Microbiome in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD), including Crohn’s Disease and ulcerative colitis, is a group of chronic diseases in the gastro-intestinal tract that already affects millions of people worldwide while the incidence is still increasing. The cause of IBD is thought to be an interplay between genetic predisposition and environmental triggers such as diet, antibiotic exposure and infections which shape the gut microbiome into a state of dysbiosis. Subsequently, the state of dysbiosis is shown to affect the severity of the disease. Current treatments for IBD mainly focus on reducing inflammation and symptom relief rather than curing the disease and the group of non-responders remains large. The need for new treatment is high and therefore more insight in the development and course of the disease is needed.

In this project we specifically focus on pediatric Crohn’s disease which is known for flares and periods of remission, in which large shifts in microbiota composition are observed. In addition to analyzing the microbiota composition in vivo, we aim unravel the functional roles of the microbiome by studying the microbial communities and the metabolites they produce in vitro. For this an interdisciplinary approach will be used involving collaboration between MBMFS group at SILS and the Tytgat Institute of Amsterdam UMC. To start with, we set up a multi-omics study involving patients with active disease and patients in remission in which analysis of the microbiome composition (both 16S and ITS2), metabolomics and proteomics will be performed.

Scientist involved in this project

Nienke Koopman

In cooporation with

Amsterdam University Medical Centers (Amsterdam UMC)


  1. Thesis: Analyzing and visualizing molecular events in bacterial spore germination

    J. Wen, 7 October 2020, UvA-DARE (Digital Academic Repository)

  2. Visualization of Germination Proteins in Putative Bacillus cereus Germinosomes

    Wang, Y.; de Boer, R.; Vischer, N.; van Haastrecht, P.; Setlow, P.; Brul, S. Int. J. Mol. Sci. 2020, 21, 5198.

  3. Integrative Analysis of Proteome and Transcriptome Dynamics during Bacillus subtilis Spore Revival

    Bhagyashree Swarge, Wishwas Abhyankar, Martijs Jonker, Huub Hoefsloot, Gertjan Kramer, Peter Setlow, Stanley Brul, Leo J. de Koning. mSphere Aug 2020, 5 (4) e00463-20; https://doi.org/10.1128/mSphere.00463-20

  4. Investigating Synthesis of the MalS Malic Enzyme during Bacillus subtilis Spore Germination and Outgrowth and the Influence of Spore Maturation and Sporulation Conditions

    Swarge, B., Nafid, C., Vischer, N., Kramer, G., Setlow, P., & Brul, S. (2020). mSphere, 5(4), e00464-20. https://doi.org/10.1128/mSphere.00464-20