Human interactions with the microbiota are mediated by chemistry.  Chemical signals are important in the establishment and maintenance of mutualism. We study the chemically-mediated interactions between gut microbiota and the gut. We seek to identify the specific molecules that function as signals mediating (1) the gut health with a main focus on changes in gut motility but also gut-brain axis, (2) bacterial ecosystem and its metabolic interactions. For example, we recently showed how bacterial metabolisation of the food supplement 5-hydroxytryptophan into a compound, which is a potent stimulant of gut motility (1).

In parallel, we look into interactions between gut bacteria and medication, which impact the effectiveness of treatment. For example, we uncovered that gut microbiota can be a threat for the effectiveness of medication for Parkinson’s patients and this can likely be circumvented by dietary interventions that change our gut microbes (2,3).

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What do we do ?

Techniques we apply 

Ex vivo system

Gut motility is a major effector of gut microbiota composition and has been associated to multiple diseases. It is thus of value to identify compounds which modulate gut motility. Traditional contractility screening system use rings of intestinal tissue mounted between hooks to measure contractions of the remaining muscles, so called organ bath system. This however does not allow for assessment of complex movement patterns which are crucial for luminal mixing and transport. In our lab, we currently have ex vivo organ bath system up and running and we aim to optimize this ex vivo organ culture system using whole sections of the intestine, simulating luminal flow and coupled with video imaging to investigate intestinal movements. Additionally, this proves suitable to study intestinal colonization by the microbiota and reduces the usage of animal experimentation.

Schematic view of the organ bath.

Gain of function libraries

The gut microbiota harbors a huge enzymatic capacity for biotransformations of diverse molecules originating from diet, medications or the host itself. It still is a major challenge in the field to identify the enzymes involved in those processes, as a great fraction of the microbiota can not be cultured in vitro. To circumvent this, we are actively developing an in vitro screening assay, building upon work proposed by (4) to express enzymes from metagenomic samples without the need to know about their organisms of origin.

Experimental design of gain of function libraries.

Presto-Tango GPCR screen

G-protein coupled receptors (GPCRs) are involved in a great variety of physiological functions, also in the intestines. They can be activated in by a multitude of ligands, while it has been shown that the microbiota can produce suitable molecules to do so (5). Thus, we are interested in identifying new ligands which modulate gastrointestinal function using a recently published assay (Presto-Tango) containing >300 GPCRs, which allows for easy expression and reporting of GPCR activation in a modified HTLA cell line (6).

GPCRs signaling principle with the Presto Tango assay.

Mini Bioreactor

The gut microbiota consists of an enormous amount of different bacteria. All these bacteria interact metabolically. Disentangling these interactions is necessary for a better understanding of the role of the microbiota in health and disease as well as development of novel therapeutic interventions. With the mini bioreactor, multiple members of the microbiota can be grown together. Here the level of oxygen and the pH can be monitored and controlled in real time, to mimic the conditions anywhere in the intestine. Furthermore, compounds or bacteria can be added to simulate dietary, medical or probiotic interventions. Lastly, samples can be obtained throughout the course of the experiment to be analyzed with every omics tool needed to fully understand the interactions within the microbiota.

Mini Bioreactor.


1. Waclawiková, B., Bullock, A., Schwalbe, M., Aranzamendi, C., Nelemans, S.A., van Dijk, G., El Aidy, S. Gut bacteria-derived 5-hydroxyindole is a potent stimulant of intestinal motility via its action on L-type calcium channels. PLoS biology. (2021) 19(1) e3001070.

2. van Kessel SP, Frye AK., El-Gendy AO, Castejon M, Keshavarzian A, van Dijk GJ, El Aidy S. Gut bacterial tyrosine decarboxylases restrict the bioavailability of levodopa, the primary treatment in Parkinson’s disease. Nature Communications (in press; doi: 10.1038/s41467-019-08294-y).

3. van Kessel, S.P., de Jong, H.R.,  Winkel, S.L.,  van Leeuwen, S.S.,  Nelemans, S.A., Permentier,H., Keshavarzian, A., El Aidy,S. Bacterial deamination of residual levodopa medication for Parkinson's disease elicits inhibitory effect on gut motility. BMC Biol. (2020) 18:137.

4.Zimmermann, M., Zimmermann-Kogadeeva, M., Wegmann, R. and Goodman, A. L. (2019). Mapping human microbiome drug metabolism by gut bacteria and their genes. Nature. 570(7762), 462–467.

5.Chen, H., Nwe, P.-K., Yang, Y., Rosen, C. E., Bielecka, A. A., Kuchroo, M., Cline, G. W., Kruse, A. C., Ring, A. M., Crawford, J. M., & Palm, N. W. (2019). A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology. Cell, 177(5), 1217-1231.e18.

6.Kroeze, W. K., Sassano, M. F., Huang, X.-P., Lansu, K., McCorvy, J. D., Giguère, P. M., Sciaky, N., & Roth, B. L. (2015). PRESTO-Tango as an open-source resource for interrogation of the druggable human GPCRome. Nature Structural & Molecular Biology, 22(5), 362–369.

+31(0)50 3632201

+31(0)50 3632088 (secretary)

Host-microbe Interactions group

Groningen Biomolecular Sciences and Biotechnology Institute (GBB)

​University of Groningen
Nijenborg 7, 9747 AG Groningen

The Netherlands