This is your EquiBiome discovery portal where you can view your horse’s interactive report and access information.


The information on this report is for educational and informational use only. The information is not intended to be used for any diagnostic purpose and is not a substitute for professional veterinary advice. You should always seek the advice of your veterinarian with any questions you may have regarding diagnosis, cure, treatment, mitigation, or prevention of any disease or other medical condition or impairment or the status of your horse’s health.

The information on this report is for educational and informational use only. The information is not intended to be used for any diagnostic purpose and is not a substitute for professional veterinary advice. You should always
seek the advice of your veterinarian with any
questions you may have regarding diagnosis,
cure, treatment, mitigation, or prevention
of any disease or other medical
condition or impairment or the
status of your horse’s health.

About the Biome

This report is an analysis of the genetic material (DNA) which is present in all microbes present in your horse’s gut. It is the most accurate method of identifying individual microbial groups and species. It provides a real time snapshot of the hindgut microbial community of your horse. Whilst the test is a powerful management and analytical tool, it is not intended to be used to diagnose any illness, please consult your vet if your horse is in discomfort.

To generate this report an advanced functional sequencing technology called Metagenomics is used which is the most accurate and up to date technology, chosen by genomic researchers around the world. It looks not only at the species present, but also their ability to perform specific functions.

In horses, the knowledge and science linking microbiome to health and disease, are in their infancy. In humans this is much more advanced because of the larger database of samples. It is our aim to gather as many samples of different groups (populations) of horses as we can, this will help to increase our knowledge and put it in line with human research, offering the best and most accurate service.

We are proud to say that to date, we have the largest library of equine data in the world. This information is used to identify and accurately describe the healthy horse biome.

In order to create our extensive database faecal samples have been gathered and analyzed from thousands of horses including; the thoroughbreds in training, the Wild Carneddau ponies, Native ponies, horses at livery and obese horses. Also from horses with Laminitis, Sarcoids, Diarrhoea, Lyme's, Grass Sickness, Infect ions, Ulcers, Hind Gut Discomfort, Faecal Water Syndrome, with Temperament and Unsoundness Problems. Horses On Medication such as antibiotics, Non Steroidal Anti-inflammatory Drugs (NSAIDs) and Antacids.

It's All About The Bugs

The microbiome comprises a community of microbes (mainly bacteria, fungi and viruses) that live in the hind gut of the horse.

This community is influenced by many factors including the breed of your horse, his age and the food he eats. The balance of this community is essential for good health and can alter through stress, the use of medications and with a change in diet.

Good Bacteria

  • Make vitamins and allow minerals to be absorbed
  • Mend the gut wall and prevent ulcers and inflammation
  • Make vitamins and allow minerals to be absorbed
  • Defend against the invasion of bad bacteria Increase energy and promote a good immune response

Bad Bacteria

  • Cause disease -colitis, colic, gastric ulcers and inflammation
  • Can cause imbalances, triggered by changes in diet, stress, commonly used medication, including the use of ulcer and pain medication

Re-balancing the Gut

Re-balancing the gut is much easier if you know what and where these imbalances are. Scientific research has linked every common gastrointestinal health problem to the gut bacteria.

We Can help

The report identifies the bacteria causing the imbalances. It gets rid of the guess work around what supplements, forage. pellets, chaff etc to feed your horse and helps to establish the best diet to improve its overall health.

Your Pet’s Report - Part One

Diversity Score – The most important measure of gut microbiome health

Who’s In There? This part looks at the top groups of bacteria at genus level. Bacteria are divided into groups to make them easier to understand and identify, the major players and highlights their nutritional contributions and benefits.

You will see in Part One, how important certain bacteria are to your pets health. You will also see how by making some small changes to the diet, beneficial bacteria can be encouraged to increase in number, providing even more benefits.

Some of the dietary changes mentioned in your report are made by adding prebiotic ingredients such as inulin. The definition of a prebiotic is ‘’a non-digestible food ingredient that beneficially affects your pet by selectively stimulating the growth and/or activity of one or a limited number of bacteria in the colon and thus improves health.’’ Inulin is only one example of how important plant chemicals can be to the biome, another group you will hear mentioned is plant polyphenols.

Probiotics are also mentioned these are live bacteria, rather than a food for the bacteria. Other recommended dietary changes will relate to imbalances between the groups of bacteria that feed or digest carbohydrates, fats and protein. Making small changes in the amount or quality of these major nutrients will significantly improve the health of the gut and prevent any future opportunity for inflammation and colitis.

Part 2 - Dietary Insights


This part refers to the bacteria identified across all of the taxonomic groups and specifically the ability of the microbiome to digest the key dietary groups; Proteins, Carbohydrates and Fiber. Excessive proliferation of either of these may indicate access is provided in the diet.

Also to assess whether the microbial population is able to provide sufficient levels of important minerals and vitamins.

Part 3 – Health Insights


This section explains how and why the bacteria contribute to the health and well being.

For example, some bacteria help rebuild the gut wall, some trigger an immune response and some talk to the brain about what and how to act, eat and rest.

Other bacteria ‘take over’ and form biofilms, taking nutrients away from your pet and reducing the pH (acidity) of the hind gut preventing fermentation and causing discomfort.

This part also looks at the relationships and the conversations between the bacteria, some relationships contribute to health, especially the health of the immune system and some contribute to ill health, increasing the opportunity for inflammation and dysbiosis.


Max's Diversity score

The diversity of your horse’s gut microbiome is important. Microbial diversity is a measure of both the different types and the amount of bacterial species in your sample. Your horse’s diet as well as other factors such as stress, age and medications will affect the overall microbial diversity. Low microbial diversity is often associated with poor health. Diversity can also increase in really sick animals especially in certain groups like alpha-proteobacteria.

The Guts of Max’s Microbiome – Genus level

Let us give you a quick refresher in biology. The pie chart below is a representation of the bacteria “families” or genus in a healthy Horse when compared to Max’s gut.

Different types of bacteria are needed to do different jobs in Max’s gut. Having the right percentage of each of them, without a single family taking too much space is the key to a balanced biome.

You can click on each family to see what they do and how their numbers can affect Max‘s health.

Key Digestive Insights

Key Health Insights


Gut Metabolism


Gut Wall Renewal


Gut Wall integrity (stress related)


Bacteria Associated with Inflammation


Bacteria Associated with Inflammation


Bad Bugs

Disease-causing (pathogenic) Microbiome

New and re-emerging diseases have been increasing steadily in the last 20 years with more than 70 percent being zoonotic in nature. Despite Australia's strict quarantine procedures, a zoonotic disease outbreak is a constant risk, the above listed pathogens are the most common and represent the highest risk. The 16s rRNA gene is used by health authorities around the world, considered to be the most effective and accurate method of identification (Socolovschi et al 2010, Srinivasan et al 2015). The List below describe the main culprits, clicks on the name of each to the more information

The List below describe the main culprits, clicks on the name of each to the more information


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  • Argenzio RA, Southworth M, Stevens CE (1974) Sites of organic acid production and absorption in the equine gastrointestinal tract. Am J Physiol 226: 1043–1050.
  • Glinsky MJ, Smith RM, Spires HR, Davis CL (1976) Measurement of Volatile Fatty-Acid Production-Rates in Cecum of Pony. Anim Sci 42: 1465–1470.
  • Al Jassim RA, Andrews FM (2009) The bacterial community of the horse gastrointestinal tract and its relation to fermentative acidosis, laminitis, colic, and stomach ulcers. Vet Clin North Am Equine Pract 25: 199–215.
  • Chapman AM (2001) Acute diarrhea in hospitalized horses. Vet Clin North Am Equine Pract 25: 363–380.
  • Weese JS, Staempfli HR, Prescott JF (2001) A prospective study of the roles of Clostridium difficile and enterotoxigenic Clostridium perfringens in equine diarrhoea. Equine Vet J 33: 403–409.
  • Daly K, Stewart CS, Flint HJ, Shirazi-Beechey SP (2001) Bacterial diversity within the equine large intestine as revealed by molecular analysis of cloned 16S rRNA genes. FEMS Microbiol. Ecol 38: 141–151.
  • Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 1635–1638.
  • Wu GD, Lewis JD, Hoffmann C, Chen YY, Knight R, et al. (2010) Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags. BMC Microbiol 10: 206.
  • Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, et al. (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75: 7537–7541.
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  • Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, et al. (2008) The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 9: 386.
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403–410.
  • White JR, Nagarajan N, Pop M (2009) Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS Comput Biol 5: e1000352.
  • Shepherd ML, Swecker WS Jr, Jensen RV, Ponder MA (2011) Characterization of the fecal bacteria communities of forage-fed horses by pyrosequencing of 16S rRNA V4 gene amplicons. FEMS Microbiol Lett 326: 62–68.
  • Middelbos IS, Vester Boler BM, Qu A, White BA, et al. (2010) Phylogenetic characterization of fecal microbial communities of dogs fed diets with or without supplemental dietary fiber using 454 pyrosequencing. PLoS One 5: e9768.
  • B, Vörös A, Roos S, Jones C, Jansson A, et al. (2009) Changes in faecal bacteria associated with concentrate and forage-only diets fed to horses in training. Equine Vet J 41: 908–914.
  • Packey CD, Sartor RB (2009) Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases. Curr Opin Infect Dis 22: 292–301.
  • Chang JY, Antonopoulos DA, Kalra A, Tonelli A, Khalife WT, et al. (2008) Decreased diversity of the fecal microbiome in recurrent Clostridium difficile-associated diarrhea. J Infect Dis 197: 435–438.
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Horse MicroBiome Methodology

Microbial total RNA is extracted, ribosomal RNA molecules are removed from total RNA, and the remaining RNA molecules are sequenced on Illumina NextSeq or NovaSeq. Proprietary bioinformatics algorithms are used to perform taxonomic classification and functional analysis of the sequencing data.

Method Limitation

Horse Microbiome’s results and recommendations are based on our ability to identify and quantify thousands of microbial taxa. There are microorganisms that thrive in the gut whose genomes have not been sequenced. Horse MicroBiome is unable to identify those specific organisms, but can identify their near neighbours, which have similar structure. There are also taxa that we cannot discriminate because of their sequence similarity, for example at the strain level. There are some RNA transcripts that may not always align and match to specific known organisms, which may be due to the fact that these sequences are poorly characterized, reliable consensus sequence may not be available for reference. Horse MicroBiome monitors the growth of public genomic databases and will update its own databases when there is sufficient new information to be worthy of incorporation.

Detection of a microorganism by this test does not imply having a disease. Similarly, not detecting a microorganism by this test does not exclude the presence of a disease-causing microorganism. Further, other organisms may be present that are not detected by this test. This test is not a substitute for established methods for identifying microorganisms or their antimicrobial susceptibility profile. Results are qualitative and identify the presence or absence of identified annotated organisms.

Terms and Conditions

The Horse Biome 5.0 analysis provides insights into your Horse’s gut microbiome environment and how it may influence your Horse’s health. The test is designed to be used solely to identify the genetic makeup and composition of gut microbiome in your Horse and no other purpose is intended, authorized, or permitted, including diagnosing diseases. This report is for informational purposes only and cannot be used to diagnose or treat medical conditions. If any of the results are of concern to you, please consult with your Horse’s veterinarian.

Every Horse’s microbiome is unique and their composition is the result of many factors, including genetics, environment, nutrition, hydration status, stress and more and training.

Upon receipt of your sample, the microbiome DNA in your Horse’s faeces is analysed to determine the microbes likely present with a reasonable degree of certainty. Our procedures are designed to provide reliable and accurate results. Horse Microbiome is not responsible for any errors in obtaining the faecal sample or for any injuries or loss that may occur as a result.

The purpose of the Horse Biome 5.0 Test is to identify the genetic makeup of the microbial population in your Horses large colon. The test is not designed to diagnose any ill health or predisposition to disease, and test results should not be relied upon as a diagnostic test.

The test is based upon an extensive database of validated microbes in published scientific literature. If your Horse biome contains other microbes, it may result in the microbes, or a combination of microbes entered in to the database.