PhD Rotavirus and intestinal microbiome interaction

PhD Rotavirus and intestinal microbiome interaction

Published Deadline Location
21 Nov 13 Dec Amsterdam
We are looking for an ambitious PhD candidate to study the interaction between the intestinal bacterial microbiome, rotavirus, and enteric intestinal immunity.

Job description

Rotavirus is the most important cause of severe diarrhea in children under the age of five worldwide. While several live attenuated oral rotavirus vaccines have been licensed for use since 2006, rotavirus vaccines are far less effective in low-income than high-income settings.

The intestinal microbiome describes the community of microorganisms that inhabit our body. We have demonstrated that the intestinal bacterial microbiome composition correlates with rotavirus vaccine performance and hypothesize that the bacterial microbiome and eukaryotic virome modify rotavirus vaccine performance in low-income settings.

This PhD position will explore underlying mechanisms explaining virome and bacterial microbiome interactions with rotavirus and our immunity to the virus. The project is translational and will incorporate analysis of human data from high- and low-income settings, and use of 3-dimensional cell cultures (enteroids), with collaborators from Zambia, Ghana, and the US.

We are looking for an ambitious PhD candidate to study the interaction between the intestinal bacterial microbiome, rotavirus, and enteric intestinal immunity.
The project will employ metagenomic sequencing analyses, analysis of host systemic and enteric immunity, analysis of human samples, virus cell culture, and novel utilisation of human intestinal organoids.

This research is embedded in long-term research partnerships with academic groups in Zambia, Ghana and the US, supporting the global relevance and context of the research line and offering extensive opportunities for cross-disciplinary research and scientific exploration.


Amsterdam UMC


  • The candidate should preferably have both an MD degree and have prior laboratory experience.
  • Experience in in virus culture and cell biology techniques are considered assets.
  • Ability to work in R and perform bioinformatic analyses are considered assets.
  • Because of the collaborative nature of the project the candidate should be an excellent team player with good communication skills.

Conditions of employment

  • A flying start to your career in research work in a metropolis with a diverse and open culture, and a multicultural society.
  • Working with motivated colleagues from all corners of the world.
  • The position is to be filled for 0.9 - 1.0 fte.
  • You will start with a contract for one year (12 months) in accordance with the CAO UMC 2022-2023, with the possibility of extension for another three years (36 months).
  • PhD students (Onderzoeker in Opleiding) are placed in scale 21, with a fulltime gross salary. The starting salary is € 2.901,- and increases to € 3.677 bruto in the fourth year.
  • In addition to a good basic salary, you will receive, among other things, 8.3% year-end bonus and 8% vacation allowance. Calculate your net salary here.
  • Pension via BeFrank
  • Reimbursement of 75% of your public transport costs. Would you rather travel by bike? Then we have a good bicycle scheme.
  • An active staff association and the Young Amsterdam UMC association, both of which organize fun (sports) activities and events.


Amsterdam UMC

The Academic Medical Center (AMC) houses the university hospital and the medical faculty of the University of Amsterdam, as well as several research institutes. Infectious Diseases represents one of the major research topics at the AMC, integrated in a multidisciplinary fashion at the Center for Infection and Immunity AMC (CINIMA).

This research will take place at the Department of Global Health and the Department of Microbiology of the Amsterdam UMC. The vision of the Department of Global Health is provision of equal opportunities for health and well-being for all. The department’s mission is to address challenges in global health and development by conducting collaborative interdisciplinary and intersectoral research, generating insights and solutions, and educating the next generation of global health experts. (see also,

The project will partly take place at the OrganoVIR Laboratories of the Department of Microbiology of the AUMC. OrganoVIR Labs has expertise in the field of organoids for virus research and is housed in the Department of Medical Microbiology in the AMC. Laboratories at the department have biosafety facilities up to level 3, state-of-the-art molecular biology and culture facilities and access to high-throughput sequencing. The department hosts the Laboratory of Clinical Virology, one of the largest clinical virology departments in the Netherlands. An important focus of basic, applied and clinical research at this Laboratory is understanding how organoid models can become a superior model for virus research.

Additional information

The first round of interviews is scheduled for half December.

In addition 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 Dr. Vanessa Harris, MD PhD, afdeling Global Health via

For more information about the application procedure, please contact Tanja Hart, Recruitment Advisor, via 06-21603178 or via

A reference check, screening and hiring test 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 is not appreciated.


  • PhD
  • €2901—€3677 per month
  • Doctorate
  • 10113



Meibergdreef 9, 1105AZ, Amsterdam

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Application procedure

Application procedure

Make sure to apply no later than 13 Dec 2023 23:59 (Europe/Amsterdam).