Emerging evidence links gut-brain axis dysregulation to psychiatric disorders. This 5-year longitudinal cohort study followed 3,400 participants, analyzing gut microbiome composition via 16S rRNA sequencing alongside validated depression assessments. Participants with lower Lactobacillus and Bifidobacterium diversity showed 2.3-fold increased odds of developing major depressive disorder (OR 2.31, 95% CI: 1.87–2.85). Probiotic supplementation in a nested RCT sub-study (n=480) reduced PHQ-9 scores by 4.2 points versus placebo.