The relationship between microbiome and metabolomics by studying the microbiota living in the human body and studying their effects on the concentration of metabolites, also to study effects of microbiota colonization on other bacteria or living organism entering the body. These microbiomes and metabolites not only act as an energy source for whole body organs but can also play a role in causing diseases as they affect beyond the gut. It is compulsory to understand the relationship of the microbiome with the food nutrients we take in. So, we will be able to improve the health by making some changes in dietary intake according to gut microorganisms. In this study, we observed the relationship of microbiome and the metabolomics they are involved in, with diseases related to them. As the number of metabolites in human body is an indicator of colonized number of microbiota and development of a disease related to it.