The selection of single nucleotide polymorphisms.
First, we identified 2047 SNPs that were associated with both gut microbiota and lobar BMB at a significance level of p < 1 × 10− 5. To further investigate the causal effects, we used more strict significance level of p < 5 × 10− 8 to select SNPs and identified 22 SNPs that fit this criteria. Then, we screened for SNPs associated with deep infratentorial BMB in the same way. 1783 (genome-wide statistical significance threshold, p < 1 × 10− 5) and 22 (genome-wide statistical significance threshold, p < 5 × 10− 8) SNPs were selected as SNPs. The F statistics of the SNPs were all largely > 10 (Table S1), indicating no evidence of weak instrument bias.
Causal effects of the gut microbiome on the lobar brain microbleeds.
Through the IVW, in the set of SNPs (p < 1 × 10− 5), the majority of gut microbiomes were not related to lobar BMB (Table S2). Meanwhile, we found that the genus Lachnospiraceae NC2004 group, class Negativicutes, order Selenomonadales, family Victivallaceae, and phylum Cyanobacteria were the protective factors against lobar BMB (genus Lachnospiraceae NC2004 group: OR [95% CI]: 0.59 [0.44, 0.80]; class Negativicutes: OR [95% CI]: 0.49 [0.30, 0.81]; order Selenomonadales: OR [95% CI]: 0.49 [0.30, 0.81]; family Victivallaceae: OR [95% CI]: 0.77 [0.62, 0.96] ; phylum Cyanobacteria: OR [95% CI]: 0.69 [0.48, 0.98]). The order Bacillales, as well as the genus Terrisporobacter, phylum Firmicutes, genus Coprobacter, and genus Ruminococcaceae UCG009, were identified as risk factors for lobar BMB (order Bacillales: OR [95% CI]: 1.33 [1.06, 1.67]; genus Terrisporobacter: OR [95% CI]: 1.61 [1.07, 2.40]; phylum Firmicutes: OR [95% CI]: 1.69 [1.08, 2.65]; genus Coprobacter: OR [95% CI]: 1.33 [1.01, 1.75] ; genus Ruminococcaceae UCG009: OR [95% CI]: 1.38 [1.00, 1.90]) (Fig. 2, Table S6). We identified the SNPs under a more stringent condition (p < 5 × 10− 8), and we found that family Streptococcaceae, genus Streptococcus, and genus Intestinibacter were causally associated with lobar BMB (wald ratio, family Streptococcaceae: OR [95% CI]: 3.87 [1.07, 13.94]; genus Streptococcus: OR [95% CI]: 3.61 [1.07, 12.20]; genus Intestinibacter: OR [95% CI]: 2.99 [1.11, 8.07]) (Table S4).
The same association between the gut microbiome and lobar BMB was still noted in the MR-egger and weighted median analyses (Table S6). MR-Egger and MR-PRESSO tests showed that there is no horizontal pleiotropy or outliers (Fig. 2). In addition, the leave-one-out method revealed that no SNP was significantly associated with the outcome. Finally, bi-directional MR analyses showed that there is no evidence that lobar BMB affects gut microbiota (Table S6). The result of the MR Steiger directionality test also supports above conclusion (Table S6).
Causal effects of the gut microbiome on the deep infratentorial brain microbleeds.
In the set of SNPs (p < 1 × 10− 5), as shown in Fig. 3, IVW analyses show that phylum Proteobacteria, genus Oscillospira, order Desulfovibrionales and family Desulfovibrionaceae were causally related to a increased risk of deep infratentorial BMB (phylum Proteobacteria: OR [95% CI]: 2.28 [1.10, 4.72]; genus Oscillospira: OR [95% CI]: 2.21 [1.02, 4.80]; order Desulfovibrionales: OR [95% CI]: 1.90 [1.01, 3.58]; family Desulfovibrionaceae: OR [95% CI]: 2.04 [1.01, 4.13]). In contrast, class Bacilli was causally related to a decreased risk of deep infratentorial BMB (OR [95% CI]: 0.40 [0.20, 0.78]). No significant correlation was found between other gut microbiomes and deep infratentorial BMB (Table S3). In the set of SNPs (p < 5 × 10− 8), we found that order Gastranaerophilales was causally associated with deep infratentorial BMB (wald ratio, OR [95% CI]: 0.30 [0.10, 0.88]) (Table S5).
The results of the MR-Egger intercept test and MR-PRESSO global test showed that there were no horizontal pleiotropic effects and The Cochran Q test did not provide any evidence of heterogeneity (Fig. 3). Results from the weighted median method and MR-egger method also supported principal analyses (IVW), which was not significant (Table S7). And the results of the leave-one-out analysis showed that no matter which SNP was removed, it would not have a fundamental impact on the results (Figure S2). Finally, through the bi-directional MR analyses and MR Steiger directionality test, we found that there was no reverse causal relationship between the deep infratentorial BMB and gut microbiota associated with it (Table S7).