Baseline Gut Microbiome and Metabolite Profiles Associate with Treatment Response in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy

<b>Background/Objectives:</b> Response to neoadjuvant chemotherapy (NAC) varies substantially among breast cancer patients and is only partially explained by tumor-intrinsic factors. The gut microbiome has emerged as a potential modulator of chemotherapy efficacy, yet its role in breast cancer remains underexplored. This study aimed to characterize gut microbial composition, functional potential, and microbially derived metabolites in breast cancer patients undergoing NAC. <b>Methods:</b> baseline stool samples from 39 chemotherapy-naïve breast cancer patients undergoing NAC were analyzed using shotgun metagenomic sequencing and targeted metabolomics. Patients were stratified by pathological complete response (pCR, <i>n</i> = 17; no pCR, <i>n</i> = 22). Microbial taxonomic and functional profiles, short-chain fatty acids (SCFAs) and bile acids were assessed, with subgroup analysis performed in triple-negative breast cancer (TNBC). <b>Results:</b> Patients achieving pCR exhibited significantly higher baseline microbial richness compared to non-responders (<i>p</i> = 0.040). Differential abundance analysis revealed enrichment of <i>Dialister</i>, <i>Kineothrix</i>, and <i>Jutongia</i> in responders, whereas <i>Rothia</i>, <i>Leuconostoc</i>, <i>Klebsiella</i>, <i>Jingyaoa</i>, <i>Cuneatibacter</i>, <i>Youxingia</i>, and <i>Bittarella</i> were enriched in non-responders. SCFAs (acetate, propionate and butyrate) positively correlated with microbial glucose catabolic pathways, while caproate was negatively associated with multiple amino acid, lipid, vitamin, and cell wall biosynthesis pathways, including peptidoglycan maturation. Metabolomic analysis identified higher deoxycholic acid (DCA) levels in non-responders and increased C6 levels in responders, although these associations did not remain significant after multiple testing correction. Similar trends were observed in the TNBC subgroup (<i>n</i> = 15). <b>Conclusions:</b> Baseline gut microbiome diversity, taxonomic composition, and functional metabolic potential are associated with response to neoadjuvant chemotherapy in breast cancer, supporting the gut microbiome and its produced metabolites as a potential biomarker of treatment efficacy.