Obesity has become an emerging global issue responsible for an increased risk of cardiovascular diseases and cancer. Gut microbiota is one of biological factors involved in the pathogenesis of obesity and metabolic disorders. Microbiome alteration has been associated with chronic endotoxemia and microinflammation, insulin resistance and hyperinsulinemia – factors playing an important role in the development of metabolic disorders such as non-alcoholic steatohepatitis (NASH), diabetes mellitus (DM) and dyslipidemia. Bariatric interventions are an important part of obesity treatment. Surgical interventions are the most effective procedures. Endoscopy assisted techniques (intragastric balloon or duodenal-endoluminal sleeve) are also very promising, clinically tested procedures. Dietary interventions changing gut microbiota are more frequently used. However, our knowledge about the mechanisms of weight loss triggered by these interventions is incomplete. Recent experimental and clinical studies provide novel data that bariatric surgery modulates intestinal microbiome and changes its potential of energy harvest in the gut. Surgically altered microbiota in the short term exert profound but beneficial metabolic effects in humans. However, long-term consequences of such modulation are unknown. Recent data from randomized clinical trials support the notion that dietary interventions and supplementation of pre- and probiotics favorably modulate gut microbiota and augment weight loss after bariatric procedures.