My main scientific interests are related to understanding how cells of the immune system communicate with other host systems and the resident microorganisms (microbiota) in complex organisms in health and disease. The microbiota exceed 10 times the number of our own body cells and contribute to many physiological processes. This co-existence is beneficial for both sides but has to be tightly regulated in order to prevent disease development. In order to disclose the mechanisms of these physiological and associated pathological processes, I make use of the systems approach and analyze host and microbiota simultaneously. This is done through host transcriptome profiling and global microbiome analysis by microarrays and next generation sequencing to identify the key regulators of the process. These findings are further validated by directed perturbations of host (knockout mice and siRNA) and microbiota (using antibiotics or colonizing germfree mice with specific bacteria or complex microbiota). My recent work on chronic enteropathy in immunodeficient hosts (human and mouse) revealed a crosstalk between the immune system, the microbiota, and the epithelial cells affecting both intestinal and systemic lipid metabolism. I plan to study further the molecular mechanisms of this interaction potentially leading to new therapeutic interventions.