In total, 13 taxa differed between those with HER2+ vs. HER2− tumours (p ≤ 0.001), 3 taxa between ER+ and ER− tumours, and 2 taxa between PR+ and PR− tumours.No significant α-diversity or phyla composition by ER/PR status, tumour grade, stage, parity, and body mass index, but had significant relationships with HER2 status and age at menarche.HER2+ vs. HER2− BC showed 12–23% lower α-diversity (p = 0.034), revealing low Firmicutes (p = 0.005), and high Bacteroidetes (p = 0.089). This evidence concerns the gene PGR and breast cancer.