Susana Fuentes (1976) is an expert in the human microbiome field. Since her appointment at the RIVM in 2016, her focus has been on translating fundamental microbiome research into applications for public health, combining the use of mechanistic models and human clinical studies to understand these complex interactions.

I have always been fascinated by the impact that this world inside us -that is the microbiome- has on our health. Microbiome-associated therapies have the potential to revolutionize public health and healthcare, from personalized treatments to the more broad implementation of disease prevention measures. A better understanding of this ecosystem and its interplay with the host is fundamental for the translation of microbiome research into applied interventions

Research projects

Susana leads the Microbiome and Immunology group, working on the following projects:

  • The intestinal microbiome of the Dutch population: What defines a “healthy” microbiome? How does the microbiome look in the Dutch population throughout all ages? How does it relate to individual characteristics or lifestyle? What is the impact of our microbiome on the immune system?
  • The microbiome, infections and vaccination: Can we identify biomarkers within the microbiome that associate with infections and different vaccinations? Can we improve vaccine response and increase our resilience to infections through modulation of the microbiome? We are particularly interested on the more vulnerable populations, such as infants and older adults.
  • Modelling host-microbe interactions: Can we mimic a microbiome with modulatory effects on the host? How do we translate these to animal and human studies for infection and vaccination? We investigate these host immune responses in in vitro systems with different levels of complexity. 
  • Tools for microbiome research: We continuously test and improve current state-of-the-art methodology of human microbiome research, either by amplicon or metagenomic sequencing.


Susana Fuentes is a microbiologist. She graduated as a Pharmacist from the University of Granada in Spain in 1999, where she went on to get a PhD in Molecular Microbial Ecology (2005) on the microbial ecology of the gastrointestinal microbiota in mice, and its effect in different models for immunosuppression and inflammatory bowel disease. She then joined Wageningen University in the Netherlands (WUR) as a postdoctoral researcher, in the Laboratory of Microbiology as well as in the Host-Microbe Interactomics groups. Her research interests involved the clinical aspects and applications of the gastrointestinal microbiota. This included a broad range of cohorts, from newborns to the ageing population, from signatures of vaccine response or effects of antibiotic treatments to the application of fecal microbiome transplantation for the treatment of recurrent Clostridium difficile infection and intestinal bowel disease. From 2016, she started up microbiome research at the RIVM, in the Center for Immunology of Infectious Diseases and Vaccines.

Areas of expertise

  • Microbiome
  • Host response
  • Microbial ecology

Team members

  • Jolanda Kool (research technician)
  • Sudarshan Shetty (postdoctoral researcher)
  • David Boverhoff (PhD student)



Key publications