Metagenomic analyses reveal E. coli-derived siderophores as potential signatures for breast cancer

Background Breast cancer remains the leading cause of cancer-related mortality among women, highlighting the urgent need for novel insights into its biology. Recent evidence suggests the gut microbiome and its metabolites may play a role in breast cancer pathogenesis. This study investigates the gut microbiome and its predicted metabolite profiles in breast cancer patients to uncover potential mechanistic links. Methods Comprehensive metagenomic analyses were conducted on the gut microbiome of pre and postmenopausal breast cancer patients where microbial species were profiled through AMPHORA2 and metabolites were predicted through antiSMASH. Multivariate association analysis (MaAsLin2) was used to identify significant associations between specific microbial species, predicted metabolites, and breast cancer status. A custom ensemble machine learning classifier was developed to classify pre- and postmenopausal breast cancer cases and controls based on microbial and predicted metabolite features. Additionally, a synthetic microbiome dataset was generated through MIDASim to validate the reproducibility of the ML results. Furthermore, we proposed the underlying mechanism of E. coli- siderophore in breast cancer through literature and statistical support. Results Our analysis profiled 471 microbial species and predicted 40 key metabolites in the metagenomic data. Statistical analysis identified significant positive associations (p-value < 0.05) of E. coli , siderophore, and thiopeptide production, with breast cancer. The custom ensemble model achieved accuracy and AUC as high as 78% and 90%, respectively, in classifying pre and postmenopausal cases and controls. The high-ranking features, including E. coli , siderophore, and thiopeptide, supported the statistical findings and reinforced their biological relevance. Lastly, we propose a mechanistic model in which E. coli secretes siderophores under iron-limiting conditions, facilitating iron sequestration from the host, that can potentially promote angiogenesis and tumor progression. Conclusion Our findings suggest that microbial iron acquisition mechanisms could be critical in breast cancer pathophysiology. Further functional analyses are warranted to validate the proposed mechanisms and assess their therapeutic potential. This study highlights the gut microbiome and its predicted metabolites as promising targets for breast cancer treatment, offering new directions for research and clinical intervention.