Obesity, a worldwide health concern with a constantly rising prevalence, is a multifactorial chronic disease associated with a wide range of physiological disruptions, including energy imbalance, central appetite and food reward dysregulation, and hormonal alterations and gut dysbiosis. The gut microbiome is a well-recognized factor in the pathophysiology of obesity, and its influence on host physiology has been extensively investigated over the last decade. This review highlights the mechanisms by which gut dysbiosis can contribute to the pathophysiology of obesity. In particular, we discuss gut microbiota’s contribution to host energy homeostatic changes, low-grade inflammation, and regulation of fat deposition and bile acid metabolism via bacterial metabolites, such as short-chain fatty acids, and bacterial components, such as lipopolysaccharides, among others. Finally, therapeutic strategies based on next-generation probiotics aiming to re-shape the intestinal microbiota and reverse metabolic alterations associated with obesity are described.