is a commensal microorganism in the human gut but occasionally causes invasive infection (ICA), especially in immunocompromised individuals. Early initiation of antifungal therapy is associated with reduced mortality of ICA, but rapid diagnosis remains a challenge. The ICA-associated changes in the gut microbiota can be used as diagnostic and therapeutic targets but have been poorly investigated. In this study, we utilized an immunodeficient Rag2γc (-/--/-) mouse model to investigate the gut microbiota alterations caused by throughout its cycle, from its introduction into the gastrointestinal tract to invasion, in the absence of antibiotics. We observed a significant increase in the abundance of , particularly and , as well as a significant decrease in the abundance of in mice exposed to either the wild-type SC5314 strain or the filamentation-defective mutant () HLC54 strain of . However, only the SC5314-infected mice developed ICA. A linear discriminate analysis of the temporal changes in the gut bacterial composition revealed as a discriminative biomarker associated with SC5314-infected mice with ICA. Additionally, a positive correlation between the abundance and fungal load was found, and the negative correlation between the abundance and fungal load after exposure to suggested that might affect the differentiation of intestinal Th17 cells. Our findings reveal the influence of pathogenic on the gut microbiota and identify the abundance of as a microbiota signature associated with ICA in an immunodeficient mouse model.