Taxonomic, predicted functional, and network-based characterization of the breast cancer-associated gut microbiome

Gut microbiome dysbiosis has emerged as a non-genetic risk factor in breast cancer (BC), yet the taxonomic, predicted functional, and microbial association patterns of the gut microbiome in BC remain incompletely understood. This study aimed to provide a combined taxonomic, predicted functional, and network-based characterization of the gut microbiome in BC using publicly available 16 S rRNA sequencing data. Publicly available 16 S rRNA V4 sequencing data from PRJNA658160 were analyzed with 804 fecal samples, including 386 BC samples and 418 healthy controls. Taxonomic profiling was performed, and predicted pathway profiling was conducted with PICRUSt2. Diversity, differential abundance, and network analyses were performed at both the genus and predicted pathway levels. Taxonomic differential abundance was evaluated using ANCOM-BC2, pathway differences using LinDA, taxonomic networks using SPIEC-EASI, and predicted pathway association networks using Spearman correlation. BC samples exhibited significantly reduced taxonomic alpha diversity, whereas genus-level beta diversity showed no strong global separation between groups. 13 genera were differentially abundant; Bacteroides , Erysipelatoclostridium , Parabacteroides , and Fusobacterium were enriched in BC, whereas Prevotella , Alloprevotella , and Coprococcus were more abundant in healthy controls. Exploratory network analysis identified Bacteroides as a prominent hub-like taxon and Erysipelatoclostridium as a bridge-like taxon in the BC inferred association network. Predicted functional analysis indicated reduced pathway alpha diversity and identified 130 differentially abundant predicted pathways. BC-enriched predicted pathways were mainly associated with carbohydrate degradation, the glyoxylate cycle, fatty acid β-oxidation, and stress-related metabolism, whereas control-enriched predicted pathways were associated with menaquinone biosynthesis, biotin biosynthesis, fermentation, and broader biosynthetic functions. Predicted pathway beta diversity also differed significantly between groups (PERMANOVA R² = 0.013, p = 0.001); however, beta-dispersion was significantly greater in BC samples, indicating that this difference may partly reflect increased within-group heterogeneity rather than only a shift in group centroids. Because PICRUSt2 infers pathway abundance from 16 S rRNA gene profiles, these pathway-level findings represent predicted functional potential rather than confirmed functional activity. BC-associated gut microbiome dysbiosis appears to involve selective genus-level alterations, descriptive differences in inferred microbial association patterns, and broader predicted pathway-level shifts rather than complete community replacement. These findings highlight candidate microbial and pathway-level signatures that require validation using shotgun metagenomics, metabolomics, and independent cohorts.