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

Stanley Brul

Jurgen Seppen (Amsterdam UMC)

Wouter de Jonge (Amsterdam UMC)

Anna Heintz Buschart

In cooporation with

Amsterdam University Medical Centers (Amsterdam UMC)


  1. Organization and dynamics of the SpoVAEa protein and its surrounding inner membrane lipids, upon germination of Bacillus subtilis spores.

    Wen J, Vischer NOE, de Vos AL, Manders EMM, Setlow P, Brul S. Sci Rep. 2022 Mar 23;12(1):4944. doi: 10.1038/s41598-022-09147-3. PMID: 35322191

  2. Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine

    Koopman, N.; Remijas, L.; Seppen, J.; Setlow, P.; Brul, S. Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine. Int. J. Mol. Sci. 2022, 23, 3405. https://doi.org/10.3390/ijms23063405

  3. History of fecal transplantation; camel feces contains limited amounts of Bacillus subtilis spores and likely has no traditional role in the treatment of dysentery.

    Koopman N, van Leeuwen P, Brul S, Seppen J (2022). PLOS ONE 17(8): e0272607. https://doi.org/10.1371/journal.pone.0272607

  4. Genetic editing of multi-resistance plasmids in Escherichia coli isolated from meat during transfer.

    Tania S. Darphorn, Stanley Brul, Benno H. ter Kuile,Plasmid,Volume 122,2022,102640,ISSN 0147-619X,https://doi.org/10.1016/j.plasmid.2022.102640.

  5. The Multifaceted Role of Serotonin in Intestinal Homeostasis

    Nienke Koopman, Drosos Katsavelis, Anne S Ten Hove, Stanley Brul, Wouter J de Jonge, Jurgen Seppen, Int. J. Mol. Sci. 2021, 22(17), 9487; doi: https://doi.org/10.3390/ijms22179487

  6. Thesis: Analyzing and visualizing molecular events in bacterial spore germination
  7. 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

  8. 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

  9. 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.

  10. Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

    F. J. Ryan, A. M. Ahern, […] M. J. Claesson. Nature Communications volume 11, Article number: 1512 (2020). doi: https://doi.org/10.1038/s41467-020-15342-5