Abstract

A staggering amount of microbes lives in a close association with eukaryotic organisms and they play key role in the evolution and functioning of the host. The microbiome concept, i.e. the collection of commensal, symbiotic, and pathogenic microorganisms living in association with a given host, was first used in the context of microorganisms sharing the human body space, and after that several other authors have used this term in other mammals, insects or plants. The human microbiome significantly contributes to the human metabolism, and provides traits that humans did not need to evolve on their own. The set of genes present in the microbiome can be considered as the secondary genome of the host. The same view can be transported to other mammals, as ruminants, or even plants, which also rely in their microbiome for specific traits. Here, we will discuss how metagenomics has shed light on understanding of the microbiomes as being the connecting layer placed between the host a nd the environment mediating a range of host physiological process, and ultimately impacting on health and disease providing life support for the host.