PhD position in Advancing Gut Architecture and Functionality (1.0 FTE)

Uren per week: 
38 tot 40
Faculteit of dienst: 
Faculteit Bètawetenschappen
Department of Pharmaceutical Sciences, UIPS
Uiterlijk reageren op: 


This PhD position is integral to the TOP-GUT MSCA DN project (details: and This project recruits 11 PhD students and we are looking for you as our new motivated and dedicated PhD student. Your research focusses on the development of a 3D gut chip aimed at overcoming the constraints of current in vitro gut models. The project's central objective is to faithfully replicate the physiological attributes of the intestinal lumen using biofabrication methods, including the incorporation of a patterned collagen scaffold to emulate the architectural characteristics of human intestinal villi within a microfluidic device. This '3D gut chip' is envisioned to deliver a 3D tissue structure exposed to fluidic shear, thereby enhancing cell differentiation and physiological function, with a particular emphasis on ameliorating absorptive permeability and biotransformation processes.

Your primary objectives:

  • develop hydrogel constructs capable of accurately replicating the crypt-villus features of the intestinal lumen;
  • cultivate intestinal organoids on the patterned hydrogels and rigorously assess their functional maturation, considering spatial cell arrangement and mucus production, among other factors;
  • integrate the developed topographical elements into a perfusable microfluidic device with both apical and basal access points;
  • investigate the barrier and biotransformation activities of various molecules, encompassing those of bacterial origin, dietary components, and pharmaceutical compounds, under both static and dynamic (flow) conditions within the '3D gut chip.'

To achieve these objectives, advanced techniques in 3D cell culturing and biofabrication will be employed. Furthermore, state-of-the-art methodologies will be applied to functionally characterise intestinal cells, including analytical techniques and spatial imaging. Additionally, microfluidic systems and flow modeling will be harnessed to elucidate the biological handling and transformation of drugs and nutrients in the context of health and disease. It is noteworthy that within the TOP-GUT project, the inclusion of stromal compartments and immune cells will expand the scope of investigation.


Excited about the position? Please check if you bring the following criteria:

  • a Bachelor's or Master's degree in a relevant field such as Bioengineering, Biotechnology, Biomedical Sciences, or a related discipline;
  • a strong background in cell culture, tissue engineering, and microfluidics;
  • experience with 3D cell culture and biofabrication techniques (highly desirable);
  • proficiency in experimental design, data analysis, and problem-solving;
  • excellent communication skills and the ability to work both independently and as part of a collaborative team;
  • demonstrated passion for translational research and an eagerness to contribute to the advancement of in vitro gut models.


As TOP-GUT is a Marie Skłodowska Curie project, we offer:

  • a position for 4 years a full time PhD position for 4 years (the first three years are funded by the Marie Curie Doctoral Networks programme of the European Commission, the fourth year by Utrecht University);
  • a full-time gross salary starting from €2,770 in the first year and increasing to €3,539 in the fourth year 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, sports and cultural schemes and you get discounts on software and other IT products. 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.

    Over de organisatie

    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. Shaping science, sharing tomorrow.

    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 on YouTube.

    Silvia Mihăilă's research group is part of the Utrecht Institute of Pharmaceutical Sciences (UIPS), Utrecht University. Her group specialises in developing advanced in vitro models that seamlessly combine biofabrication techniques and organoid cultures. The primary goal is to advance our comprehension of health and disease by harnessing microenvironmental cues, particularly through the manipulation of topographical and geometrical parameters, to fine-tune and optimise cellular processes, which can be pharmaceutically targeted. This multidisciplinary approach holds the promise of deepening our insights into the intricate mechanisms underlying health and disease.

    Yvonne Vercoulen’s research group is part of the Center for Molecular Medicine, University Medical Center Utrecht. Dr. Vercoulen’s team investigates how cellular interactions and inflammatory signaling promote tissue disease, such as inflammation and cancer. We develop advanced imaging technology in primary tissues and make use of culture systems (oganoids) that mimic the human gut. The team fosters collaborations with expert clinicians in gastroenterology through research meetings for optimal exchange of knowledge, promoting clinical impact.

    Aanvullende informatie

    If you have any questions that you’d like us to answer, please contact Silvia Mihăilă (assistant professor of in vitro models of disease) at

    Do you have a question about the application procedure? Please send an email to
    Are you an international applicant? Our International Service Desk can answer your questions about living in the Netherlands as international staff.

    Disclaimer: Another member of the consortium could be excited about your skills and experiences and may want to ask you to join their subject within this consortium. In your application e-mail, please explicitly state if you permit the UU to share your cv and motivation letter with consortium partners. If you do not, or if you explicitly state you do not want this, we will not share the provided information with others. The UU does not guarantee that you will be approached by partners. The personal data you provide will not be used for any other purpose than this internal sharing and possible further recruitment as described in our privacy statement, and will be deleted permanently 4 weeks after a new candidate has been found for this position. If you have any questions about this processing of your personal data, do not hesitate to ask


    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.

    If you are enthusiastic about this position, you could read more about the consortium at the TOP-GUT page

    To apply for this position please send Silvia Mihăilă ( an email with you application including a single document containing: 

    • a cover letter that includes the motivation for the position, emphasising the candidate’s strength regarding the project and the requirements (max 3 pages).
    • a CV (max 2 pages).
    • a scanned copy of all relevant diplomas or certificates that formally entitle the candidate to embark on a doctorate. Typically, these documents will include Bachelor’s and Master’s degree certificates. In case the Master’s degree has not been obtained yet at the closing date for application, the candidate has to submit a declaration signed by their supervisor or University official stating that the degree will be obtained by the time of PhD enrolment.
    • a Letter of Recommendation from two appropriate referees or contact details of two referees.

    Uiterlijk reageren op 30 november 2023.