In order to verify the effects of FMT and Lactobacillus transplantation on the composition of gut microbiota in PCOS rats, PCOS rats were treated with FMT or Lactobacillus and the bac-teria described above were examined. As showninTable2,on day 36,the copy number of Lactobacillus and Clostridium were increased in both FMT group and Lactobacillus transplantation group, to levels similar to that of the control group. The abundance of Prevotella was decreased in both treated groups and the changes in FMT group were more significant than that in Lactobacillus transplantation group. Though Prevotella in both groups still have significant differences with the control, it decreased significantly when compared with the PCOS group. There were no significant differences in the copy number of Bifidobacterium, Escherichia coli ,Enterococcus, Bacteroides and Ruminococcus in the two treated groups when compared with PCOS group. These data indicated that PCOS resulted in a significant variation of gut microbiota composition. Both FMT and Lactobacillus transplantation were beneficial for restorations of normal gut residents in letrozole induced PCOS rats.