The microbiome in health and disease

Principle investigator

Prof. Dr. E.J. (Ed) Kuijper

Description of the research

In recent years the importance of the microbiome for health and disease has been increasingly acknowledged. The composition of the microbiome plays a role in different diseases, ranging from diseases with clear causes like Clostridium difficile infection, to multifactorial diseases like inflammatory bowel disease, obesity and type II diabetes.
The laboratory of experimental bacteriology has extensive experience with faecal microbiota transplantation (FMT) for the treatment of Clostridium difficile infection (see also The research group is now moving forward investigating the mechanisms behind the curing effect of FMT in this disease, as well as its effect and underlying mechanisms in other diseases (e.g. irritable bowel syndrome). This research includes traditional microbiological work like culturing of bacterial species and consortia, as well as computational work in the field of high-throughput sequencing and metagenomics.

Research objectives
  • Do patients with various diseases affecting the intestinal tract have a different gut microbiome than healthy people?
    • Are specific bacterial species involved, and can a defined consortium be developed?
    • Are these differences cause or consequence of the disease? 
    • Are these bacterial species participating in characteristic networks?
  • What is the importance of other microbiome components like viruses, eukaryotes and metabolites?
  • What (immune) mechanisms underlie to the curing effect of faecal transplantations?
  • In general the study of the relation between the human microbiome and various health outcomes
Key publications
  • Faecal microbiota transplantation in clinical practice. Terveer EM, van Beurden YH, Goorhuis A, Mulder CJJ, Kuijper EJ, Keller JJ; Working Group of The Netherlands Donor Feces Bank. Gut. 2018 Jan;67(1):196 doi: 10.1136/gutjnl-2017-313909
  • How to: Establish and run a stool bank. Terveer EM, van Beurden YH, Goorhuis A, Seegers JFML, Bauer MP, van Nood E, Dijkgraaf MGW, Mulder CJJ, Vandenbroucke-Grauls CMJE, Verspaget HW, Keller JJ, Kuijper EJ. Clin Microbiol Infect. 2017;23(12):924-930
  • [Faecal microbiota transplantation: indications in perspective]. van Beurden YH, Terveer EM, Keller JJ, Kuijper EJ, Mulder CJJ, Vandenbroucke-Grauls CMJE. Ned Tijdschr Geneeskd. 2017;161(0):D1623
  • Fecal Microbiota Transfer for Multidrug-Resistant Gram-Negatives: A Clinical Success Combined With Microbiological Failure. Stalenhoef JE, Terveer EM, Knetsch CW, Van't Hof PJ, Vlasveld IN, Keller JJ, Visser LG, Kuijper EJ. Open Forum Infect Dis. 2017 Mar 13;4(2):ofx047
  • Is the Lower Gastrointestinal Route Really Preferred Over the Upper Gastrointestinal Route for Fecal Microbiota Transfer? Terveer EM, van Beurden YH, van Dorp S, Keller JJ, Kuijper EJ. J Clin Gastroenterol. 2016 Nov/Dec;50(10):895
  • Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, Visser CE, Kuijper EJ, Bartelsman JFWM, Tijssen JGP, Speelman P, Dijkgraaf MGW, Keller JJ. N Engl J Med. 2013; 368(5):407-15 
Research group
  • Ed Kuijper, MD, PhD - Medical microbiologist
  • Bastian Hornung, MSc - Bioinformatician
  • Romy Zwittink, MSc - Microbiologist
  • Quinten Ducarmon, MSc - PhD student
  • Liz Terveer, MD - Medical microbiologist
  • Jeroen Corver, PhD - Molecular biologist
  • Wiep Klaas Smits, PhD - Molecular biologist
  • Jeroen Laros, PhD - Bioinformatician
  • Anoe Geelen - Technician

  • Vedanta Biosciences Inc
  • Wageningen University: dr. Clara Belzer and prof. dr. Willem de Vos