Gut microbiome has been analysed using metagenomics approach which combines the power of genomics, bioinformatics, and systems biology, providing new ways to access the microbial world. Gut microbiome evolves from the pre-birth exposure onwards in a child, as a result of its interaction with its environment; and is apparently influenced by various environmental factors all through the life, most important being diet and its composition. Metagenomic analysis of gut microbial communities of a malnourished and a healthy child revealed an abundance of enteric pathogens leading to intestinal inflammation and nutrient malabsorption. The change in diet from vegetarian to non-vegetarian also influences the composition and dynamics of the intestinal microbes. Gut microbiota have been observed to vary with age due to physiological changes in the gastrointestinal tract, modifications in lifestyle, nutritional behavior and weakened functionality of the host immune system. Studies in apparently healthy individuals and patients suffering from intestinal or metabolic disorders revealed differential microbiome compositions, proving that an imbalance of gut microflora leads to dysbiosis which is the major cause of metabolic disorders such as irritable bowel syndrome (IBS), obesity, diarrhea, etc. The investigational studies are trying to assess the relationship between intestinal microbiota dysbiosis and various metabolic diseases. Nutritional interventions in the form of probiotics and prebiotics as investigational new drugs (INDs) are being assessed for correcting dysbiosis in disease states. The current paper focuses on the recent knowledge and databases for the same with pointers to future investigations as the need of the hour studies.