Obesity is an enormous public health problem, arising from the abundance of food, eating behavior, and body regulation on energy intake, expenditure, and storage. Recent evidence suggests that the gut microbiota may play a role in obesity by increasing the host's energy-harvesting efficiency. Obesity surgery, a well-accepted tool for weight reduction, contributes to alterations in gut microbiota through anatomical changes and through modifications of dietary components. The mechanisms of the microbiome activity consist of modulating the host metabolism, inflammatory processes including insulin resistance, and by affecting the endocrine and the nervous systems.The type of bacteria present in the gut regulates fatty acid metabolism by using specific short chain fatty acids as metabolites. Bacterial fermentation of dietary fibers producing these fatty acids turns the dietary fibers into mediators for bacterial communication with the organs, thereby modulating the host metabolism. Bariatric surgery changes the ratio of microbiome components. Studies suggest that there is not only a starvation-like adaptation of the gut microbiota but also a change in the relative abundance of different bacteria that are associated with metabolic and inflammatory processes. These changes were found at three months post-surgery, and are persistent at longer follow-ups, indicating a stable gut modification.The literature review presented may suggest that specific analysis of the microbiota can help in selecting the preferred type of surgery and the prospect of surgery success in terms of long term weight reduction. We thought it would be beneficial for scientists interested in obesity to enrich their knowledge about the highlights of the relations between the microbiota and obesity, and more specifically with that of bariatric surgery.