PhD in Equine Intestinal Microbiome and Resistome

Organisation/Company Utrecht University Research Field Medical sciences » Veterinary medicine Researcher Profile Recognised Researcher (R2) First Stage Researcher (R1) Final date to receive applications 29 Mar 2026 - 21:59 (UTC) Country Netherlands Type of Contract Temporary Job Status Not Applicable Hours Per Week 40.0 Is the job funded through the EU Research Framework Programme? Not funded by a EU programme Is the Job related to staff position within a Research Infrastructure?

No

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.

• 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.

• 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…