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Amsterdam Microbiome Initiative

Amsterdam Microbiome Initiative

The Amsterdam Microbiome Initiative (AMI) is an Amsterdam wide initiative to bundle the expertise available in our area at the UvA, VU, Amsterdam UMC and ACTA. Its members meet at the Amsterdam Microbiology SeminArs (AMSA) and have as aim to study microbial consortia in biotechnological, biomedical and environmental settings using multidisciplinary approaches.

These cover high resolution microscopy, omics technologies, specific culture systems to assess microbial physiology  and system biology tools. AMI members collaborate at the UvA with the Research Priority Area Systems Biology (RPA-SB).  The tools to be developed in the RPA-SB will be highly valuable to all members of the AMI as it focuses on combining the strengths of bottom-up and top-down systems biology approaches for modelling microbial communities as examples of complex biological systems.


AMI maintains close links with the Microbiota Centre Amsterdam at the Amsterdam UMC location AMC. AMI is meant as a platform and bottom-up organisation and therefore its exact composition is subject to regular update. If you feel your research will benefit from joining let us know! 


Prof. Stanley Brul is coordinating the AMI.  
Contact AMI via  

prof. dr. S. (Stanley) Brul

Faculty of Science

Swammerdam Institute for Life Sciences

  • AMI news

    Recruiting two new assistant professors

    May 2019

    The faculty of Science (FNWI) has defined a Research Priority Area Systems Biology (RPA-SB)  with a focus on modeling host-microbe interactions in different fields of biology. We are currently selecting two new assistant professors as part of this RPA-SB to help build networks in this RPA-SB together with microbiome specialists in the microbiology groups at SILS and IBED of the faculty as well as  AMC (Tytgat Institute) with Prof. Wouter de Jonge and ACTA with dr. Bastiaan Krom.

    One assistant professor will be based in the SILS Molecular Biology and Microbial Food Safety group. The central mission of this group is to understand the interaction of microbes and their environment. We focus on the molecular physiology and importance of environmental interactions as signals for growth, survival and death. There is growing evidence that host-microbe interactions play a significant role in many organisms. In a biomedical context such interactions are crucial for a better understanding and future treatment of inflammatory bowel diseases such as IBS and Crohn’s disease as well as diseases of the upper digestive tract. Since the development of the genomic technologies molecular host-microbe interaction can be studied holistically from a mechanistic point of view. An outlook towards the study of interactions of the microbiome and the human brain is under development.

    Another assistant professor will be based in the SILS Plant Hormone Biology group of prof. Harro Bouwmeester (recently appointed as KNAW member). The central mission of this group is to understand the interaction of microbes and their environment. The group focuses on the role of plant hormones and other signalling molecules in the communication of plants with beneficial and harmful organisms, particularly in the rhizosphere. An important example of signalling molecules that are used by plants for communication in the soil, are the strigolactones. These are used by the friends of plants, the symbiotic arbuscular mycorrhizal fungi, for host detection but also by their enemies, root parasitic plants. 

    Data interpretation of the dynamics of microbial consortia in terms of their metabolome, proteome, transcriptome and genome is central for the new positions. The new assistant professors will be active in generating descriptive and predictive models of microbial behavior to underpin our mechanistic understanding of  the microbial consortia under study.


    Three PhD plus positions

    March 2019

    Recently, research within AMI got an impulse by earmarking the first three "PhD plus" positions: five year PhD positions for research areas involving the oral microbiome and the gut microbiome, with extra education tasks and possibilities to obtain a University Teaching Qualification. Research in the gut microbiome focuses on microbial communities and the development and progression of Crohn's disease.

AMI partners

Microbiotica Centre Amsterdam

Related projects

Research Priority Area Systems Biology