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Gut microbiota plays an important role in health and disease, but this ecosystem remains incompletely characterized and shows a wide diversity. This review discusses new findings that may explain how gut microbiota can be involved in the control of energy and metabolic homeostasis.Over the past 5 years studies have highlighted some key aspects of the mammalian host–gut microbial relationship. Gut microbiota could now be considered a ‘microbial organ’ placed within a host organ. Recent data suggest that the modulation of gut microbiota affects host metabolism and has an impact on energy storage. Several mechanisms are proposed that link events occurring in the colon and the regulation of energy metabolism.Gut microflora may play an even more important role in maintaining human health than previously thought. The literature provides new evidence that the increased prevalence of obesity and type 2 diabetes cannot be attributed solely to changes in the human genome, nutritional habits, or reduction of physical activity in our daily lives. One must also consider this important new environmental factor, namely gut microbiota. Scientists may take into consideration a key question: could we manipulate the microbiotic environment to treat or prevent obesity and type 2 diabetes? This opens up a new area in nutrition research.