The gut microbiota is in close contact with the intestinal epithelium and affects the development and maturation of the mucosal immune system. Diet is one of the most substantial factors that modulate the microbiota composition in the gut. In this project, we try to understand better the interaction between diet, gut microbiota and mucosal barrier function. We perform sequencing of the gut microbiota by 16S rDNA gene sequencing or metagenomics, we analyze host tissue transcription by RNAseq analyses and we perform metabolomics of the intestinal content to identify microbial molecules that signal to the host. Integrating the different -omics technologies will allow us to identify processes that are crucial for the maintenance of mucosal barrier function in the healthy gut and will reveal microbiota-host signalling pathways that may lead to a diseased gut.