Research
Our research focusses on microbial interactions in a wide variety of environments and contexts, including innate and adaptive immunity in acute and persistent infections, microbial pathways in the phyllosphere, host pathogen interactions in Salmonella infections, protein glycosylation in yeast and prokaryotes, interactions of fungi with microbes and biosynthesis of natural products from bacterial symbionts in various host animals. Our research groups show a high level of interaction and integration.
Defense mechanisms against antagonists, including competitors, pathogens, parasites and predators, are a hallmark of all kingdoms of life. In our laboratory, we study the chemical defense mechanisms of multicellular fungi against bacterial competitors and animal predators at molecular, cellular and organismal level.
Infectious diseases, caused by various microorganisms, have major medical, social and economic consequences and are a major cause of death worldwide. Analyzing the ways of how the immune system recognizes and reacts towards pathogenic infections resulting in eradication or control is relevant for our basic understanding of complex host-pathogen interactions.
Natural products are the basis of many drugs and an inspiration for synthetic chemists. We aim to understand how structurally complex natural products are made by organisms. We then use biosynthetic knowledge to generate structural diversity not yet encountered in Nature and to create sustainable sources of rare bioactive compounds. To achieve these goals, scientists from diverse backgrounds, including analytical and synthetic chemistry, molecular biology, pharmacology and bioinformatics, collaborate in our group.
Our work is focused on the understanding of the mechanisms that control T cell priming and regulate cytokine production and homing capacities. These questions are addressed primarily in the human system, where we combine the ex vivo analysis of memory T cell subsets with in vitro priming of naive T cells. This approach has led to the identification of chemokine receptors expressed in human Th17 and Th22 cells, and to the dissection of the cytokines that drive naive T cells polarization and modulate T cells effector functions. In parallel, we have used the mouse system to address fundamental questions on the regulation of lymphocyte trafficking during inflammation and in autoimmunity. We also developed a method for the analysis of human naive and memory CD4 and CD8 T cell repertoires based on high throughput cellular screenings of human T cell libraries. This method is currently used to dissect the human T cell response to pathogens, allergens, and self-antigens.
We are interested in studying ecological and evolutionary factors that determine the structure, function and diversity of microbial communities – with a focus on the ocean ecosystem and the gastrointestinal tract of animals and humans. To this end, we develop and combine bioinformatic and experimental approaches to integrate quantitative ‘meta-omics’ readouts with contextual information, with the goal to better understand and predict the role of environmental microorganisms and the underlying mechanisms of host-microbial homeostasis.
The primary interest of our laboratory is to learn how bacterial physiology is shaped by the environment and to identify microbial interactions within the phyllosphere. We perform structure/function analyses at different hierarchical scales, from the level of key proteins, to individual cells, to bacterial communities, to the ecosystem. Our research involves a range of disciplines and approaches, including functional genomics, metaproteogenomics, and systems and synthetic biology, as well as novel tools in nanotechnology.
Immune response in the central nervous system need to be finely tuned in order to limit excessive inflammation in this delicate and critical organ. We are interested in understanding how the local microenvironment, in particular fibroblastic stromal cells, influences key processes during the activation of and surveillance by immune cells in the brain and its associated lymphoid organs.