ESR Project 3

The PhD student will be enrolled in the AMC Graduate School and supervised by an academic and non-academic supervisor, equally exposing the candidate to the academic and non-academic sector. He/she will study the role of fungi in intestinal failure in neonates by capitalizing on a large cohort with a collection of daily fecal samples (>17.000) of 1,500 preterm and term neonates combined with a close clinical follow-up on health status from 9 Neonatal Intensive Care Units in The Netherlands. He/she will perform microbiota (16S) and mycobiota (ITS1) sequencing of pre-term fecal material, develop mouse and human fetal organoids, study organoid exposure to fungi and validate presence of fungi in a clinically relevant animal model. The second part of this project entails the investigation of fungal pathogens in inflammatory bowel disease (IBD), establish IBD flare related fungi in fecal and bowel tissue material, upon culturing, transplant these into experimental colitis models and perform fungal exposome proof of principle studies.


- Academic Medical Center (Tytgat Institute for Liver and Intestinal Research & Microbiota Center Amsterdam)

- Imperial College London (National Phenome Center)

- University Hospital Bonn (Dept. of Surgery)

- Westerdijk Fungal Diversity Center (Dept. of Yeast Research)

- TNO Research (Dept. of Microbiology & Systems Biology)

Host Institution

Gut Research


  • Drs. P. Bessems
  • Dr R. van den Wijngaard