PhD Position in Equine Intestinal Microbiome and Resistome at Utrecht University

PhD in Equine Intestinal Microbiome and Resistome

Veterinary Medicine, Microbiology, and Antimicrobial Resistance
Utrecht University
Utrecht, Netherlands
Application Deadline: 29 March 2026

Fully Funded PhD: Equine Microbiome and Resistome Research

The Utrecht University invites applications for a four-year PhD position at the Faculty of Veterinary Medicine, within the Department of Clinical Sciences.

This project focuses on understanding the intestinal microbiome and resistome of horses and their role in gastrointestinal health and antimicrobial resistance. The research aims to identify strategies to promote health and limit the spread of antimicrobial resistance, potentially leading to new clinical interventions and improved stewardship programs.

Research Focus

The PhD candidate will:

• Investigate how the equine intestinal microbiome and resistome affect gastrointestinal health.
• Explore interventions such as faecal microbiota transplantation (FMT) to influence microbiome composition and reduce antimicrobial resistance.
• Conduct laboratory experiments and collect equine samples for analysis.
• Use molecular and bioinformatics techniques including 16S rRNA sequencing, shotgun metagenomics, and qPCR.
• Work with existing datasets and design new studies to assess microbiome dynamics.
• Co-supervise Bachelor’s and Master’s students as part of the research program.

This PhD is a collaboration between the Equine Internal Medicine group and the Clinical Infectiology group, combining expertise in veterinary clinical research, microbiology, and bioinformatics.

Academic Field and Research Domain

This PhD lies primarily in:

Primary Field

• Veterinary Medicine

Core Disciplines

• Molecular Microbiology
• Microbiome Research
• Antimicrobial Resistance

Applied Research Areas

• Equine Gastrointestinal Health
• Resistome Dynamics
• Translational Veterinary Interventions
• Bioinformatics and Sequencing Analysis

The project bridges clinical veterinary science, molecular microbiology, and data-driven approaches to combat antimicrobial resistance.

Candidate Profile

Applicants should have:

• MSc in Veterinary Medicine, Microbiology, Bioinformatics, or a related field
• Strong interest in molecular microbiology and antimicrobial resistance
• Experience or interest in bioinformatics analysis
• Ability to work independently and collaboratively in a multidisciplinary team
• Effective written and verbal communication skills in English

Employment Conditions

• Full-time position, 36–40 hours per week
• One-year initial contract with extension to four years upon successful evaluation
• Gross monthly salary: €3,059 to €3,881 (scale P, full-time)
• 8% holiday allowance and 8.3% year-end bonus
• Pension scheme and partially paid parental leave
• Professional development support and flexible terms of employment

Research Environment

The PhD is conducted at the Utrecht University Equine Hospital and within the Clinical Infectiology Research Group (KLIF).

• The Equine Internal Medicine group focuses on equine clinical health, regenerative medicine, and applied veterinary research.
• KLIF conducts research on animal and zoonotic pathogens, antimicrobial resistance, and epidemiology, collaborating with global organizations such as the World Health Organization and Food and Agriculture Organization of the United Nations.
• Candidates will benefit from state-of-the-art facilities and an ambitious, interdisciplinary team of veterinarians, microbiologists, clinicians, and bioinformaticians.

Career Prospects

Graduates will gain expertise in:

• Veterinary microbiology and equine health
• Antimicrobial resistance management
• Translational research in animal health
• Bioinformatics and molecular techniques

Career opportunities include academia, veterinary hospitals, research institutes, and policy or consultancy roles in animal health and antimicrobial stewardship.

This PhD in Equine Intestinal Microbiome and Resistome is ideal for candidates interested in veterinary clinical research, molecular microbiology, and antimicrobial resistance.

Apply now at: https://www.uu.nl/en/organisation/working-at-utrecht-university/jobs/phd-candidate-in-equine-intestinal-microbiome-and-resistome