The plastic nature of the gut microbiome facilitates its modulation through non-invasive methods, which makes it an attractive intervention target. Given the gut microbiome’s influence on health and disease, microbiome modulation in principle aims at reverting disease-associated constellations (dysbiosis) back into a healthy state (eubiosis). However, despite a wealth of human microbiome studies, we still lack a precise understanding of how diet and lifestyle factors, including medication, shape the gut microbiome. In the past we have collaborated with other groups at EMBL to characterise the effects of antibiotics and non-antibiotic drugs on commensal gut microbes in vitro and are now shifting focus from these chemically defined to more complex dietary interventions to study their effects on the microbiome. To model the impact of dietary effects, including fasting, we analyse gut metagenomic and other -omics data in collaborative settings with clinical partners. With this work, we ultimately aim to more rationally design dietary interventions to effectively restore gut health (eubiosis) in an individual-specific way.