Abstract Background Upon migrating to the injured sites, bone marrow mesenchymal stem cells (BMSCs) play critical roles in the repair of bone lesion caused by chronic apical periodontitis. Emerging evidences have shown that Enterococcus faecalis is always associated with apical periodontitis, especially refractory apical periodontitis. But the mechanism underlying how Enterococcus faecalis affects the migration of BMSCs remains unclear. Methods The effects of Enterococcus faecalis supernatants on the migration of BMSCs were determined by transwell migration assays. miRNA sequencing was performed to detect the significantly differentially expressed miRNAs of BMSCs. Proteomics analysis was used to detect the protein expression alterations of BMSCs. Luciferase report assays were deployed to verify the targets of miRNA. Western blot analysis was performed to examine the expressions of matrix metalloproteinases-3, matrix metalloproteinases-9, Forkhead Box Protein J1 (FOXJ1), and nuclear factor kappa B (NFκB). The activations of NFκB were detected by luciferase assays with NFκBluc reporter. Results We found that Enterococcus faecalis supernatants could promote the migration of BMSCs. The upregulation of miR-200a-3p in this process contributed to BMSC migration through downregulating its target Forkhead Box Protein J1. Moreover, FOXJ1/ NFκB axis was found to regulate matrix metalloproteinases (MMPs) in this process. Conclusions These results above suggest that miR-200a contributes to the migration of BMSCs induced by the secretions of E. faecalis via FOXJ1/NFκB/MMPs axis. Keywords: Bone marrow mesenchymal stem cells, Cell migration, Nuclear factor kappa B, Enterococcus faecalis, miRNA, Host-pathogen interactions Background Apical periodontitis, which is characterized by the inflammation and destruction of the apical periodontium, is always caused by the host immune response to microbial infection in the root canal system [[35]1]. Those species originated from intestinal flora, such as E. faecalis, have been identified as dominant factors causing apical periodontitis [[36]2]. E. faecalis is always isolated as a monoculture in retreated root canals [[37]3]. It belongs to facultative aerobic species and is usually found in secondary infection or post-treatment of apical periodontitis, especially in the refractory inflammation [[38]4]. E. faecalis is tolerated to antimicrobials and contains the ability of surviving in a nutrient-deficient environment. Thus, persisting infections in root canal or apical periodontium are always associated with E. faecalis [[39]5]. There are various virulence factors produced by E. faecalis, such as lipoteichoic acid, aggregation substance protein, and surface adhesion [[40]6, [41]7]. During the development of pulpitis, E. faecalis can invade and colonize at dentinal tubules. Studies on the etiology of refractory apical periodontitis have revealed that E. faecalis biofilms in the dentinal tubules contribute to the retaining of apical periodontitis [[42]8]. Since apical periodontitis is characterized by inflammation and bone resorption [[43]9], cells associated with this process should be carefully taken into consideration. Belonging to multipotent stem cells and widely presenting in bone marrow, bone marrow mesenchymal stem cells (BMSCs) can differentiate into osteoblasts, chondrocytes, or adipocytes [[44]10]. Meanwhile, BMSCs have shown certain ability of moving from niche to the peripheral circulation, and further to the target tissues [[45]11]. The recruitment of BMSCs is required for the repair of bone lesion, and the migration of BMSCs is usually attracted by the environmental factors at the site of injury [[46]12]. There are various factors gathering at the injury, including infectious factors and those produced by injured tissues. With bacterial infection, BMSCs contact with bacterial components and recognize them through the receptors on the cell membrane. Studies on human BMSCs have revealed that lipopolysaccharide (LPS), the cell wall component from gram-positive bacteria, can increase their migration [[47]13], while the synthetic lipopeptide could inhibit the migration of mouse BMSCs [[48]14]. The migration of human dental pulp stem cells were also increased with the stimulation of Toll-like receptor 2 (TLR2) ligands [[49]15]. Studies above remind us that it depends on the type of mesenchymal stem cell in which migration effect would be caused by bacterial components. In fact, it is hard to ensure the regeneration of the tissue without the efficient migration of BMSCs into the injured sites. It requires more acknowledgments in this field to induce BMSCs