PhD Rotavirus and intestinal microbiome interaction

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.

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, www.aighd.org)

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.