In the present study, the FMTs from patients with IBD caused colitis and depression in the transplanted mice: they induced the NF-κB+/Iba1+, LPS+/Iba1+ and IL-1R+ cell populations and IL-1β and IL-6 expression in the hippocampus and myeloperoxidase activity and IL-1β and IL-6 expression and suppressed tight junction protein expression in the hippocampus and colon. This evidence concerns the gene AIF1 and inflammatory bowel disease.