Microorganisms basically cover all the mucosal surface in their host: digestive, respiratory tissues and urogenital tracts, but it is the gastro intestinal tract (GIT) that has drawn most attention because of its important role in many aspects of the host function. The coexistence in an intimate and close way between multicellular life and its associated microbiota and its importance in host evolution is unmistakable. The dynamic and complex interactions between the microbiota and its host have been formed through evolution in all larger organisms. The metagenome of host microbiota has a large genetic potential with a genome with more orders of magnitude than their host genome itself. However, it is vastly ignored or unknown. Host gut microbiome (the diversity of commensal microbes that colonize gut host) has the potential to answer some of the questions that were raised after genetics and genomics studies of multicellular organisms.