We utilized multiple approaches to evaluate the potential causal relationships between gut microbiota and IBS. These methods included the fixed/random-effects inverse-variance weighted (IVW) method, weighted median method, MR-Egger regression, and MR pleiotropy residual sum and outlier (MR-PRESSO) test. The IVW method served as our primary analysis due to its precise effect estimates and widespread usage in MR-analysis [24–26]. Initially, the IVW method calculated ratio estimates for individual SNPs using the Wald estimator and Delta method. Then, these estimates were combined to derive the primary causal estimate [27]. To assess heterogeneity among selected SNPs, Cochran’s Q test was employed. If heterogeneity existed (p < 0.05), we employed the random-effects IVW method; otherwise, we used the fixed-effects IVW method [28].
Given that the IVW method can be influenced by valid instruments and potential pleiotropic effects, we conducted sensitivity analyses to evaluate the robustness of associations. Firstly, we employed the weighted median method as it provides reliable estimates of causal effects when valid instruments are lacking [29]. This approach yields valid causal effect estimates even if less than 50% of information is derived from invalid instruments [29]. Secondly, MR-Egger regression was utilized to examine potential horizontal pleiotropy. If the p-value of the intercept was below 0.05, it indicated possible horizontal pleiotropy of SNPs [30]. Finally, we performed the MR-PRESSO test to detect outliers among SNPs by conducting a global test of heterogeneity. Following identification and removal of potential outliers, a corrected association result was obtained [31].
To further assess potential directional pleiotropy, each SNP used as instrumental variables (IVs) was scanned for their associations with secondary phenotypes using the GWAS Catalog (http:// www. ebi. ac. uk/ gwas, last accessed on November 22, 2022). MR analyses were then repeated after excluding SNPs associated with other phenotypes.
The associations between human gut microbiota and the risk of IBS were presented as odds ratios (ORs) with 95% confidence intervals (CIs). All MR analyses were conducted using R version 4.2.2 (https://www.r-project.org/) with the “Mendelian Randomization,” “TwoSampleMR,” and “MR-PRESSO” packages.
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