The gastrointestinal tract is indispensable for an animal's well-being. Food is consumed through the mouth and digested by host enzymes in the stomach and small intestine, and nutrients are extracted and absorbed in the small and large intestines. In this nutrient-rich environment, microorganisms can colonize and grow, and as a result, numerous interactions or symbioses between microorganisms and the animal exist that impact the health and well-being of the host animal.

Symbiosis is defined biologically as ''the living together in more or less intimate association or even close union of two dissimilar organisms'' and this, in a broad sense, includes pathogens. Thus, symbiosis is living together, irrespective of potential harm or benefit, and living together is no more apparent than in the animal gastrointestinal system. This symbiosis can be relatively defined by the degree of benefit to one or both partners within the association, as well as by the closeness of the association.

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