Through the integrated analysis of untargeted metabolomics and 16S rDNA sequencing data, we explored the mechanism of improvement of glucose and lipid metabolism disorders in pre-DM mice, which may be regulated through the Lactococcus–TCA/TCDCA–FXR–CYP7A1 and Lactococcus–LCA–TGR5–GLP-1 axes. The gene discussed is NR1H4; the disease is Disorder of lipid metabolism.