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Health begins in the gut. This is the same for horses. There are now countless studies that have compared what changes in the horse’s large intestine microbiome (‘gut flora’) when external circumstances change, such as feeding or medication, or in the case of illnesses such as colic or laminitis

More and more laboratories are now also offering so-called ‘intestinal gut flora analysis’, in which the microorganisms present are determined to identify any imbalances in the intestinal gut flora and take appropriate countermeasures. There are a wide variety of test protocols on offer. Some laboratories simply adopt the analysis that are also used for human intestinal gut flora analysis. As expected, the results never match, because the human microbiome is definitely very different to that of horses. While humans are omnivores by nature, horses are optimised for the utilisation of cellulose as an energy source, which requires a completely different intestinal gut flora. Other laboratories only analyse the bacterial species and ignore the complex interaction of bacteria with other microorganisms such as fungi, protozoa or viruses. Logically, these analyses cannot provide a comprehensive picture of whether we are dealing with ‘healthy’ or ‘altered’ intestinal gut flora.

The ‘good’ and the ‘bad’ gut bacteria

Even if we assume that the bacteria essentially determine the health of the horse’s large intestine, it is still not clear which bacteria are ‘good’ and which are ‘bad’. This is because in a system as complex as the large intestine microbiome – as is so often the case in biological systems – it is not so easy to differentiate between ‘good’ and ‘bad’. Only when a form occurs extremely frequently, or the ratios of certain genera are reversed can conclusions be drawn about the health of the horse. But which conditions are considered ‘healthy’ and from which shifts one must assume a pathological change or just an adaptation to a change in feeding or management has not yet been researched in horses.

Lactic acid bacteria are among the ‘bad’ bacteria, cellulose-digesting bacteria are among the ‘good’ bacteria

It is already well researched that an increased occurrence of certain lactic acid bacteria can be associated with diseases. The lactate produced by the lactic acid bacteria causes the pH value in the large intestine to drop, which can result in colic or laminitis. This does not mean that recognisable symptoms are outwardly visible; both colic and laminitis can be subclinical and lead to constant discomfort in the horse without the disease showing the well-known symptoms. Researchers therefore advise against the administration of lactic acid bacteria in the form of probiotics or haylage, as well as feeding starchy feed, which promotes the proliferation of lactic acid bacteria in the large intestine. The presence of lactic acid bacteria in the large intestine is also associated with a disturbed intestinal gut flora.

The good bacteria include the metabolisers of plant fibres, especially cellulose, which provide the horse with short-chain fatty acids from which it draws its energy. It is still unclear which bacteria and which other microorganisms in the large intestine are involved in the digestion of cellulose and how. It is already known that, in addition to bacteria, various fungi also digest cellulose in the horse’s large intestine and are therefore involved in fibre utilisation. According to previous hypotheses, it is assumed that there is always ‘teamwork’ between different microorganisms and that there is not just one type of bacteria that breaks down the fibres into energy. However, it is not yet known how the various microorganisms involved in fibre digestion interact.

And even among these ‘good’ and ‘bad’ bacteria, there is no ideal of what the perfect microbiome should look like.

Not to mention that circumstances under which the composition changes are extremely varied. Feeding, movement management and even the stress level play an important role here.

What is certain is that there is a balance between the different bacteria. If this is disturbed, diseases can occur. But what ‘disturbed’ means has yet to be researched.

Hand on the coat of a horse
©Adobe Stock/Sonja

Influences of geographical location, management and feeding

If you compare horses from different continents, the findings are that each region shows a completely different intestinal gut flora, depending on what feed is offered and digested. If you then look at domestic horses and wild horses in the respective region, you can see that the domestic horse has more starch-digesting bacteria in its gut and fewer fibre-digesting bacteria. This indicates that feeding by humans already has a considerable influence on the microorganisms in the large intestine. At this stage we do not know when to speak of a ‘pathologically disturbed’ intestinal gut flora and up to what point it is simply normal.

Another important factor is the horse’s feed intake as well as general daily management. For example, breaks in feeding, such as those that occur when feeding hay in mealtimes or via automatic roughage feeders, can lead to a significant reduction in fibre-digestible bacteria. Exercise also plays a major role – not only quietly hacking out in tranquil surroundings but also the demands of training for sports performance. Metabolic imbalances such as EMS are reflected in the intestinal flora, but stress factors also influence the composition of the microbiome. This often raises the ‘chicken and egg’ question: is the disturbed microbiome the cause of the excess weight? Or has the obesity led to a disruption of the microbiome? The answer to this question, in regard to the Equine Biome has yet to be found.

Other factors that have an influence on the microbiome of the large intestine are also differences on the breed, age, and sex of the horse and, of course, depending on the medication that the horse has received in the past.

In conclusion, it can be said that in individual cases of prolonged illnesses such as diarrhoea, it can be useful to search specifically for the pathogen to be able to treat the horse.

In principle, the intestinal gut flora analysis as offered by the laboratories should be seen as followed: if we do not know what a healthy microbiome should look like, we cannot decide on the basis of analysis whether an intestinal flora is pathologically altered or merely adapted to the living conditions of the horse.

What we know and this applies to all horses is that hay is the best prebiotic because it contains a high proportion of cellulose, which the ‘good’ microorganisms need as a vital food source.

As nothing is ever straight forward, when feeding hay, one must be aware of the fibre content and the composition of grasses and herbs in the hay as they, also have an influence on the Equine gut microbiome.

Scientific proof:

  1. Fazio, F., Gugliandolo, E., Nava
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