Defined as microscopic organisms these include bacteria, protozoa, fungi, archaea, bacteriophages, and viruses. Most are harmless, many are beneficial and some cause disease (pathogens). Of particular importance in equine nutrition are the bacteria responsible for fermentation which break down complex carbohydrates (starch & fibre) to yield sugars and volatile fatty acids in the large intestine which can be absorbed and utilised as energy sources. Gut microbes also produce a range of useful nutrients, particularly vitamins and after they die are themselves digested yielding amino acids and other nutrients.

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