Evidence suggests a relationship between the obesity phenotype and the gut microbiome. This study investigated the effect of bariatric surgery on changes to gut microbiota composition and related metabolites and pathways, as well as the relationship of these to metabolic parameters following surgery. Microbial composition by 16S rRNA gene sequencing and circulating biomarkers of inflammation and microbial metabolism were studied in subjects with severe obesity before and 3 ,6, and 12 months after surgery. We observed that bariatric surgery persistently increases alpha diversity and alters microbiota composition and putative function up to one year after surgery. Network analysis identified groups of bacteria significantly correlated over time with levels of circulating metabolites. The association between changes in microbiome with decreased circulating biomarkers of inflammation, increased bile acids and products of choline metabolism suggest that the microbiome may, in part, mediate improvement of metabolism following bariatric surgery.