BACKGROUND: The objective of the study was to compare gut microbiota post Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG). METHODS: Sprague-Dawley rats were randomized to RYGB, SG, or sham surgery. Body weight was measured. Fecal samples were collected before and 1, 3, 6, and 9 weeks postoperatively. Fecal microbiota was profiled by 16S ribosomal DNA gene sequencing and analyzed using Quantitative Insights into Microbial Ecology (QIIME) to determine the α and β diversities of gut microbiota. RESULTS: The body weight of the RYGB and SG group was significantly lower than that of the sham group. Unweighted UniFrac-based principal coordinate analysis of 5,323,091 sequences from 85 fecal samples from 17 rats revealed a distinct cluster of gut microbiota post RYGB from SG and sham surgery. The percentage of Proteobacteria in the SG and sham group remained markedly lower than that of the RYGB group from 3 weeks postoperatively, while the proportion of Gammaproteobacteria in the RYGB group was significantly higher than that of the SG group and the sham group from 3 weeks postoperatively. Furthermore, the RYGB group was postoperatively enriched for Gammaproteobacteria and Bacteroidaceae, whereas the SG group was postoperatively enriched for Desulfovibrionaceae and Cyanobacteria. Compared to the pre-operative parameters, the RYGB group had a persistent increase in the relative abundance of Gammaproteobacteria and a decrease in the Shannon index, while the SG group only transiently exhibited these changes within the first week after surgery. The relative abundance of Gammaproteobacteria was negatively correlated, whereas the Shannon index was positively correlated with weight after surgery. CONCLUSIONS: RYGB, but not SG, alters the gut microbiota of Sprague-Dawley rats. RYGB also reduces the diversity of gut microbiota. Furthermore, the abundance of Gammaproteobacteria negatively correlates with postoperative body weight and may be one of the potential contributors to stable weight loss after bariatric surgery.