The human microbiome contains a vast array of microbes and genes that show greater complexity than the host's own karyome; the functions of many of these microbes are beneficial and show co-evolution with the host, while others are detrimental. The microbiota that colonises the gut is now being considered as a virtual organ or emergent system, with properties that need to be integrated into host biology and physiology. Unlike other organs, the functions that the gut microbiota plays in the host are as yet not fully understood and can be quite easily disrupted by antibiotics, diet or surgery. In this review, we look at some of the best-characterised functions that only the gut microbiota plays and how it interacts with the host's endocrine system and we try to make it clear that the 21st-century biology cannot afford to ignore this facet of biology, if it wants to fully understand what makes us human.