Supplementary Material for: Genetical predicted causal relationship between gut microbiota and different types of kidney diseases

Introduction: Although recent research suggests that alterations in gut microbiota play a critical role in the pathophysiology of kidney diseases, the causal relationship between specific intestinal flora and the risk of kidney diseases remains unclear. Here, we investigated the causal relationship between gut microbiota and different kidney diseases through Mendelian randomization analysis. Methods: Gut microbiota and three types of kidney diseases, including diabetic nephropathy, IgA nephropathy, and membranous nephropathy, were identified from large-scale genome-wide association studies summary data. Inverse variance weighted method was employed to estimate causal relationships. Cochran’s Q test was utilized to uncover any heterogeneity. The Mendelian randomization Egger intercept test was employed to detect horizontal pleiotropy, and the leave-one-out method was used for testing the stability. In addition, the reverse, multivariable, and two step Mendelian randomization analysis was conducted to assess the causation possibilities. Furthermore, the associations between three types of kidney diseases and immune infiltration were determined. Results: We identified 1,531 single nucleotide polymorphisms. There were 6 positive and 9 negative causal effects between gut microbiota and three types of kidney diseases. Specifically, Dialister was a protective factor for diabetic nephropathy while LachnospiraceaeUCG008 was a risk factor. Clostridiuminnocuum was a protective factor for IgA nephropathy, while ChristensenellaceaeR.7, Clostridiumsensustricto1, LachnospiraceaeUCG004, LachnospiraceaeUCG010, Oscillospira, RuminococcaceaeUCG010, and Terrisporobacter were risk factors for IgA nephropathy. Butyricicoccus, Catenibacterium, Flavonifractor, and Lachnospira were associated with an increased risk of membranous nephropathy, while RuminococcaceaeUCG011 was associated with a decreased risk of membranous nephropathy. Sensitivity analysis indicated the results were robust. No significant pleiotropy or heterogeneity was identified. Notably, the reverse Mendelian randomization analysis did not reveal any causal relationship. After adjusting for environmental confounders, including CO, PM 2.5, PM10, and exposure to tobacco smoke at home, these causal relationships still exist. Additionally, immune infiltration analysis indicated unique immune cell distribution in each type of kidney disease, which are largely consistent with later two step approach. Conclusion: This study uncovered the causal relationship between gut microbiota and three types of kidney diseases. This discovery provides fresh perspectives on how microbes contribute to kidney diseases, paving the way for more in-depth clinical studies.

引言：尽管近期研究表明肠道菌群（gut microbiota）的改变在肾脏疾病的病理生理学中发挥关键作用，但特定肠道菌群与肾脏疾病发病风险之间的因果关联仍未明确。本研究通过孟德尔随机化（Mendelian randomization）分析，探究了肠道菌群与不同类型肾脏疾病之间的因果关联。
方法：本研究从大规模全基因组关联研究（genome-wide association studies）汇总数据中获取了肠道菌群与三种肾脏疾病（糖尿病肾病、IgA肾病、膜性肾病）的相关信息。采用逆方差加权法估算因果关联；使用科克伦Q检验（Cochran’s Q test）检测异质性；采用孟德尔随机化埃格特截距检验检测水平多效性（horizontal pleiotropy），并通过留一法（leave-one-out method）检验结果稳定性。此外，还开展了反向、多变量及两阶段孟德尔随机化分析，以评估因果关联的可靠性。同时，本研究还分析了三种肾脏疾病与免疫浸润之间的关联。
结果：本研究共筛选得到1531个单核苷酸多态性（single nucleotide polymorphisms）位点。肠道菌群与三种肾脏疾病之间共存在6个正向因果关联和9个负向因果关联。具体而言，小杆菌属（Dialister）是糖尿病肾病的保护因素，而毛螺菌科UCG008（LachnospiraceaeUCG008）则为其危险因素。无害梭菌（Clostridiuminnocuum）是IgA肾病的保护因素，而克里斯滕森菌科R.7（ChristensenellaceaeR.7）、梭菌属sensu stricto 1（Clostridiumsensustricto1）、毛螺菌科UCG004（LachnospiraceaeUCG004）、毛螺菌科UCG010（LachnospiraceaeUCG010）、颤螺菌属（Oscillospira）、瘤胃球菌科UCG010（RuminococcaceaeUCG010）及土孢杆菌属（Terrisporobacter）均为IgA肾病的危险因素。丁酸球菌属（Butyricicoccus）、链杆菌属（Catenibacterium）、黄酮降解菌属（Flavonifractor）及毛螺菌属（Lachnospira）与膜性肾病的发病风险升高相关，而瘤胃球菌科UCG011（RuminococcaceaeUCG011）则与膜性肾病的发病风险降低相关。敏感性分析结果显示本研究结论具有稳健性，未检测到显著的水平多效性或异质性。值得注意的是，反向孟德尔随机化分析未发现任何反向因果关联。在校正包括一氧化碳（CO）、细颗粒物（PM2.5）、可吸入颗粒物（PM10）及室内烟草烟雾暴露在内的环境混杂因素后，上述因果关联依然成立。此外，免疫浸润分析显示三种肾脏疾病均具有独特的免疫细胞分布特征，该结果与两阶段孟德尔随机化分析结果基本一致。
结论：本研究明确了肠道菌群与三种肾脏疾病之间的因果关联。该发现为解析菌群如何参与肾脏疾病的发生发展提供了全新视角，为后续更深入的临床研究奠定了基础。