Functional analysis based on all differential genera identified 19 MetaCyc signaling pathways, twelve of which were significantly enriched in BC patients by containing 165 genes Top-ranked 10 genes mdh, pykF, gapA, zwf, pgi, tpiA, pgk, pfkA, ppsA, and pykA were identified as BC-causing bacterial key genes (bKGs) through protein-protein interaction network analysis. This evidence concerns the gene MDH2 and breast cancer.