An insight into Equine Microbiome

Difference in the gut microbiome of (a) wild and (b) domesticated horses. (Left part of the figure recreated by author using images from creative common sources and using information from Kauter et al., 2019).

Microbes have been an integral part of our ecosystem since the origin of life. These tiny creatures have proved their worth to humans in various ways and they continue to do so. The latest addition to this growing list of microbial applications includes the study of microbiomes of different organisms. The microbiomic research has shown that these microorganisms play a crucial role in the proper functioning of vital systems (like digestive, immune, nervous) of multicellular organisms.

It is known that various genes present in different organisms make necessary instructions in the form of various proteins. These proteins help to carry out all the metabolic activities required for the effective functioning of the organism. But, it is not just the genetic material of an organism, which is able to narrate the entire biological story of that organism. In fact, the detailed insight about an organism’s performance can be studied by the combination of organism’s own genetic material as well as the genetic material of the microbes present on or inside the body of that organism.

So, in a quest to understand the hidden part of the organisms-that is their microbiomes, there has been a technological revolution in high throughput sequencing methodologies to sequence the genetic material of all the microbes which form a dynamic association with different organisms. These sequences have opened up new avenues of ‘omic’ based studies, which have greatly enhanced the existing biological concepts using in silico or bioinformatic analysis. So, with use of sequence analysis, many questions were answered and it also allowed the researchers to explore new emerging questions. For instance, the human microbiome could answer many questions which the human genome project could not explain completely. For example, how the body responds to different kinds of diet, diseases and drugs or antibiotics. Thus, keeping in view of the great potential of this novel molecular toolkit, microbiome studies have been conducted over a wide range of animals. Some of these researches have yielded novel insights that have significantly contributed towards understanding the factors which affect the functional and ecological roles of animals in their natural habitat and the overall animal health. For instance, the microbiome in livestock, domestic and wild animals is strongly influenced by their diet. In this respect, a recent study by Meredith K. Tavenner, Sue M. McDonnell and their team at the Department of Animal and Food Sciences, University of Delaware, Newark, USA has compared the gut microbiome of domesticated and wild horses and have found significant differences in diversity and community structure between the two microbiotas. They found that while the wild horses had a distinct and diverse bacterial community and had higher abundance of the orders Fibrobacteres, the domestic horses had a higher abundance of Spirochaetales (Fig. 1). Additionally, young feral (wild) horses of less than a year of age had a less diverse microbial community but it was quite different from that of the horses which were older than 1 year. Further, the bacteria related to fat and protein digestion were found to be less in foals of higher age. It was further reported that the domestic conventionally managed foals had higher abundance of Lactobacillus spp. and other Lactobacillaceae genera, especially during their second and third week of life. This may be due to the fact that mare’s milk is high in lactose content (6.15%), followed by protein (2.64%) and fat (2.07%), in the first few weeks of lactation (Wells et al., 2012). But, the fat as well as protein content decreases in mare’s milk in the later weeks of lactation, which may explain the decreasing number of bacteria related to fat and protein digestion in adult horses. Also, the domesticated horses have access to concentrate feeds, which are generally rich in energy and/or protein but low in fiber. On the other hand, the main diet of wild horses is fiber-rich grasses and other edible shrubs and plants. 

Interestingly, it was found that there were very less differences in the microbiome of foals and adults of domesticated horses. It is interesting because the microbiomes of adult organisms usually differ from the microbiomes which are present at the time of birth, suggesting that age is one of most influencing factor of an organism’s enteral microbiome composition. However, in case of certain domestic animals like horses, the difference in microbiomes of adult and young horses could be due to the availability of a uniform as well as limited diets and an increasing adaptation of domestic horses towards digestion of concentrate feeds. Also, the use of drugs or antibiotics to treat infectious diseases with timely medical treatment to domesticated horses may have been the major drivers in shaping their microbiome structure. On the other hand, the wild ones have access to a variety of plants and vegetation at all ages, with exposure to climatic fluctuations and social interaction with other horses in their natural environment as well as environmental exposure to pathogens and different kinds of stress levels. This suggests that the establishment of microbiome composition in the domesticated and wild horses is largely dependent on the management factors such as access to grazing, exercise, social interaction and diet, which overall contributes to the equine health (Tavenner et al., 2020). 

Further it has been observed that the fecal microbiomes of the domesticated group had a considerably lower abundance of Phascolarctobacterium (Clostridia genus) while a significantly higher abundance of Methanocorpusculum archaea in microbiomes of non-domesticated horses. These methanogens or producers of enteric methane consume hydrogen and carbon dioxide, which are produced as waste products by the cellulose-degrading gut microbes. Thus, the higher abundance of methanogens in non- domesticated horses’ points towards their access to cellulose rich grass-based diet in the wild. 

So, the above findings related to equine microbiome will be extremely useful in investigating changes which are linked with certain disorders like equine grass sickness, laminitis or colitis, intestinal disorders including inflammatory bowel disease, infectious diseases. It will also be helpful to study the effects of drugs or antibiotics in horses. Thus, such studies will help us to assess the health state of horses if their microbiome is disturbed and hence the effective treatment strategies could be developed accordingly. In other words, the study of equine microbiome would be a major step in attainment of one of the sustainable development goals of United Nations: “Ensure healthy lives and promote wellbeing for all at all ages”, which goes beyond human health and includes animal, plant and environmental health also.



  • Tavenner, M.K., McDonnell, Sbe.M. & Biddle, A. Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals. AnimMicrobiome 2, 43 (2020).
  • Kauter, A., Epping, L., Semmler, T. et al. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. AnimMicrobiome 1, 14 (2019).

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