The term “microbiome”, was coined by microbial ecologists, combining the word “microbe” and the word “biome” – with the latter meaning “community of organisms in a certain environment”. Purpose of this was to describe better microbial communities living at the same place under the same environmental conditions. In general, microbiome is defined as “collection of all microbial genes” (or “collection of all microbial genetic material”) found in a certain environment.
Another term, often found in similar context as microbiome, is “microbiota” – meaning “collection of all microbes in a certain environment”. Strictly speaking, these two are not to be confused because in a given sample we could have more microbial genes than known microbial species. Remember, there are many microbial species which we don´t know! Therefore, microbiome is somewhat broader term than microbiota.*
Microbiomes (as well as microbiota) are often named based on the type of the host organism (human, plant or animal) or the organ where they are found such as gut, skin, root, etc.
The debate which microbiome definition is the “correct” one is still ongoing and we won´t go here into the details. Anyway, mixed microbial communities are found everywhere on this planet: on- and in- human bodies, animals and plants as well as in soil, in air and in water. Without them, our life and life on Earth would not be possible.
*Author´s note: it´s a common mistake in the literature that the terms “Microbiome” or “Microbiota” were coined by the Nobel laureate Joshua Lederberg. Indeed, the word “Microbiota” doesn´t appear a single time in his often cited 2001 article (Lederberg J, McCray AT. Ome sweet omics: a genealogical treasury of words. Scientist 2001;15:8.) and the term “Microbiome” can be traced many times earlier, back to 1988. More details can be found in the 2017 article by Susan L. Prescott – History of medicine: Origin of the term microbiome and why it matters…