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Gut microbiota drug biotransformation as a tool to unravel the mechanisms of metabolic microbiota-host interactions

Project description

Unveiling the gut microbiota-host relationship

The microorganisms that reside in the intestine – collectively known as the gut microbiota – have an important role in human health. They produce bioactive molecules and metabolites that influence the host metabolism and its gene expression. To fully delineate the precise metabolic interactions between the microbiota and the host requires methods that discriminate between host and microorganism-generated metabolites. To overcome these limitations, the ERC-funded GutTransForm project proposes to develop a systematic approach that uses drug molecules to probe the gut microbiota’s capacity to modify chemicals. This approach will help unveil key aspects of the microbiota-host relationship that may be useful in the design of medical interventions.


The variability of the human gut microbiome (entirety of microorganisms inhabiting the intestine) far exceeds human genome variability, and has been connected to various aspects of human health. Although microbiome differences are often linked to altered metabolism, the current view on metabolic interactions between the microbiota and the host remain mostly descriptive due to several limiting factors. First, most sequencing-based human microbiome studies rely on correlative analyses between microbiome composition and human phenotypes, depend on largely incomplete microbial genome annotations, and are not targeted to identify community-mediated functional traits. Second, many metabolites can be both of microbial and human origin, which makes it conceptually and methodologically challenging to disentangle metabolic microbiota-host interactions.
To overcome these limitations, I propose a systematic bottom-up strategy to mechanistically study metabolic microbiota-host interactions by harnessing gut microbiota’s capacity to biotransform (chemically modify) drug molecules. The large chemical diversity and exogenous origin makes medical drugs ideally suited for experimental in vitro and in vivo approaches to probe microbiota-host interactions in a controlled way. We will combine high-throughput culturing protocols, genetics, metabolomics measurements, genomics analyses, gnotobiotic mouse work, and computational modeling to connect interpersonal differences in microbiome composition to differences in metabolic functions of individuals’ gut microbiota, and ultimately link them to molecular host phenotypes. Generating these mechanistic insights and transformational resources is essential to understand the fundamental principles of the microbiota-host relationship. In addition, this project has direct medical relevance, as it provides actionable microbiome-based links to interpersonal differences in medical drug response, which remain a widespread problem in clinical practice.



Net EU contribution
€ 1 894 858,75
Meyerhofstrasse 1
69117 Heidelberg

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Baden-Württemberg Karlsruhe Heidelberg, Stadtkreis
Activity type
Research Organisations
Other funding
€ 0,00