Description of the role that the microbiota may play in human health, energy harvest, and obesity. The adult human gut may contain up to 100 trillion microbial organisms, known as the microbiota. Major advances in defining the quality, quantity, and physiologic activity of the intestinal microbiota were precipitated by the conversion from culture-based techniques to metagenomics. The microbiota may serve various functions including promoting development of the human immune system, modulating inflammation, and affecting calorie extraction. Recent evidence, in humans and animal models, supports a role for the microbiota in obesity. Not only is the presence of bacteria important, but also the relative proportions of microbial communities, specifically Firmicutes and Bacteriodetes, appear to be important in energy homeostasis. The microbiota may also affect the immune and inflammatory response in human organisms. Although there is limited data supporting the manipulation of the gut microbiota, using probiotics, antibiotics, and/or prebiotics to treat obesity, novel therapeutic agents may be developed.