The entirety of the microorganisms in different parts of the gut is known as the Microbiota and the corresponding entirety of their genetic material is the Microbiome. In the large intestine of horses, the Microbiota includes bacteria, fungi, protozoa, archaea, viruses, and parasites. These organisms contribute a substantial amount of the horse’s energy needs by digesting complex carbohydrates like cellulose from plant material. The population of different organisms include those which are beneficial in terms of digestion and supporting the immune system, and some which are pathogenic or potentially harmful. In the small intestine the range of organisms is more highly variable than in the large bowel, in part because of the throughput of environmental bacteria with the feed.

The composition of the microbiota varies over time and in response to the local environment according to the available nutrient supply with some groups favoring different foods such as fibre or starch and sugars. As different foods pass through the gut the various populations will take advantage and expand in size, or contract if their best substrate nutrient source is in short supply. Despite this, in a healthy hind gut the microbiota tends to be fairly stable. Diversity of the microbiome seems to be important for healthy function and this declines with age – a possible cause of reduced digestive efficiency in older horses. Domesticated horses tend to have less diversity than non-domesticated, perhaps due to diet, pasture access, human contract etc.

The microbiome is susceptible to Dysbiosis, disturbance in composition which may result from or be a cause of intestinal disease. Triggers for dysbiosis may be changes in feed, dehydration, parasitism, infectious disease lie Salmonellosis, toxins from mould (mycotoxins) or other sources like poisonous plants, or antibiotic treatment. These triggers upset the balance of microorganisms in the microbiome and may result in intestinal disease with symptoms such as diarrhoea or colic.

In domestic horses one of the most common causes of dysbiosis is feed related and caused by starch entering the hind gut where it promotes overgrowth of certain lactic acid forming bacterial populations. The acid can damage and inflame the gut lining and lead to escape of toxic materials into the bloodstream – so called ‘’leaky gut syndrome’’. This in turn can result in colic, circulatory changes, and in some cases laminitis.

Antimicrobial therapy has been associated with dysbiosis resulting in inflammation of the colon (colitis) with associated diarrhoea which may be acute and profuse. Penicillin’s, Tetracycline, Cephalosporins and Fluoroquinolone antibiotics have all been associated with colitis. Changes to the normal flora may take 3-4 weeks to reverse and re- establish a more normal balanced microbiome.

Prevention of dysbiosis is obviously desirable and until specific strategies are available the most promising methods revolve around maintaining steady diets, making ration changes gradual, and providing sufficient forage feeds to promote the population of beneficial fibre digesting gut bacteria. In essence, following a natural diet which the horse evolved to handle, so far as possible.

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