Toward a Deeper Understanding of Gut Microbiome in Depression: The Promise of Clinical Applicability

The emergence of the coronavirus disease 2019 pandemic has dramatically increased the global prevalence of depression. Unfortunately, antidepressant drugs benefit only a small minority of patients. Thus, there is an urgent need to develop new interventions. Accumulating evidence supports a causal relationship between gut microbiota dysbiosis and depression. To advance microbiota‐based diagnostics and therapeutics of depression, a comprehensive overview of microbial alterations in depression is presented to identify effector microbial biomarkers. This procedure generated 215 bacterial taxa from humans and 312 from animal models. Compared to controls, depression shows significant differences in β‐diversity, but no changes in microbial richness and diversity. Additionally, species‐specific microbial changes are identified like increased Eggerthella in humans and decreased Acetatifactor in rodent models. Moreover, a disrupted microbiome balance and functional changes, characterized by an enrichment of pro‐inflammatory bacteria (e.g., Desulfovibrio and Escherichia/Shigella) and depletion of anti‐inflammatory butyrate‐producing bacteria (e.g., Bifidobacterium and Faecalibacterium) are consistently shared across species. Confounding effects of geographical region, depression type, and intestinal segments are also investigated. Ultimately, a total of 178 species and subspecies probiotics are identified to alleviate the depressive phenotypes. Current findings provide a foundation for developing microbiota‐based diagnostics and therapeutics and advancing microbiota‐oriented precision medicine for depression. Microbiota‐based therapeutics is a promising intervention approach and might be the next breakthrough in depression treatment. By integrating and analyzing the microbial alterations in depression reported worldwide, a depression‐associated microbial database is constructed. Identifying the species‐specific and trans‐species microbial changes and explicating the confounding effects is critical to developing microbiota‐based diagnostics and therapeutics and advancing microbiota‐oriented precision medicine for depression.