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PhD position to study the role of fungi in intestinal failure in neonates.

  • Full or part time
  • Application Deadline
    Tuesday, April 30, 2019
  • Funded PhD Project (Students Worldwide)
    Funded PhD Project (Students Worldwide)

Project Description

PhD position at Gut Research & Academic Medical Center to study the role of fungi in intestinal failure in neonates. This project is part of the GROWTH Innovative Training Network, where a position for a Marie-Sklodowska Curie (MSCA) PhD student is offered in the area of early life nutrition and chronic intestinal (inflammatory) disease.


GUT RESEARCH is a young and innovative company headed to accelerate the microbiome and mycobiome R&D in functional and intestinal inflammatory diseases. GUT RESEARCH premises are closely affiliated to the Academic Medical Center (Amsterdam) and the University Hospital Bonn emphasizing the open and collaborative atmosphere in our company. The GUT RESEARCH team in Amsterdam consists of scientists, business developers and technicians lead by a principle scientist.


The GROWTH consortium, funded by the European Commission (2019-2023), is made up to train a new generation of researchers working on new pathological insights, biomarker diagnostics and personalized nutritional interventions for intestinal failure in neonates and preterm infants. Academic and industry partners, covering various disciplines ranging from fundamental research to clinical paediatrics and analytical chemistry to organoid and gut-on-chip applications, have teamed up in the EU:
- Gut Research BV (The Netherlands)
- University Hospital Bonn (Germany)
- Imperial College London (United Kingdom)
- Reckitt Benckiser (United Kingdom)
- Academic Medical Center (The Netherlands)
- Cherry Biotech (France)
- VU Medical Center (The Netherlands)
- TNO Research (The Netherlands)
- Radboud University Medical Center (The Netherlands)

GROWTH is a European Industrial Doctorate programme that requires PhD students to spend at least 50% of their time (18 months) in the non-academic sector.

GROWTH website url:


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.

The candidate 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.


During the first 36 months of the ESR project, the candidate will have the opportunity to spend 18 months at Imperial College London (National Phenome Center, United Kingdom) to deploy (un)targeted fungisome, lipidome and metabolome analyses on fecal samples of preterms and neonates integrate these datasets supported by machine learning approaches under supervision of Dr James Kinross.


Applicants can be of any nationality and must be Early Stage Researchers and shall at the date of recruitment by GUT RESEARCH, be in the first four years (full-time equivalent research experience) of their research careers and have not been awarded a doctoral degree. Furthermore. the applicant must not have resided or carried out his/her main activity (work, studies, etc) in the country of his/her host organisation for more than 12 months in the 3 years immediately prior to his/her recruitment.

The per annum MSCA PhD student living and mobility allowance (plus family allowance if applicable, family status is assessed at recruitment) is in line with EU-MSCA requirements. This amount will be subject to tax and employee’s National insurance deductions and will be paid in EURO.

Complete applications in English should include the GROWTH Application Form and its mandatory attachments ( Please note that applications that do not meet these requirements WILL NOT BE CONSIDERED.

Please send the complete package as 1 PDF file via email to before 30 April 2019 18:00h - Europe/Brussels.

Please familiarize yourself also with the other 7 ESR postings (PhD positions) within the GROWTH consortium ( Selected applicants will be invited to an Onsite Recruitment Event in Amsterdam on 13 May 2019. Awarding decisions will be announced shortly thereafter, and candidates are expected to be available to start their projects between June and October 2019.

Funding Notes

A degree (MSc, or equivalent) in Health and/or Life Sciences (Biology, Microbiology, Molecular Biology, Immunology, Biomedical Sciences, Biochemistry or closely related fields) or Data Sciences (Bio-informatics, Machine Learning). Candidates in the final stages of obtaining their degree are eligible to apply

ENGLISH: Excellent, both written and spoken.

We expect a Master´s degree (or equivalent) in Health and/or Life Sciences and/or Data Sciences. Furthermore, the applicant should be able to perform team-oriented as well as independent work. Desirable methodological skills: excellent background in molecular/cell biology, biochemistry, immunology and/or microbiology, hands-on knowledge of analytical methods.

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