PhD candidate in Equine Intestinal Microbiome and Resistome

Faculty: Faculty of Veterinary Medicine Department: Department Clinical Sciences Hours per week: 36 to 40 Application deadline: 29 March 2026

A healthy intestinal microbiome is essential for equine health. In this project, we will investigate the intestinal microbiome and resistome and their roles in gastrointestinal health and the development and spread of antimicrobial resistance. By influencing the microbiome and resistome, we aim to promote positive health effects and limit the spread of antimicrobial resistance. This project may lead to new clinical interventions and provide insights to improve current antimicrobial stewardship programmes.

Your job

This PhD project is a collaboration between the Equine Internal Medicine group (Department of Clinical Sciences, CS) and the Clinical Infectiology group (Department of Biomolecular Health Sciences, BHS). It builds on previous work by Dr Aldert Zomer (BHS), Dr Mathijs Theelen (CS), Dr Rosa Houben (CS), and Prof Jaap Wagenaar (BHS).

As a PhD candidate, you will be part of the Equine Internal Medicine group and closely collaborate with Clinical Infectiology. You will explore strategies to influence the microbiome and resistome (e.g. faecal microbiota transplantation, FMT) to promote positive health effects and limit the spread of antimicrobial resistance. You will work with existing datasets and set up new studies, collecting samples from horses and performing laboratory experiments followed by data analysis. Techniques such as 16S rRNA sequencing, shotgun metagenomic sequencing, and qPCR will be used to study the microbiome and resistome.

You will conduct innovative, integrative research and have access to state-of-the-art facilities at Utrecht University Equine Hospital and within the Clinical Infectiology Research Group. You will work in an ambitious, motivated, multidisciplinary team of veterinarians, clinicians, molecular microbiologists, and bioinformaticians. In addition, you will co-supervise Master’s and Bachelor’s students during their research projects as part of your PhD. You will be enrolled in the Utrecht Graduate School of Life Sciences and receive training, supervision, and guidance for both your research and personal and professional development, providing an excellent foundation for an independent academic career.

Your qualities

• Master’s degree in veterinary medicine, microbiology, bioinformatics, or a related field.
• Strong interest in (molecular) microbiology and antimicrobial resistance.
• Quick learner who thrives in a multidisciplinary research environment.
• Ability to work independently and foster both collaboration and independent thinking.
• Effective communication of scientific ideas, both written and verbal.
• Knowledgeable in your field and committed to keeping up with recent advances in the literature.
• Experience with bioinformatics analyses is an advantage.
• Proven proficiency in written and spoken English.

Our offer

• A position for one year, with an extension to a total of four years upon successful assessment; ((go/no-go decision after one year);
• A full-time working week of 36-40 hours and a gross monthly salary between €3,059 and €3,881 (salary scale P 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 also offers a range of its own schemes for employees. This includes arrangements for professional development , various types of leave, and options for sports and cultural activities . You can also tailor your employment conditions through our Terms of Employment Options Model. In this way, we encourage you to keep investing in your personal and professional development. For more information, please visit Working at Utrecht University .

About us

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.

Clinical Sciences

At the Department of Clinical Sciences , you will work alongside approximately 150 veterinarians and a similar number of support staff. Approximately two-thirds of the veterinarians are specialists in various disciplines; the remaining one-third consists of interns, residents and PhD candidates. Together we are responsible for the education of veterinary students, provision of clinical services to horses and companion animals, and both clinical and more fundamental research in the areas of regenerative medicine, locomotion, genetics and reproduction.

Biomolecular Health Sciences (Clinical Infectiology)

Research at Clinical Infectiology (KLIF) focuses on animal and zoonotic pathogens and the emergence of antimicrobial resistance which poses a threat for veterinary and public health. The generation and analysis of sequencing data is part of our daily work for epidemiological analysis which we use to determine search for virulence and antimicrobial markers, to assess the effects of interventions, and for diagnostics. KLIF offers a stimulating work environment at the forefront of scientific research. We do not only work with academic partners, but also with global organizations like the World Health Organization and the Food and Agriculture Organization of the United Nations.

More information

For more information, please contact Dr. Mathijs Theelen at m.j.p.theelenuu.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.

Knowledge security screening can be part of the selection procedures of academic staff. We do this, among other things, to prevent the unwanted transfer of sensitive knowledge and technology.

To apply, please send your curriculum vitae, including a letter of motivation, via the ’apply now’ button.

The application deadline is 29 March 2026.