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Frequently Asked Questions About The Horse’s Hind Gut

At EquiBiome, we work with state-of-the-art technology to push the boundaries of what we know about how our horses’ bodies work. We discover more about the equine hind gut all of the time, but there is still so much more to learn. Understandably, we get asked a lot of questions about the equine hindgut and the evidence behind our work. This blog article covers some of the frequently asked questions about the science behind equine gut health and the microbiome.


What Can Equine Faecal Testing Tell Us About Our Horses’ Digestion?


At EquiBiome, we use state-of-the-art MiSeq NGS technology to produce a snapshot of the microbial community in the horse’s hind gut. Using this technology, we can understand the types and numbers of different microbes are present in the horse’s hindgut. The level of biodiversity within the sample, as well as the presence (or absence) of certain microbes, can help us to understand a horse’s health and how we can manage their feeding to support a healthy microbiome.


The EquiBiome Report explores the role of digestion and gut bacteria and puts this into easy-to-understand language. This report is there to help owners better understand their horses’ microbiome and how to support a healthy gut.


The horse’s digestive system is large and complex, so equine faecal testing cannot tell us everything. However, examining the microbiome of the hind gut can provide a useful snapshot and insight into what is going on. 


Information From Current Science:


From Chaucheyras-Durand, F., Sacy, A., Karges, K., & Apper, E. (2022). Gastro-intestinal microbiota in equines and its role in health and disease: The black box opens. Microorganisms, 10(12), 2517. (Emphasis added)


‘Discussion: The Microbiota of Horses, a Crucial “Organ” Largely Associated with

Health and Diseases in Horses’


“Gut health is a multidimensional concept related to diet, host and microbiota in which structure and functioning of the gastrointestinal barrier, gut microbial profile, and diet composition is continuously interacting (Figure 5). A stressful situation (e.g., sport, transportation), a high starch diet, or a digestive disorder may lead to an alteration of the gut environment, to higher gut permeability, to inflammation and to a change in the gut microbiota profile. Epithelial metabolism is supposed to play a crucial role as an intersection between gut microbiome, immune cells and epithelial permeability and regeneration, as demonstrated in humans suffering from obesity, diabetes, or intestinal bowel disease [126–128]. The intestinal epithelium represents the frontline of the complex pathogenesis, lying at the interface of luminal inflammatory triggers such as the microbiome and host immune cells, and a breach of this well-structured barrier is suggested as a cornerstone of chronic inflammation. Differentiated colonocyte is supposed to shape the microbiota, notably by performing mitochondrial β-oxidation to use fatty acids (mainly butyrate) as a source of energy and consumption of oxygen through oxidative phosphorylation; thus, creating a hypoxia in the intestinal lumen, which in turn will favor strict anaerobes growth, and fibrolytic activity to produce SCFAs, creating a virtuous cycle for the colon health. However, this cycle can be interrupted by epithelial injury or by an external factor (e.g. antibiotic) and colonocyte metabolism can switch towards anaerobic glycolysis, leading to lactate, nitric oxide (transformed into nitrate used as electron acceptor by Proteobacteria) and oxygen release in the lumen, which will favor the growth of facultative anaerobes like Proteobacteria [126]. Remarkably, certain opportunistic and potentially pathogenic bacteria can influence the colonocyte metabolism to expand their colonization. Therefore, to understand how the availability of respiratory electron acceptors becomes elevated during gut dysbiosis or inflammation could be a new area of research to develop novel preventative or therapeutic strategies in horses.


How Closely Does the Faecal Sample Reflect What is Found in the Gut?


Early studies (prior to 2016) concluded that the bacteria in the faeces were not exactly the same as those found in the horse’s hindgut. However, later studies demonstrated that changes in the microbiome relating to diet to reveal patterns of dysbiosis mirrored in the gut and the faeces, concluding that equine faecal testing would be useful as a diagnostic tool for hindgut microbial disturbances, especially during dietary changes. 


To avoid discrepancies, we use the IBERS (Institute of Biological, Environment and Rural Studies) research lab with the leading geneticist Dr. Matt Hegarty, and the same lab technician each time. This is both expensive and slow, but the results are far superior to any results we have received back from the commercial / NHS type labs such as Eurofins. The results were often unusable from these sources, though the turnaround time was much quicker at just 2 weeks and cost less than a quarter of the IBERS charge. You might say that you get what you pay for!


There are also clear and careful instructions on the timing and process of faecal sample collection, and the collection and extraction processes remain the same.


Information from Current Science:


From Grimm, P., Philippeau, C., & Julliand, V. (2017). Faecal parameters as biomarkers of the equine hindgut microbial ecosystem under dietary change. Animal, 11(7), 1136-1145. (Emphasis added)


’The “Common Core Microbiota” of the Adult Healthy Horse: A Myth or a Reality?’


“Because of its importance in healthy and sick horses, the GIT microbiota of horses should be looked at with careful consideration of the digestive site. Richness and evenness increase towards the distal part of the GIT [4], indicating the complexity of this environment. A “common core microbiota” i.e., a group of microbial taxa that are shared by all or most horses [3,5] could exist in the various GIT segments, with strong differences highlighted between foregut and hindgut (Figures 1 and 2). In the feces, the core community at the Operational Taxonomic Unit (OTU) level has been defined by “being present in all samples included in the study at 0.1% relative abundance (or greater)” [3]. Several studies report that fecal bacterial communities are not significantly different from the ones found in the colon [6], or even from the ones in the caecum [7], but differs from the upper tract. Thus, feces are interesting to be used as a non-invasive marker, although not complete, of what happens in the hindgut (especially the colon) but not in the foregut.’’


From Chaucheyras-Durand, F., Sacy, A., Karges, K., & Apper, E. (2022). Gastro-intestinal microbiota in equines and its role in health and disease: The black box opens. Microorganisms, 10(12), 2517. (Emphasis added)


‘’We also lack information about functions of the microbiota, i.e., the “functional core microbiota”. In addition, methodological differences in DNA extraction protocol, type of sequencing platform, selected region of the 16S rRNA gene and type of corresponding primers may play a role in the discrepancies that can be seen between results [3,35]. Alterations of fecal microbiota may appear, and Stewart et al. (2018) demonstrated that bacterial community varies significantly between center and surface of the fecal balls, while being stable from 0 to 6 h after defecation’’.


Given there are differences between the microbial population of the caecum and the colon, how can equine faecal tests be useful to understanding a horse’s gut health?


Yes, there are differences between the microbial population of the caecum and the colon. However, the biomarkers of dysbiosis will be mirrored from the gut into the faeces. This means that equine faecal tests can be a useful and non-invasive tool for helping us to understand our horses’ gut health.


What Is The “Ideal” Microbiome, Or Is There An “Ideal” Microbiome?


The purpose of the microbiome analysis is to look for markers of disease and dysbiosis, rather than for a perfect or ideal microbiome. There have been numerous studies relating to the links between imbalances in the microbiome and disease. For example, verrucomicrobia is a bacteria that has been proposed as a biomarker for EMS (equine metabolic syndrome). Other studies have discussed biomarkers for acidosis.


See the relevant papers below: 


Durham, A. E., Frank, N., McGowan, C. M., Menzies‐Gow, N. J., Roelfsema, E., Vervuert, I., ... & Fey, K. (2019). ECEIM consensus statement on equine metabolic syndrome. Journal of veterinary internal medicine, 33(2), 335-349.


Davies, J., Thomas, C., Rizwan, M., & Gwenin, C. (2021). Development of electrochemical DNA biosensor for equine hindgut acidosis detection. Sensors, 21(7), 2319.


How Do We Take Into Account Normal, Healthy Differences in Equine Hindgut Bacteria?


As with many areas of equine health, there are normal, healthy differences in the hindgut bacteria of different horses. These variations can occur between individuals, and horses of the same or different breeds, ages and workloads. Based on data from over 20,000 horses on our database, the EquiBiome Report highlights healthy bacteria and differences (diet, age, breed, work) between horses. We have extensive population data from wild / feral horses, competition and racehorses and horses with disease. 


The report also highlights and identifies True Pathogens - i.e. those that always cause disease (e.g. clostridium difficile and rickettsia). The report will also provide information relating to zoonotic bacteria and overgrowths from the introduction of new factory farmed ingredients (e.g. insects, fishmeal).


About EquiBiome 


At EquiBiome, we believe that new technology and science can help us better understand horses and improve the way we care for them. We use MiSeq NGS (Next Generation Sequencing) technology to gather information about the numbers of different types of bacteria and other microorganisms in the horse’s hind gut. Our test kits contain clear and straightforward instructions, and we take great care to ensure accuracy by using the IBERS lab and the same lab technician for each test. The EquiBiome Report explains the test results in an easy-to-understand format, making it useful and informative for horse owners who want to gain a better understanding of their horse’s hind gut health. Visit our shop to order the EquiBiome Test today.

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