Depression is a leading cause of disability worldwide, but the effectiveness of usual antidepressant treatments is still suboptimal. Rising evidence shows that depression is associated with changes in the gut microbiota. Thus, the gut-brain-interaction became a promising treatment-target for depression, even though the mechanisms underlying this bidirectional regulation are still not fully understood. To this point, all existing studies investigated the impact of modulating the gut microbiota on depressive symptoms but neglected the other way around. To address this direction, we used electroconvulsive therapy (ECT) to investigate the brain’s role within the gut-brain-interaction in depression. As ECT exclusively stimulates the brain without any direct effect on the gut, investigating its influence on the gut microbiota has the potential to demonstrate the importance of specific bacterial genera in depression when their abundance changes in course of a successful ECT-treatment. Therefore, we collected stool samples of 23 depressed patients who underwent ECT for clinical reasons at five different time points during their ECT treatment. In a preliminary analysis, we found that the composition of the gut microbiome did not changes during the ECT-treatment over all patients. However, when we compared responders to non-responders, we found significant changes in the abundance of several bacteria in the responders’ gut microbiome but not in the non-responders’. Understanding the effect of ECT on the gut microbiota’s composition and function will allow us to potentially identify specific gut bacteria, which could be used for a novel, individualized drug approach in depression.