How do phages kill dormant bacteria

Are you excited about exploring the biology behind phages infecting dormant bacteria? Join forces to uncover fundamental biology with great potential for clinical impact. We offer a fully funded PhD position on how phages kill dormant bacteria.

How do phages kill dormant bacteria

Your function

Scientific background: If you take a bus, you probably want the driver to be awake. Similarly, bacteriophages (viruses that infect bacteria) have long been assumed to require metabolically active hosts. However, several recent studies and our own findings challenge this assumption. We have identified over a dozen phages capable of replicating in growth-arrested E. coli, suggesting that dormancy-killing is far more common than previously recognized. How do phages replicate in dormant cells? The phages we discovered are genetically diverse and differentially respond to bacterial knock-outs, pointing to multiple, evolutionarily distinct solutions to this challenge.

Project: you will integrate high-throughput phenotypic screening with state-of-the-art genetic tools to understand how phages bypass bacterial dormancy. Furthermore, you will engineer these genes into phages that lack this capability, expanding their activity towards persistent bacterial populations.

Impact: Your work will reveal fundamental new mechanisms in phage biology and has urgent clinical relevance: uropathogenic E. coli (UPEC), a leading cause of recurrent urinary tract infections, and M. tuberculosis (Mtb), which evades antibiotics by entering dormancy, both exemplify the medical challenge of treating persistent infections. By developing novel phages active against dormant UPEC and Mtb, you will provide powerful new therapeutic options for the world’s most frequent and most deadly infections.

Embedding: Your PhD project is funded by an NWO-M2 grant, supervised by Yuval Mulla (VU) and co-supervised by Coen Kuijl (VUmc). You will be embedded in the molecular microbiology department of the VU and will closely collaborate with a PhD student at the medical microbiology section of the Amsterdam UMC. The start date is flexible between September 1, 2026, and December 1, 2026.

Your duties

• Genome-wide mutant generation (transposon library, CRISPR-I) to find phage genes involved in dormancy-killing
• High-throughput phenotypic screening (imaging-based)
• Targeted verification of hits via molecular cloning
• Isolation and design of dormancy-killing phages against key pathogens (UPEC, Mtb)
• Contributing to publications and presentations
• Teaching, including supervision of interns and groups of students in practical courses

Your profile

• A master’s degree (MSc) in biomolecular science, biomedical science, biophysics, or a closely related discipline. People currently still in their master's can apply if they expect to finish their program in time to start December 1, 2026, at latest.
• Experience with wet lab research, including molecular cloning via internships, is required. Experience in transposon/CRISPR-I libraries, microbiology, or specifically phages, is a plus but not required.
• Basic programming experience is required, including setting up bioinformatic pipelines via, for example, Bash and basic data analysis via, for example, Python. More extensive programming experience including image analysis is a plus but not required.
• Strong motivation to work in an interdisciplinary research environment.
• Excellent command of English, both written and spoken.

Good grades for courses and especially for internships, as evidenced by an uploaded university-certified overview, are a strong plus.

What do we offer?

• An employment contract of initially 1 year. If there is sufficient perspective, this will be extended to a total of 4 years. Your dissertation at the end of the fourth year forms the end of your employment contract.
• 8% holiday allowance and 8.3% end-of-year bonus
• Discount on, and occasionally exclusive access to, theater performances and courses at the Griffioen Cultural Center
• Space for personal development
• A wide range of sports facilities which staff may use at a modest charge

About us

About the team

The Molecular Microbiology section concentrates on the microbial cell envelope, protein secretion systems, novel antibiotics and phage biology. Our section is located together and works closely with the Medical Microbiology and Infection Prevention unit of the AUMC focusing on infection models. Combined, the two groups have approximately 35 members.

In this project you will work closely together with one more PhD student and be part of a larger group working on mycobacterial secretion systems.