Current nutrition research is focusing on health promotion, disease prevention and physical performance improvement and adjuvant therapeutic approach for individuals and communities around the world. The provision of humans with required nutritional ingredients depends on both how well the individual is provided with balanced foods and what state of gut microbiota the host has. Studying the mutually beneficial relationships between gut microbiome and host is drawing ever-increasing attention in biomedical science. Increasing biome-based evidences show that gut microbiota can affect host energy balance, especially fat deposition and lipid metabolism. Our previously study demonstrated that increased gluconeogenesis from non-carbohydrate carbon backbone and glycogenesis lead to abnormal energy metabolism and excessive glycogen accumulation in the liver of gut microbiota-lacking mice. In addition, many studies have been reported that gut microbiota regulates host energy balance by potential important mediators such as fasting-induced adipose factor and short-chain fatty acids. Therefore, this literature review will introduce how gut microbiota affects the nutrition and biochemical pathways in the host and its roles on the metabolic diseases development.