The MicroSusDiet project uses a transdisciplinary approach to study the roles of microbes across the Swiss Agri-food system to support sustainable, healthy Swiss diets. From microbes in foods to sustainable dietary pattern, the bi-directional relationship between diet and gut microbiome is explored by combining metagenomics and metabolomics tools, using population data and nutritional intervention studies. The true impact of changes in nutrient composition of foods via fermentation will be tested using novel measures of nutrient bioavailability, including metabolomics profiling in urine and breath. The project finally examines the effects of changing the agricultural environment on microbes and their metabolites along the food chain from soil to plant, plant to consumer.