Background Changes in the gut microbiome following bariatric surgery have been causally linked to metabolic benefits. Objectives We sought to characterize and assess the stability of gut microbiome shifts following sleeve gastrectomy (SG). Setting University laboratories. Methods Diet-induced obese mice were randomized to SG or sham surgery. Mice were housed individually or cohoused such that one SG mouse was housed with one weight-matched, sham-operated mouse. Fecal samples were collected before and on postoperative days 7 and 28. Bacterial composition in feces was characterized by using next-generation Illumina sequencing of 16 S rRNA. Results SG mice lost more weight and were more insulin sensitive than sham mice independent of housing status (P<.05). One week following surgery, fecal samples from all mice showed shifts in the microbiome that only persisted in SG-operated mice. Cohousing did not alter the microbial composition of SG-operated mice. Cohoused sham-operated mice showed a unique shift in microbial composition on postoperative day 28 that differed from individually housed, sham-operated mice (P<.001). Cohousing did not affect metabolic outcomes of either SG or sham surgeries. Conclusion SG results in acute and sustained shifts in the gut microbiome. SG associated shifts are not altered by reexposure to obesity-associated gut microbiota.