Jennifer Little BSc Hons MSc RNutr,
Equinutrition, Independent Equine Nutritionist

Antibiotics are medications used to treat bacterial infections. They work by interfering with the structure of the bacteria’s cell wall, its protein metabolism and replication, resulting in the death of the bacteria. They are extensively used in veterinary medicine as one of the leading options to treat a plethora of bacterial infections and to prevent postoperative and secondary infections [1].

When treating or preventing bacterial infections the use of antibiotics is a significant treatment course as recommended by vets. Their usage increases survival rates, as well as reducing disease transmission from horse to horse [2]. However, their use is known to have some potential side-effects in horses, relating to their hindgut.

The Horses Hindgut
The horse has a rather unique digestive system, in that it is referred to as a ‘hindgut fermenter’. This means that the site where fibre is broken down and converted into an energy source that the horse can use is the hindgut. This is a process driven by the bacterial population housed within the hindgut, collectively known as the microbiota, or gut biome. These bacteria have the capabilities to breakdown otherwise indigestible carbohydrates within the fibre, to produce an energy source in the form of Volatile Fatty Acids (VFAA’s) [3]. The bacteria that make up this biome play a major functional role in critical metabolic processes, the production of fatty acids, bile acids, the production of vitamins and amino acids, the regulation of the inflammation within the gut, and the modulation of the immune system [4]. Factors that effect and change the make-up of this biome can impact these important metabolic processes, and are associated with disease.

Antibiotics and the Hindgut
The potential unwanted side effects of antibiotics relates to the disruption of the bacterial population within a horses hindgut [5]. Resulting in a reduction in the beneficial celluloytic bacteria and proliferation and overgrowth of pathogenic bacteria [3;5;6]. The biodiversity and bacterial abundance in a horses hindgut is negatively impacted by antibiotic treatment, with a decline in numbers and a loss of richness [4]. This affects the activity of the bacteria responsible for breaking down fibre and the intestinal immune balance [3]. The oral administration of antibiotics can significantly alter the whole hindgut biome in just 2 days from the first dosage [3].

The treatment of antibiotics can increase the water content of the faeces produced from day two [3], and if significant enough it can result in diarrhoea. Antimicrobial-associated diarrhoea (ADD) is a common and serious adverse effect of antibiotic use in horses [4;3]. The exact incidence level is not well defined, but for those housed in veterinary referral centres it has been reported at 22-94% [4]. The onset of symptoms can occur within just 48hrs of the first antibiotic treatment [3]. The severity of the symptoms can range from mild to severe and life-threatening [7], in milder cases symptoms can be long lasting [4]. Even in horses that do not develop diarrhoea as a result of antibiotic administration the bacterial diversity in the gut biome is still know to be diminished, and metabolic processes effected. Again these changes can occur rapidly after the first antibiotic treatment [4].

Generally the bacteria that are considered to be beneficial decrease and the types of bacteria associated with gastrointestinal diseases such as colitis and colic, known as pathogenic bacteria, increase [4]. The reduction of beneficial bacteria can be detrimental to a horses digestive function and overall health [3]. The overgrowth of pathogenic bacteria has been linked with a increased gut mobility, a reduction in the protective mucous layer, the promotion of inflammation and autoimmunity, and the decrease in barrier function of the gut wall [3;4]. There is also evidence to suggest that the ability of the hindgut to absorb the VFF’s produced from fibre breakdown is diminished [3]. The production and absorption of VFA’s should account for half or more of a horses energy requirements, a reduction in the guts ability to absorb these molecules could significantly contribute to the horse entering an energy deficient state [3].

The disruption of the gut biome has an effect on the whole of the horse, affecting the production and absorption of energy and vitamins as well and impacting on the immune defences, at the gut mucosa and the systemic systems [3].

Protecting the Biome Under an Antibiotic Challenge
This piece is in now way implying antibiotics should not be administered, just to highlight some of potential implications of their use. Implications a vet will have weighed up against the health risks of a current infection or the need to prevent a probable infection.

It is important to consider factors which could avoid adverse effects of antibiotic use on horses health [1]. When administering antibiotics many veterinarians will also recommend the supplementation of Probiotics [5]. Supplementation of Probiotics at the time of antibiotic use can help to maintain the gut biome, making it more resistant to disturbances as a means to delay or prevent anti-biotic related adverse effects [3]. The use of Probitoics has been shown to contribute to an improved recovery following antibiotic therapy. Helping to avoid the typical decreases in the beneficial celluloytic bacteria, supporting the integrity of the gut wall and in contributing to overall equine health [3].

The supplementation of Prebiotics, such as MOS & FOS, has significant evidence for supporting the horses gut biome. But more research is required to establish the combined supportive effect of Pro and Prebiotics in the face of an antibiotic challenge. Some recent studies have indicated that their use during an antibiotic treatments is sufficient to strengthen the integrity of the digestive tract wall, reduce the risk of increased faecal water, as well as improved digestion, resilience and absorption of VFA’s [3;5]. These early findings for this combined approach were significant enough for me (the author) to ensure I provided the supplementation of the Probiotic Saccharomyces cerevisia (yeast) and the Prebiotics, MOS and FOS in my own horses diet following a surgical procedure that required a course of antibiotics.

The horse’s digestive system is rather unique in comparison with many animals that have also evolved to survive on a forage or grass-based diet. The horse can function on high volumes of forages that contain lower nutritional values, compared to those grasses often more suitable for livestock, such as dairy pastures. The horse can achieve this due to the structure of its digestive system.

The average horse’s digestive system is around 100ft in length and runs from their mouth to their anus and comprises of sections referred to as the foregut and the hindgut.


  1. Khusro,A., Aarti,C., Buendia-Rodrigues,G., Arasu,M.V., Al-Dhabi,N.A., Barbabosa-Pliego,A. 2021. Adverse effect of antibiotics administration on horse health: an overview. Journal of Equine veterinary science (97) 103339 . 
  2. Gustafson, R.., Bowen,R.E. 1997 Antibiotic use in animal agriculture. J.  Appl Microbiology (83) 531-541. 
  3. Collinet,A., Grimm,P., Julliand, S., Julliand, V. 2022. Multidimensional approach for investigating the effects of an anti-biotic combination on the equine hindgut ecosystem and microbial fibrolysis. Frontiers in Microbiology (12) 646294
  4. Arnold,C., Pilla,R., Chaffin,K., Lidbury,J., Steiner,J., Suchodolski,J. 2021. Alterations in the faecal microbiome and metabolme of horses with antimicrobial-associated diarrhea compared to antibiotic-treated and non-treated healthy case controls. Animals (11) 1807
  5. Wagner,A.L., Span,A., Biddle,A.S., Girard,I.D. 2022 13 Impact of biome fix on the faecal microbiome response to antibiotic challenge in horses. Journal of Equine Veterinary Science (100) 103476
  6. Elghandour, M.M.Y., Khusro,A., Greiner,R., Salem, A.Z.M., de la Fuente,J.L., Marquez-Molina, O. 2018 Horse fecal methane and carbon dioxide production and fermentation kinetics influenced by Lactobacillus farmiminis supplemented diet. J.Equine Vet Sci (62) 98-101
  7. McGorum,B.C., & Piri,R.S. 2010. Antimicrobial associated diarrhoea in the horse. Part2: which antimicrobials are associated with AD in the horse? Equine vet. Educ (22) 43-50

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