Effects of gut microbiome, plasma metabolome, and immune cells on diabetic nephropathy: a two-sample Mendelian randomization study and mediation analysis

Background Diabetic nephropathy (DN) is a leading cause of end-stage renal disease. Emerging evidence implicates the gut microbiome (GM), plasma metabolome, and immune cells in DN, but the causal relationships remain unclear. Methods A two-sample Mendelian randomization (MR) analysis was performed using genome-wide association study (GWAS) summary statistics for GM (n = 7,738), plasma metabolites (n = 8,299), immune cell traits (n = 3,757), and DN (cases = 6,043). Five MR methods were applied, with inverse-variance weighted (IVW) as the primary approach. Mediation analysis was conducted to assess whether plasma metabolites or immune cells mediated GM effects on DN. FDR correction was applied to pre-specified candidate associations for GM and immune cells, and within metabolite classes for metabolites. Results Three GM taxa had positive causal effects on DN risk (family Veillonellaceae, genus Dorea , species Haemophilus parainfluenzae , all q < 0.05), while five taxa demonstrated protective effects (family Micrococcaceae, Lactobacillaceae, genus Rothia , Lactobacillus , species Bacteroides eggerthii , all q < 0.05). Sixty-two causal associations between plasma metabolites and DN were identified (all q < 0.05 after class-stratified FDR correction), along with 31 associations between immune cell traits and DN (all q < 0.05). Mediation analysis revealed that Haemophilus parainfluenzae exerted its effect via CD16−CD56 on HLA DR+ natural killer cells (mediation proportion = 6.0%, P = 0.045), while Dorea acted through an unannotated metabolite (X-22834; mediation proportion = 22.6%), though the indirect effect of Dorea did not reach significance based on confidence interval criteria. Conclusion This study systematically elucidated the causal relationships and potential mechanisms of GM, plasma metabolites, and immune cells in DN pathogenesis using MR and mediation analyses. These findings offer novel insights into DN's pathophysiology and highlight potential targets for future therapeutic strategies, advancing our understanding of DN etiology and informing the development of more effective interventions.