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Breast cancer patients frequently experience debilitating cancer-related fatigue (CRF) during chemotherapy. Emerging evidence implicates the gut microbiota (GM) and the gut-brain axis in CRF pathogenesis, yet whether pre-chemotherapy GM profiles can predict CRF remains unclear. This prospective cohort study enrolled 100 breast cancer patients initiating chemotherapy. GM profiling and fatigue assessment (Visual Analogue Fatigue Scale, Cancer Fatigue Scale) were performed at baseline and the third chemotherapy cycle. Serum levels of neuroimmune-endocrine markers were also measured. Multivariate logistic regression was used to build a predictive model for moderate-to-severe CRF. Patients experiencing moderate-to-severe CRF at the third chemotherapy cycle demonstrated higher baseline Baseline GM characteristics predict the risk and severity of chemotherapy-induced CRF, potentially through modulation of neuroimmune-endocrine pathways via gut-brain axis. These findings underscore the potential role of GM as a predictive biomarker and a therapeutic target for chemotherapy-induced CRF.