Background: Intestinal bacteria are closely related with inflammatory bowel disease (IBD), and regulatory cell-mediated immune tolerance is important to inhibit IBD. Commensal intestinal bacteria play key roles in regulating immune tolerance cell, however, bacterial strains directly involved in this regulation remain to be identified.Results: In the present study, metronidazole, among nine antibiotics, was found to have the best effect on protecting mice against DSS-induced colitis. Enterobacter ludwigi, abundant in mouse feces after metronidazole treatment, was identified to decrease mice susceptibility to DSS-induced colitis with or without the presence of complex intestinal bacteria. E. ludwigii gavage increased CD103+DCs and Foxp3+Treg cells in intestinal microenvironment, and effects of E. ludwigii on diminishing colitis were lost in DC or Treg depletion mice. CD103+DCs isolated from E. ludwigii-treated mice showed enhanced ability to promote the Treg differentiation from naive T cells. DCs, directly stimulated by live E. ludwigii strain or its culture supernatant, had increased immune tolerance ability for Treg differentiation in vitro. Conclusions: Overall, our findings identify a facultative anaerobe bacterial strain E. ludwigii, which directly enhances CD103+DC and Treg-mediated immune tolerance, resulting in protecting mice against DSS-induced colitis.