Growing evidence suggests that alterations of gut microbial composition and function result in an increasing risk of ulcerative colitis. The present study investigated whether microbial imbalance is the causal factor and how it contributes to the intestinal disorder in colitis using a dextran sulfate sodium (DSS)-induced experimental colitis rat model plus fecal microbiota transplantation (FMT). Based on the 16s rRNA sequencing data, our findings support that alteration of gut microbiota is a causing factor and contribute to colitis development.