From Gut to Brain: Data-Driven Evidence Suggests Causal Contribution of Gut-Microbiota to Major Depressive Disorder in Humans

Major Depressive Disorder (MDD) is a highly prevalent, severe mental health condition that constitutes one of the leading causes of disability worldwide. While recent animal studies suggest a causal role of the gut microbiome in the pathophysiology of MDD models, evidence in humans is still unclear due to small sample sizes, inconsistent clinical assessment of MDD diagnosis, and methodological limitations regarding causal inference in cross-sectional data. Here, we explicitly address these shortcomings to investigate the potential causal link between the gut microbiome and MDD: First, we replicate previously reported microbiome-depression associations using one of the largest multicenter MDD cohorts for which microbiome data and in-depth diagnostic assessment are available (N = 1,269 MDD patients and controls). We find a significant difference between healthy controls and MDD patients for the relative abundance of four taxa: Eggerthella, Hungatella, Coprobacillus, and Lachnospiraceae FCS020. Second, we employ state-of-the-art, fully data-driven causal inference tools within Judea Pearl's framework, allowing us to derive model constraints from the data rather than relying on potentially strong, unrealistic assumptions. Using this approach, we found evidence for Eggerthella and Hungatella as potential causal contributors to MDD. Furthermore, we show that the potential causal effects of Eggerthella and Hungatella on MDD persist beyond the influence of body mass index, revealing two distinct potential causal pathways linking the gut microbiome to MDD. Finally, the difference in relative abundance of these taxa between healthy and MDD patients was independent of antidepressant medication. Our study provides the first data-driven evidence for a potential causal role of gut microbiota in the pathophysiology of depression in humans.