BACKGROUND: Roux-en-Y gastric bypass (RYGB) surgery is one of the most efficient procedures for treating morbid obesity and results in weight-loss and improvements in metabolism and inflammation. OBJECTIVE: We examined the impact of RYGB on modifications of gut microbiota and its potential associations with changes in gene expression in white adipose tissue (WAT). DESIGN: Gut microbiota were profiled from fecal samples by using pyrosequencing in morbidly obese individuals, explored before (0 mo), 3 mo after, and 6 mo after RYGB. WAT gene expression was studied at 0 and 3 mo. We explored associations between microbial genera and differentially expressed genes in WAT and clinical markers. RESULTS: The richness of gut microbiota increased after RYGB; 37% of increased bacteria belonged to Proteobacteria. The associations between gut microbiota composition and WAT gene expression increased after RYGB. Fourteen discriminant bacterial genera (7 were dominant and 7 were subdominant) and 202 WAT genes changed after RYGB. Variations in bacterial genera correlated with changes in both clinical phenotype and adipose tissue gene expression. Some genes encode metabolic and inflammatory genes. Almost half of the correlations were independent of the change in calorie intake. CONCLUSION: These results show an increase in gut microbiota richness and in the number of associations between gut microbiota and WAT genes after RYGB in obesity. Variations of gut microbiota were associated with changes in WAT gene expression. These findings stimulate deeper explorations of the mechanisms linking gut microbiome and WAT pathological alterations in human obesity and its changes after weight loss.