The global prevalence of obesity is greater in women compared to men. The gut microbiome is implicated in the sexual dimorphic nature of metabolic disease development. Understanding how the composition and function of the gut microbiome differs between sexes and determining the factors that regulate these differences is critical to develop improved gut-based therapeutic strategies to improve metabolic health for all. Here, we identify Bacteroides thetaiotaomicron (Bt) as a probiotic that associates with insulin sensitivity and report its beneficial effects on fortifying the gut epithelium and improving host metabolism when it is supplemented in HFD-fed female mice. This work highlights the therapeutic potential of leveraging the gut microbiome to improve metabolic health outcomes for women.