundamental and applied bioinformatics research in the green life sciences. In particular, they develop and apply novel computational methods for the analysis and integration of –omics data. The group has a strong track record in genome analysis, algorithm development, and tool construction. There are many national and international collaborations with researchers studying plant and microbe metabolism, biotechnology and genomics.
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For more information, please contact Professor Celia Berkers at c.r.berkers@uu.nl or Dr Justin van der Hooft at justin.vanderhooft@wur.nl. Candidates for this vacancy will be recruited by Utrecht University.

As Utrecht University, we want to be a home for everyone. We value staff with diverse backgrounds, perspectives and identities, including cultural, religious or ethnic background, gender, sexual orientation, disability or age. We strive to create a safe and inclusive environment in which everyone can flourish and contribute.

To apply, please send your curriculum vitae via the ‘apply now’ button. Please also include a letter of motivation in which you also comment on the various qualities we are looking for.