PhD student nec and sepsis in preterm infants

Necrotizing enterocolitis (nec) and sepsis are life-threatening complications in very preterm infants. Probiotic treatment reduces nec incidence by up to 50% in Dutch neonatal intensive care units, yet the underlying mechanisms remain unclear.

This PhD project aims to uncover how microbial metabolites and bioactive molecules drive early gut maturation, immune regulation and barrier function. You will study both beneficial and potentially pathogenic effects of the intestinal microbiota, with a focus on host–microbe interactions in the immature gut.

You conduct fundamental biomedical research using human intestinal epithelial organoid models and microbiological culture systems. Techniques include barrier integrity assays (teer, translocation assays), gene expression analysis (qPCR, RNA sequencing), protein detection and quantification, and targeted metabolomics. The project is embedded in an NWO-VIDI-funded research line and closely connected to clinical neonatology.

Would you like to know more about the different phases within the PhD trajectory? You can read more about this on this page.

As a PhD candidate, you investigate mechanisms underlying nec and sepsis in preterm infants. You work with clinical samples and advanced in vitro models to translate fundamental insights into improved prevention strategies.

Your tasks include:

• Designing and performing experiments in intestinal organoid and cell culture models;
• Conducting (an)aerobic microbial culture experiments;
• Assessing epithelial barrier function using teer and translocation assays;
• Analysing gene and protein expression using qPCR, RNA sequencing and immunoassays;
• Interpreting data and presenting results in team meetings and scientific publications.

You actively collaborate with clinicians, microbiologists and bioinformaticians and contribute to conferences and consortium meetings.

You are driven to improve neonatal health through fundamental and translational research. You enjoy working in a multidisciplinary environment and take ownership of your project.

You have:

• A master’s degree (or equivalent) in biomedical sciences, molecular biology, medicine or a related field; applicants in the final stage of their degree are welcome to apply;
• A strong background in cell biology, molecular biology, microbiology and/or immunology;
• The ability to work independently as well as collaboratively in a multidisciplinary team;
• Strong analytical skills and a proactive research attitude;
• Excellent English communication skills, written and spoken.

Technical skills

• intestinal organoid models and mammalian cell culture (2D/3D systems, e.g. Caco-2, HT29, THP1);
• (an)aerobic microbial culture techniques;
• barrier integrity analysis, including TEER and translocation assays;
• RNA isolation, qPCR and gene expression analysis;
• ELISA and immunofluorescent staining;
• protein detection and quantification techniques;
• RNA sequencing and metagenomic sequencing;
• targeted metabolomics and HPLC;
• flow cytometry (FACS);
• data analysis using R and/or Python.

• A flying start to your career in scientific research.
• Plenty of room for your drive to shape tomorrow's healthcare.
• Working on large-scale and in-house research, with motivated colleagues from all over the world.
• You will be employed by Amsterdam UMC Research BV.
• A contract for 12 months, with the intention to extend for a total of 4 years. The Guideline PhD contract applies to this vacancy.
• Salary scale OIO: € 3.108 to € 3.939 gross based on full-time employment (depending on education and experience) and a year-end bonus of 8.3%. Calculate your net salary here.
• Holiday hours: 190.4 per year for fulltime and a possibility to save additional hours.
• Pension accrual with BeFrank, a modern, comprehensible and fairly priced pension.
• For >7 km each way, 100% reimbursement for public transport travel costs and, for private transport, €0.18 per km up to a maximum of 40 km each way.
• Do you prefer walking or cycling? Take advantage of our good bike scheme. Moreover, you will receive a reimbursement of €0.18 per km.

Watch this video with more information about joining Amsterdam UMC Research BV.

You join a multidisciplinary research team within the department of Pediatric gastroenterology and the Tytgat Institute for Liver and Intestinal Diseases at Amsterdam UMC. Both are embedded in the Pediatric Abdominal Center (Kinderbuikcentrum Lab) at Amsterdam UMC, location AMC.

You work in a team of clinicians, PhD candidates, postdocs and technicians who closely collaborate across neonatology, microbiology and immunology. The atmosphere is ambitious, supportive and collaborative. We value scientific curiosity, open discussion and teamwork.

Amsterdam UMC offers state-of-the-art research facilities, including advanced imaging, genomics, transcriptomics and metabolomics platforms. Our lab hosts organoid and iPSC culture systems, single-cell and spatial sequencing workflows and dedicated bioinformatics support. This setting enables you to perform high-impact, directly translatable research in neonatal gastroenterology.

Amsterdam UMC Research BV supports non-profit scientific research. In doing so, we provide researchers with everything they need to excel. Our principal investigators (PIs) and project leaders offer support in the field of project management, finance and human resources. In medical scientific research projects, legal support is also provided.

Watch the video to find out more.

Please submit your application including a CV that lists two referees and a motivation letter.

The interviews will take place in the week of March 23 and the week of March 30. We kindly ask you to take this into account.

During the publication period, applications will be handled continuously. If the vacancy is filled, it will be closed prematurely.

If you have any questions about this position, please feel free to contact Yannick van Schajik, at y.vanschajik@amsterdamumc.nl or Dr. Tim de Meij MD, at t.demeij@amsterdamumc.nl or Prof. Dr. Wouter de Jonge, at w.j.dejonge@amsterdamumc.nl.

For more information about the application procedure, please contact Chey Edwards, recruitment advisor, at c.i.edwards@amsterdamumc.nl.

A reference check, screening and hiring assessment may be part of the procedure. Read here whether that applies to you. If you join us, we ask you for a VOG (Certificate of Good Conduct).

Internal candidates will be given priority over external candidates in case of equal suitability.

Acquisition in response to this vacancy will not be considered.