The human microbiome is the collective genomes of all microorganisms living at the multiple sites of the human body (oral and nasal cavity, skin, gastrointestinal tract (GI) and vagina). Human (Homo sapiens) and their commensal microorganisms have evolved together over the last 200,000 years and have become dependent on one another. Interaction between humans and their symbiotic microbiota is essential to many aspects of normal ‘mammalian’ physiology, ranging from metabolic activity to immune homeostasis. Ecological or genetic changes that disturb this mutualism can result in disease. It reflects the evolutionary selection pressures acting at both the levels of the host and the microbial cells and has a direct profound impact on human health. The commensals include eubacteria, archaebacteria, viruses and fungi, which together form the human microbiome.