Bariatric surgery is the most effective treatment for weight loss. Vertical sleeve gastrectomy (VSG) involves the resection of ~ 80% of the stomach and was conceived to purely restrict oral intake. However, evidence suggests more complex mechanisms, particularly postoperative changes in gut microbiota, in facilitating weight loss and resolving associated comorbidities. VSG in humans is a complex procedure and includes peri-operative antibiotics and caloric restriction in addition to the altered anatomy. The impact of each of these factors on the intestinal microbiota have not been evaluated. The aim of this study was to determine the relative contributions of each of these factors on intestinal microbiota composition following VSG prior to substantial weight loss. Thirty-two obese patients underwent one of three treatments: (1) VSG plus routine intravenous peri-operative antibiotics (n = 12), (2) VSG with intravenous vancomycin chosen for its low intestinal penetrance (n = 12), and (3) caloric restriction (n = 8). Fecal samples were evaluated for bacterial composition prior to and 7 days following each intervention. Only patients undergoing VSG with routine peri-operative antibiotics showed a significant shift in community composition. Our data support the single dose of routine peri-operative antibiotics as the most influential factor of intestinal microbial composition acutely following VSG.