PhD student position, gut microbiome evolution in human health

Position overview and working environment

We are seeking a motivated and enthusiastic PhD student to join a fully funded project exploring the evolution of the human gut microbiome and its impact on health. This position focuses on computational biology, evolutionary biology, bioinformatics, and microbiome analysis. The PhD is part of the NWO Vidi project “Within-host evolution of the human gut microbiome in health and disease” and offers the opportunity to work in an international group of leading scientists. The position is based in the Department of Gastroenterology and Hepatology at the University Medical Center Groningen (UMCG) and is embedded in the dynamic, interdisciplinary Groningen Microbiome Hub, which brings together several international teams studying diverse aspects of the human microbiome. The University of Groningen is a top 100 research university renowned for its world-class scientific environment. You will engage in courses and research within small groups, ensuring close interaction with your supervisor and team members.

Background

The human gut hosts trillions of bacteria, fungi, and viruses that collectively influence health and disease. These microbial communities are highly individualized and evolve continuously due to their short generation times and large population sizes. Despite their importance, the long-term evolution of gut microbes - especially in chronic conditions like inflammatory bowel disease (IBD) - remains largely unexplored. Fundamental questions include: How rapidly do gut microbes evolve? Which genes are under selective pressure? How does strain-level variation affect health? Addressing these questions is critical to understanding the dynamics of the gut microbiome and its role in human disease.

Project aims
This project combines computational and experimental approaches to understand gut microbiome evolution in health and disease. The PhD student will:

• Analyze longitudinal microbiome datasets spanning up to 15 years.
• Reconstruct bacterial genomes and model evolutionary mechanisms, including selective pressures, strain switching, and horizontal gene transfer.
• Compare evolutionary patterns across species and between healthy and dysbiotic gut microbiomes.
• Validate computational findings experimentally using culturomics, in-vitro models of oxidative stress, and host-microbiome interaction assays.

The project will generate novel insights into gut microbiome dynamics and their implications for human health, with potential to guide microbiome-based therapies.

Whom are we looking for

Required qualifications and skills:

• Master’s degree (or equivalent) in computational biology, bioinformatics, evolutionary biology, microbiome research, or microbiology.
• Proficiency in R, Python, or Linux command-line tools.
• Basic understanding of microbiology.
• Strong collaboration, communication, and organizational skills.
• Fluency in English, both written and verbal.

What are we offering

This is a fixed-term appointment available for 4 years. The candidate will be provided with a stimulating work environment within the Groningen Microbiome Hub with opportunities for professional development in microbial bioinformatics. Your salary will be a minimum of € 3.108 gross per month in the first year and a maximum of € 3.939 (schale PRO). Additionally, the UMCG offers an 8% holiday allowance, an 8.3% year-end bonus.The conditions of employment comply with the Collective Labour Agreement for Medical Centres (CAO-UMC).

To apply, kindly utilize the digital application form located at the bottom of this page. Only submissions made through this form will be considered. To ensure full consideration, please submit a complete application consisting of a cover letter, curriculum vitae, and the contact details of two professional references. We are looking forward to your application and the possibility of you joining our team to contribute to this groundbreaking research endeavour.

Link
UMCG Research
UMCG Research Gastroenterology and hepatology
NWO

For questions about the position

Any questions? Do contact us.

How to apply

Please use the the digital application form at the bottom of this page - only these will be processed. You can apply until 14 October 2025. Within half an hour after sending the digital application form you will receive an email- confirmation with further information.
 

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