Decoding the Gut-Brain Axis: A Two-Step MR Study Unmasking Causal Microbes Across Neurodegenerative and Psychiatric Disorders

Abstract

Background & Objective: Observational studies link gut microbiome dysbiosis to a spectrum of brain disorders, yet confounding and reverse causation impede causal inference. The gut-brain axis represents a paradigm shift, but clinical translation is stalled by a "causality conundrum." To investigate causal relationships between gut microbiota and Alzheimer's Disease (AD), Parkinson's Disease (PD), Multiple Sclerosis (MS), and Major Depressive Disorder (MDD), and explore mediation pathways. Methodology: This study employed a bidirectional two-sample and two-step Mendelian Randomization (MR) framework. We analyzed summary-level GWAS data for gut microbiota (MiBioGen, N=18,340) and neurological outcomes. Genetic variants (SNPs) robustly associated with exposures served as instrumental variables. Two-Step Mediation Analysis quantified the proportion of the effect of gut microbiota on outcomes mediated through potential intermediates (e.g., lipids, immune cells). Inverse-Variance Weighted (IVW) was the primary analysis method. Sensitivity Analyses (Cochran's Q for heterogeneity, MR-Egger intercept for horizontal pleiotropy, MR-PRESSO, leave-one-out) and reverse MR were performed to validate robustness and test for reverse causation. Results: Parkinson's Disease: Ruminococcus torques increased PD risk (OR=1.213, 95% CI:1.006–1.462, P=0.043), while Parabacteroides goldsteinii was protective (OR=0.810, 95% CI:0.768–0.999, P=0.049). Alzheimer’s Disease: Selenomonadales increased AD risk (OR=1.13, 95% CI:1.03–1.24, P=0.01); Mollicutes was protective (OR=0.87, 95% CI:0.79–0.95, P=0.00). Multiple Sclerosis & MDD: Ruminococcus torques increased MS risk (OR=1.213, 95% CI:1.006–1.462, P=0.043). Bacteroides plebeius influenced MDD, partially mediated by phosphatidylcholine (mediation proportion=10.9%, 95% CI:0.0110–0.2073). Sensitivity Analyses: No significant heterogeneity or horizontal pleiotropy was found for these findings, confirming robustness (P > 0.05). Conclusion: This study provides robust genetic evidence for causal gut-brain links, identifying specific microbial taxa and mediation pathways as potential therapeutic targets. Key Words: Gut-Brain Axis, Neuro-degenerative, Psychiatric disorders, MR Scan.