From these two sub-networks, these eight novel lncRNAs (4930417H01Rik, AI480526, 5930412G12Rik, 6430628N08Rik, A530013C23Rik, A930007I19Rik, Gm15489, and Gm16251), two miRNAs (mmu-miR-883b-3p and mmu-miR-377-3p) and five mRNAs (Adcy1, Nr4a2, Six4, Stx16, and Ube3a) were speculated as key molecules in gut microbiota-dysbiosis-induced depression, and these molecules could be recognized as potential genetic and epigenetic biomarkers in microbial-associated depression. Here, NR4A2 is linked to major depressive disorder.