Microbiome

A microbiota is an "ecological community of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. A microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host. The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.

The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genomic characteristics, sometimes collectively referred to as a holobiont. The beneficial microorganisms are involved in human health and well being.

All plants and animals, from protists to humans, live in close association with microbial organisms (see for example the human microbiome). Up until relatively recently, however, biologists have defined the interactions of plants and animals with the microbial world mostly in the context of disease states and of a relatively small number of symbiotic case studies. Organisms do not live in isolation but have evolved in the context of complex communities. A number of advances have driven a change in the perception of microbiomes, including:

Increasingly, biologists have come to appreciate that microbes make up an important part of an organism's phenotype, far beyond the occasional symbiotic case study.

Commensalism, a concept developed by Pierre-Joseph van Beneden (1809-1894), a Belgian professor at the University of Louvain during the nineteenth century is central to the microbiome, where microbiota colonize a host in a non-harmful coexistence. The relationship with their host is called mutualistic when organisms perform tasks that are known to be useful for the host,parasitic, when disadvantageous to the host. Other authors define a situation as mutualistic where both benefit, and commensal, where the unaffected host benefits the symbiont. A nutrient exchange may be bidirectional or unidirectional, may be context dependent and may occur in diverse ways. Microbiota that are expected to be present, and that under normal circumstances do not cause disease, are deemed normal flora or normal microbiota.

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