ObjectiveTo investigate the effect of Roux-en-Y gastric bypass (RYGB) on the composition of intestinal microbiota among the biliopancreatic limb, the Roux limb, and the common channel in normal Sprague-Dawley (SD) rats. MethodsSixteen SD rats were randomly divided into sham surgery group (Sham group) and RYGB group, each group enrolled 8 rats. Rats in Sham group underwent sham surgery of end to end anastomosis in situ after cutting off the stomach and jejunum, and rats in RYGB group underwent RYGB. Then quantitative real-time PCR (RT-PCR) method was used to detect the expression of total bacteria, Bifidobacterium, Bacteroides, and Lactobacillus mRNA at biliopancreatic limb, the Roux limb, and the common channel. At last the comparison of mRNA in 4 kinds of bacteria was performed. ResultsCompared with Sham group, the weight of rats in RYGB group was lower at 8 weeks after surgery (P<0.01). RT-PCR results showed that, expression levels of total bacteria, Bifidobacterium, and Bacteroides mRNA at the Roux limb and the common channel in RYGB group were higher than corresponding site of rats in Sham group (P<0.05), but there was no significant difference at biliopancreatic limb between the 2 groups (P>0.05). Expression level of Lactobacillus mRNA at the Roux limb in RYGB group was higher than corresponding site of rats in Sham group (P<0.05), but there was no significant difference at biliopancreatic limb and the common channel between the 2 groups (P>0.05). ConclusionRYGB can significantly improve expression levels of the total bacteria, Bifidobacterium, and Bacteroides mRNA at Roux limb and the common channel, increase the level of Lactobacillus mRNA at Roux limb, while has no influence on biliopancreatic limb.