Gnotobiotic systems

Microbiome imaging

Organismal and cellular systems

To model human disease, we use a wide range of experimental systems from cell culture platforms to mammalian organisms.

In-vivo systems

We use the CRISPR/Cas9 system to generate new mouse models of human disease, combined with a large range of state-of-the-art phenotyping platforms and in vivo imaging technologies.

Organoids and explants

To study the mechanisms underlying host-microbial interactions at mucosal surfaces, we use ex vivo systems of intestinal organoids and explants.

Cellular screening assays

We are using high-throughput screening assays to identify ligands for innate immune receptors, cellular responses to external stimuli, and genetic elements in control of cellular physiology.

Omics technologies

The lab contains a large number of platforms enabling the comprehensive profiling of cellular and organismal systems.

DNA and RNA sequencing

The lab is home to metagenomic sequencing platforms that aim at deciphering the genomic and transcriptional functions of both host and microbiome – from the single cell to the population level.


We use metabolomics to decipher the interactome between the intestinal epithelium and the outside world.


Epigenetic studies enable us to gain insights into the organization of the genome that determine epithelial responses to differentiation and stimulation.