• Rebecca Watson MSc RVN

What is the equine microbiome?

Rebecca Watson, reveals its influence on health, disease and... personality!


We have learned a great deal about microbes since the godfather of microbiology Louis Pasteur, proposed the theory of lactic acid fermentation in 1857. He was the first to suggest ‘germ theory’ – that living microorganisms in the environment could cause disease and, by preventing these microorganisms from growing, better human health (and subsequently animal health) could be achieved.


The equine microbiome is defined as the population of microbes: bacteria, viruses, fungi, and protozoa that are present in or on our horses’ bodies. These microbes exist everywhere on the body, from the nasal passages to the lungs, to the skin, with the largest and most diverse population found within the gastrointestinal tract.


Amazing research results

Scientists in Sweden conducted a study in laboratory mice; they were separated into two groups depending on their personality: ‘extrovert’ or outing mice, and ‘introvert’ or shy mice. The study found that when the gastrointestinal tract of the extrovert mice was inoculated with the GI microbiome of the shy mice, the personality of the mice changed. The once extroverted mice became shy. The same happened in reverse – shy mice inoculated with the GI microbiome of the extrovert mice became more outgoing. This suggests that the microbiome of the gastrointestinal tract is not only important in gut health, but could also have important implications in behaviour too.


Each horse has an entirely unique microbiome that is originally determined by its DNA (the foal is first exposed to microorganisms at birth, in the birth canal and then through the mare’s colostrum and milk) but, the microbiome will also be influenced by bodily health, stress, environment, and diet. The change in the composition of the foal’s microbiome goes from sterile (in utero) to an abundance following birth, when foals begin to nurse, graze, and consume other feedstuffs, including coprophagia or ingestion of faeces (usually the dam’s).

By 60 days of age, foals have a relatively stable microbiome that is comparable to that of the adult horse. Some of the important bodily functions of the microbiome includes digestion, immunity, and the synthesis of vitamins.


Disruption of the microbiome, the wrong bacteria in the wrong place or, a sudden increase in numbers of a specific type of bacteria, can cause health issues including laminitis, diarrhoea, colic, or colitis.

Human research on the gastrointestinal (GI) microbiome has been linked to many diseases and conditions from obesity to anxiety and autism. The human GI microbiome has also been linked to how individuals respond to certain drugs, including how cancer patients respond to chemotherapy and, has even been tentatively linked to how well we sleep.


Researchers have taken faecal microbiome from overweight humans and transplanted it into ‘germ-free’ mice in the laboratory, these mice began to gain weight quite dramatically, without any changes to their diet. A similar study was performed with the faecal microbiome from wild brown bears in Canada. The brown bear’s microbiome differs dramatically during the summer months (when it can practically double its body fat), compared to the wintertime when it is hibernating. Germ-free mice that were inoculated with the bear’s summertime microbiome demonstrated a dramatic gain in both body weight and body fat in comparison to the mice that were inoculated with the bear’s wintertime microbiome.


Scientists have been studying equine GI microbiome for the past 20 years and are still working on improving the techniques used to examine it. The GI microbiome is vast and varied and, unique to each area of the intestine, for example, the microbiome represented in faeces collected from the horse’s rectum is similar to that of the caecum but, markedly different to that of the small intestine. The colon has the most diverse microbiome of all the equine intestinal tract.


Scientists in both Europe and the USA have examined the microbiome in horses with and without diarrhoea. Researchers found that intestinal microbial diversity was significantly less in horses with diarrhoea. Horses that had diarrhoea also had different species of bacteria present in the faecal microbiome, including Fusobacteria. Researchers also identified Clostridioides difficile in 3.7% of the horses without diarrhoea. Those horses also had decreased diversity of intestinal microbes compared to horses that did not test positive for C. difficile. This suggests that diarrhoea is not necessarily caused by an overgrowth of a single pathogen, e.g., C. difficile or Salmonella spp. but, may in fact be a disease of microbial imbalance or ‘gut dysbiosis’. Studies have been undertaken on the alterations to the intestinal microbiome, following treatment with antibiotics. Horses treated with intramuscular penicillin, ceftiofur or oral trimethoprim­sulfadiazine, were found to have resulting reduced variety or richness of the microbiome, which could predispose the horse to diarrhoea or other illness, such as diarrhoea, colic or laminitis.


We know that the horse’s intestinal microbiome can change rapidly with dietary concentrate or forage adjustments, potentially leading to GI upset. Researchers from the University of Liverpool and the University of Leicester also found that during a year-long study, pasture-kept horses’ microbial populations are in a slow, but constant, state of change in response to multiple factors, including season, climate, and the type of forage they are eating.


The same research team also evaluated the GI microbiome in broodmares around the time of foaling – a group of horses known to be at higher risk from colic. Samples of the broodmares’ faecal microbiome were collected and evaluated five weeks before and twelve weeks after foaling. None of the mares succumbed to colic during the time of the study and, their faecal microbiome was consistent. However, they did find that the microbial population varied between the mares.If differences in GI microbiome are associated with colic in broodmares after foaling, risk could be due to the makeup of the microbiome, rather than being related to management changes that occur around this time.


Another team of researchers collected faecal microbiome samples from 26 mares pre- and post-foaling; 50% of which went on to develop colic after foaling. The team identified differences between the colic group and the non-colic group of mares, as such they identified certain species of bacteria that could be important in future tests to predict and prevent colic in the post-foaling mare.


Researchers are making great advances in understanding the horse’s GI tract and how the microbiome impacts not just singular disease processes, but overall health. However, we still have a long way to go to fully understand what is ‘normal’ and what is not, there is a lot more to learn which could impact how we care for our horses in the future.

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