AbstractBackgroundGut microbiota plays a role in the pathophysiology of ischaemic stroke (IS) through the bidirectional gut–brain axis. Nevertheless, little is known about sex‐specific microbiota signatures in IS occurrence.MethodsA total of 89 IS patients and 12 healthy controls were enrolled. We studied the taxonomic differences of the gut microbiota between men and women with IS by shotgun metagenomic sequencing. To evaluate the causal effect of several bacteria on IS risk, we performed a two‐sample Mendelian randomisation (MR) with inverse‐variance weighting (IVW) using genome‐wide association analysis (GWAS) summary statistics from two cohorts of 5959 subjects with genetic and microbiota data and 1,296,908 subjects with genetic and IS data, respectively.Resultsα‐Diversity analysis measured using Observed Species (p = 0.017), Chao1 (p = 0.009) and Abundance‐based Coverage Estimator (p = 0.012) indexes revealed that IS men have a higher species richness compared with IS women. Moreover, we found sex‐differences in IS patients in relation to the phylum Fusobacteria, class Fusobacteriia, order Fusobacteriales and family Fusobacteriaceae (all Bonferroni‐corrected p < 0.001). MR confirmed that increased Fusobacteriaceae levels in the gut are causally associated with an increased risk of IS (IVW p = 0.02, β = 0.32).ConclusionsOur study is the first to indicate that there are gut microbiome differences between men and women with IS, identifying high levels of Fusobacteriaceae in women as a specific risk factor for IS. Incorporating sex stratification analysis is important in the design, analysis and interpretation of studies on stroke and the gut microbiota.