Technically the term refers to the combined genetic material of all the microbes in a particular environment, but the term is commonly used to simply describe all those microorganisms (the Microbiota is the correct term for the whole living organism collection, as opposed to their genetic material or genome).  The environment can include parts of the body such as the skin, ear, mouth, digestive tract etc.

Identification of the vast diversity of microbes in different microbiomes has been made possible by advances in gene sequencing technology. The ‘’Core Microbiome’’ is a concept referring to groups or families of microbes normally occurring in a host species microbiome. So, for example there may be a core microbiome specific to the caecum of most normal horses fed on pasture based diets. Changes to the microbiome may signal or precede some disease processes and there may be some potential in future to manipulate aspects of the microbiome to exert a beneficial effect. The different microbiomes of the horse are as yet poorly understood and much commentary on the subject is extrapolated from human research which may or may not be applicable.

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