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Hindgut Disturbances, Fecal Consistency Problems, and Associated Risks

First, what constitutes a hindgut disturbance?  This includes a wide range of symptoms and signs, affecting a variety of organ systems and tissues, with both acute and chronic onset versions. 

Chronic Disturbances
Typical chronic/more mild indicators for disturbances of the GI tract include gas, bloating, loud and/or frequent gut sounds, and “abnormal” fecal/defecation characteristics, such as changes in: defecation frequency (more or less often than normal), fecal size (larger or smaller fecal balls and/or fecal piles), fecal consistency (more liquid, greasy/oily, watery contents in addition to normal fecal balls, harder/drier fecal balls, etc.), fecal color (green vs. brown vs. black vs. red vs. yellow all have meaning), fecal smell (could be due to changes in diet or microbes, possibly due to organ function), presence of feed or forage particles, signs of parasites or foreign objects, etc.  With chronic disturbances, overall health of the horse can suffer, as digestion and/or absorption can be impaired.  Signs of this can include low body condition despite adequate feed intake, dry/dull coat, poor hoof quality, lack of energy, slow to heal from wounds/injuries, etc.  Often, these chronic signs are related to diet, parasite load, stress, hydration, or even dental problems (Loving, 2016).  If you are concerned about hindgut disturbance behaviors, reach out to your veterinarian or your Science Supplements nutritionist to discuss the problems to determine ways to help your horse. 

Acute Disturbances
More acute signs include the horse seeming unusually agitated, giving excess attention to their abdomen, getting up and down repeatedly with rolling, sweating without notable cause, possible changes in mucus membrane color and capillary refill time, trying to urinate without producing urine, very quiet/infrequent/absent gut sounds, etc. (American Association of Equine Practitioners, 2020).  Of note, sometimes acute disturbances may occur without the horse owner’s awareness, with a variety of outcomes possible, but in most cases this is a veterinary emergency.  Some horses may recover without medical intervention, but it can be difficult to tell the severity of the issue or if the horse is truly improving without diagnostics, and often a mild colic can be corrected if treated early but may develop into a more severe issue that becomes life threatening – sometimes without notable deterioration of the horse until it’s too late to help.    

Also, in some instances with or without medical intervention for the disturbance, the horse may go on to have a bout of laminitis – where changes in the microbial population of the hindgut result in pH changes and systemic toxicity alterations that affect blood flow to the hooves, resulting in inflammation that damages sensitive hoof tissues (Al Jassim and Andrews, 2009).  With repeated laminitic incidences, this can lead to founder, where the coffin bone rotates downward and potentially penetrates the sole of the horse’s hoof – an often career ending condition. 

Hindgut Ulcers – Both Chronic and Acute
Hindgut ulcers can present as both acute or chronic symptoms, as signs may include frequent but mild colic behaviors, fluid accumulation along the right dorsal abdomen, pain or sensitivity along the right abdomen, dull coat, diarrhea, and/or weight loss, though horses may have few if any symptoms at times (Andrews and McConnico, 2020).  Diagnosis includes a thorough medical history, ultrasound of the hindgut, and blood work showing specific indicators, and treatment includes reducing stress, limiting bulk of meals by replacing high fiber forage with pelleted feeds fed in frequent meals, addition of high Omega 3 content oil to the diet, and administration of sucralfate – a medication that helps coat the ulcers and improve their healing capacity (Andrews and McConnico, 2020; Cohen et al, 1995; Jones et al, 2003).  Contact your veterinarian if you suspect hindgut ulcers in your horse to rule out other problems and find the right treatment plan.

Dietary Influence on Hindgut Microbes
Before getting into how diet affects the hindgut, you can review this overview on the equine digestive tract for basics on how each organ contributes to digestion.  The hindgut microbes – being living creatures – have a preference for foods, are sensitive to environmental changes, reproduce when well fed, and die when their environment changes or food isn’t available.  When they reproduce, the population needs more food to maintain their new numbers, and when they die, they decompose.

All this is to point out that when a horse’s diet changes – and particularly if it changes abruptly – the microbes are affected in drastic ways that impact their population and can have detrimental effects on the horse.  For instance, if your horse had always eaten a high fiber/all forage diet, this means the microbes within its hindgut were predominantly fiber loving microbes with just a small population of starch loving microbes.  If you suddenly switch out some of your horse’s forage feed for 5 lbs of high starch feed, two results inevitable occur in the hindgut:

  • Some of the fiber loving microbes don’t have enough to eat, so they starve, die, and start decomposing. Decomposition results in a drop in pH and toxins within the hindgut at minimum, but decomposition may also result in toxins being released and absorbed by your horse.  The drop in pH and toxins will kill some other microbes of the hindgut (exacerbating the problem), and the toxins in your horse’s tissues may result in changes in blood flow that are associated with laminitis development.  Whatever type of by-products they were making (some used by the horse) declines.
  • The small population of starch loving bacteria eat… and EAT… AND EAT. They start reproducing at a substantial rate, increasing their numbers, taking up more space and competing with other microbial species.  They create their own by-products, which may or may not be helpful to the horse, and potentially affect pH of the hindgut due to their by-products.  Even worse, if they’ve multiplied too quickly without having enough starchy feed to follow up with their population boom (like if your horse is only getting that 5 lbs of starchy feed once a week), these starch loving microbes will also die off over time… with the same effects we saw with the rapid decline of the fiber loving microbes.

Especially if this cycle continues with an unstable diet and weakens the population of microbes that aid in digestion, ultimately more dangerous microbes may be able to grow their numbers, increasing the changes of a pathogenic infection developing.

Protecting Your Horse from Hindgut Disturbances
Diets predominantly based on forage promote a wider range of microbe species and are considered to be more stable and less subject to drastic changes in productivity, and thus reduce occurrence of hindgut disturbances (Garber et al., 2020). Clearly, having a stable diet and making slow, gradual changes to diet when needed (covered in the first part of this post) are a key component of reducing hindgut disturbances.  Hydration is also important to GI tract function and motility, so ensuring your horse has access to clean, fresh water at all times helps support the hindgut and absorption of water soluble nutrients.  If you’re concerned your horse doesn’t consume enough fluids, adding electrolytes to their daily intake can help stimulate water consumption (Pagan et al., 2013).  

Intestinal parasites should be controlled to support healthy function of the GI tract through appropriate use of dewormers, fecal counts, pasture and waste management, and water sources should be monitored for insect and water borne parasites.  Consult with your veterinarian for the best course of intestinal parasite control for your horse, based on its age, environment, risk factors, interaction with other horses, and health history.  Additionally, when horses must be given antibiotics for an infection, they have a higher threat to hindgut health because antibiotics can kill the beneficial microbes of the hindgut along with the intended pathogenic microbes, creating opportunity for microbial imbalance and increases in populations of resistant pathogenic microbes.  

When to Include Probiotics and Prebiotics
To help stabilize the hindgut of horses with antibiotic use, regular hindgut disturbances, history of repeated colic, difficult gaining weight despite adequate feed intake, and/or frequently changing feeds or environments (such as due to travel and competition schedules), the inclusion of probiotics and prebiotics to the horse’s diet can help stabilize and improve the efficiency of the hindgut and reduce the risk of colic (Al Jassim and Andrews, 2009; Moore-Coyler, 2019; Phillips et al., 2018).  For horses who have antibiotic administration – and especially long-term antibiotic use – the addition of probiotics can help replace the lost microbes, stabilize the microbial environment, and help contribute to digestion.  Horses with frequent hindgut disturbances or who don’t seem to gain weight well, the microbial population may be imbalanced due to stress, diet, or unknown feed contamination.  Probiotics and prebiotics can help normalize the microbial population, affect the hindgut environment to support ideal microbes and reduce less desirable microbes, activate the immune function of the GI tract, regulate fecal consistency, reduce hazardous impacts from feed contaminants, and overall improve digestion and availability of nutrients for absorption. 

Selecting Probiotics and Keeping Them Alive
Of course, not all probiotic/prebiotic blends are equal in their ability to aid digestion.  First and foremost, products that include probiotics can include any number of live (hopefully!) microbes intended to support GI tract health, although many commercially available probiotic species have not been proven effective or helpful.  Currently, the European Union (who are much stricter on animal feed safety and efficacy than the regulations in the US) only sanctions the inclusion of yeast (Saccharomyces cerevisiae) in animal feeds for both safety and efficacy reasons (European Union, 2020).  Other species may be impactful, though their inclusion is not regulated and research is limited on differences in probiotic species and their effectiveness (Schoster et al., 2014).  Yeast, on the other hand, have shown positive impacts on digestion and hindgut stability without notable side effects, even with abrupt diet changes and particularly when feeding low fiber/high starch diets (Elghandour et al., 2016; Garber et al., 2019; Glade and Biesik, 1986; Lattimer et al., 2002; Medina et al., 2002; Pagan, 1990).

Another major factor to consider is the amount of probiotics included and whether or not the levels are high enough to be capable of facilitating positive effects.  Probiotics should be live and active in order to help build their population, and so the amounts included should be listed as “CFU” which stands for “Colony Forming Units” and implies their capacity to thrive.  Further, it’s recommended to have CFU levels in at least the billions (National Research Council, 2007).  It’s common for the amount to be written as exponents – for instance, 1.0 x 109 would indicate 1 billion (as “1” with 9 zeros after is equal to 1,000,000,000), and 2.3 x 1011 would indicate 230 billion (230,000,000,000). 

Of note, the number of CFU is the amount of probiotic the producer indicates is alive and functioning at the time of packaging.  As living creatures – bottled in a container and likely without food or water – their livelihood is at risk and inevitably the number of living creatures declines steadily over time.  Ways to determine the probiotics’ likelihood of survival and that the company cares about their longevity:

  • Look for indication from the product’s information that the probiotics are specifically “alive” or “live” or “living” and that they are “protected” or “encapsulated” – which means they are more stable and are coated. This coating helps them stay safe not only while packaged but also helps them survive the horse’s upper GI tract more successfully, as the goal is for them to reach the hindgut undigested so they can set up camp and thrive!
  • Look that the packaging also indicates safe storage recommendations, such as “keep at room temperature”, “store below ___ degrees”, “keep out of direct sunlight”, “refrigerate”, “keep stored in an airtight container”, etc.

A few things to help keep probiotics alive:

  • Choose distributers, retailers, or suppliers that adhere to the storage recommendations whenever possible. Even if your probiotics were alive and well at packaging, if the product was then stored in a hot, humid warehouse for months, likely at best the number alive had declined drastically and at worst you have a rancid, fermented product that could make your horse sick.  The warmer probiotics get, the faster they die, and once they die 1. they’re not helpful and 2. the product may even be dangerous to feed. 
  • Follow storage directions when your bring the probiotics home, and keep the probiotics stored properly for as long as possible leading up to feeding them to your horse, ideally only taking them out of storage right before putting them in the feed bucket for the horse. For instance, recognize that even with proper storage for months and living probiotics in the container, if you set out all your supplements on Sunday, placing probiotics into hot baggies or daily dose containers that are not airtight and/or are in the sun, the probiotics are dying all week long and possibly going bad before your horse eats them later that week.
  • Keep probiotics separate from other feeds or water until right before giving them to your horse. If probiotics are mixed with feeds/water, they start to get more active too soon, and this can lead to fermentation in the bucket.  Horses shouldn’t be given fermented feeds – save that action for the hindgut!  Also, some feed components such as salt can kill probiotics if they are in contact for too long before consumption.  Sitting together for a few minutes before feeding is fine, but contact for extended periods can affect probiotic function.

Selecting Prebiotics
Prebiotics includes ingredients assumed to support the probiotics/microbes of the horse’s GI tract or have benefits to the horse beyond directly nutritional (such as regulating fecal consistency or stimulating the immune system), but this is a wide range of potential ingredients since anything that could be consumed by microbes could be considered “beneficial” and technically applies.  Thus, if your horse is consuming forage and/or fiber sources (which of course it should be as educated readers of this post!), seek out prebiotics that are not already typically found in your horse’s diet AND that have research to support their inclusion for digestive and health benefits.  Of even more specific interest would be to include prebiotics that have low digestibility in the upper GI tract, which (beyond fibrous feeds) includes pectins, betaglucans, and oligosaccharides, among others.  A prebiotic supplement that simply relies on ingredients like beet pulp, oat hulls, or other feeds you may already give your horse isn’t really adding a new element to your horse’s digestion, and the truly “prebiotic portion” of the ingredient may not be at high enough levels to make any impact.  Seek out more purified sources that list the levels of the actual prebiotic compound so you can determine actual efficacy.

For example, one well research group of prebiotics is the oligosaccharides, which have demonstrated benefits for both digestion and immune function.  One variety is fructooligosaccharides (FOS for short, thankfully!), a prebiotic that supports both beneficial microbial growth and improved digestion.  Research has shown FOS both promotes and feeds nonpathogenic bacterial growth while suppressing pathogenic bacteria (Campbell et al., 1997; Roberfroid 1997; Flickinger et al., 2003).  Older horses have been proven to have reduced capacity for digestion and absorption of nutrients in general, however supplementing older horses with FOS improved multiple areas of digestibility to mimic the level of digestion seen in average aged horses (Heaton et al., 2019).  Younger horses supplemented with FOS have increased signs of fiber digestion and reduced E. Coli populations (Berg et al., 2005).  FOS also helps prevent some of the drastic effects on hindgut microbial populations with sudden inclusion of starch-rich feeds to the diet, meaning FOS is protective against hindgut disturbances as a result of diet changes (Respondek et al., 2008).

Another prebiotic in the oligosaccharide group is mannanoligosaccharides (MOS), which strengthens the immune function of the GI tract by helping prevent pathogenic bacteria from infiltrating digestive tract cells (Ofek and Beachey, 1978), and MOS was shown to increase immunity proteins and reduce diarrhea in foals when their mothers were supplemented during pregnancy (Ott, 2002).  Beta-glucans (or ϐ–glucans) are also often included in digestive supplements for their ability to absorb excess water in the GI tract, regulate passage rate of feed through the GI tract, and stabilize fecal consistency (Duss and Nyberg, 2004), but they are also are known to help regulate immune responses to pathogens (Jacobs et al., 2017; Paap and Roberti, 2014) and to have substantial antioxidant capacity (Kofuji et al., 2012).

While many factors can lead to hindgut disturbance, some are within our control as horse owners to help reduce the likelihood of developing discomfort or dangerous hindgut events.  With healthcare and management, thoughtful diet development, gradual feed changes, and the inclusion of pro- and prebiotics in your horse’s diet, you can help keep the hindgut and all those microbes stable and supportive of your horse’s health.

See our Science Supplements line of Probiotic/Prebiotic blends


Al Jassim RAM, Andrews FM. The bacterial community of the horse gastrointestinal tract and its relation to fermentative acidosis, laminitis, colic, and stomach ulcers. Veterinary Clinic of North American Equine Practitioners. 2009;25:199-215

American Association of Equine Practitioners. Colic: Minimizing its Incidence and Impact in your Horse. Horse Health Fact Sheets. 2020.

Andrews FM, McConnico R. Colonic Ulcers: A Pain in the Hindgut! Department of Veterinary Clinical Sciences, Louisiana State University. 2020.

Berg EL, Fu CJ, Porter JH, Kerley MS. Fructooligosaccharide supplementation in the yearling horse: effects on fecal pH, microbial content, and volatile fatty acid concentrations. Journal of Animal Science. 2005;83:1549-1553.

Campbell JM, Fahey Jr. GC, Wolf BM. Selected indigestible oligosaccharides affect large bowel mass, cecal and fecal short chain fatty acids, pH and microflora in rats. Journal of Nutrition. 1997;127:130-136.

Cohen ND, Carter GK, Mealey RH, Taylor TS. Medical Management of Right Dorsal Colitis in 5 Horses: A Retrospective Study (1987–1993). Journal of Veterinary Internal Medicine. 1995;9(4):272-276.

Duss R, Nyberg L. Oat soluble fibers (ϐ -glucans) as a source for healthy snack and breakfast foods. American Association of Cereal Chemists. 2004;49(6):3320-325.

Elghandour MMY, Kholif AE, López S, Mendoza GD, Odongoe N, Salema AZM. In Vitro Gas, Methane, and Carbon Dioxide Productions of High Fibrous Diet Incubated With Fecal Inocula From Horses in Response to the Supplementation With Different Live Yeast Additives. Journal of Equine Veterinary Science. 2016;38:64-71.

European Union. Register of Feed Additives. Publications Office of the European Union. 2020.

Garber A, Hastie P, Murray J-A.  The effect of yeast supplementation on equine fecal microbial population dynamics following abrupt dietary changes. Journal of Equine Veterinary Science. 2019;76:79

Garber A, Hastie P, Murray JA. Factors Influencing Equine Gut Microbiota: Current Knowledge. Journal of Equine Veterinary Science. 2020;88: 102943

Glade MJ, Biesik JM. Enhanced nitrogen retention in yearling horses supplemented with yeast culture. Journal of Animal Science. 1986;62:1635-1640.

Heaton CP, Cavinder CA, Paz H, Rude BJ, Smith T, Memili E, et al. Are prebiotics beneficial for digestion in mature and senior horses? Journal of Equine Veterinary Science. 2019;76:87-88

Heaton CP, Cavinder CA, Paz H,Rude BJ, Smith T, Memilia E, Harris P, Liburt N, Krotky A. Are prebiotics beneficial for digestion in mature and senior horses? Journal of Equine Veterinary Science. 2019;76:87-88

Flickinger EA, Van Loo J, Fahey GC. Nutritional responses to the presence of inulin and oligofructose in the diets of domesticated animals: a review. Critical Reviews of Food Science Nutrition. 2003;43:19-60

Jacobs RD, Gordon ME, Felippe MJ, Raub RH. Beta 1-3,1-6 glucan supplementation modulates the immune response of horses undergoing a glucocorticoid challenge. Journal of Animal Science. 2017;95(Suppl 4):165

Jones SL, Davis J, Rowlingson K. Ultrasonographic findings in horses with right dorsal colitis: five cases (2000–2001). Journal of the American Veterinary Medical Association. 2003;222(9):1248-1251

Kofuji K, Aoki A, Tsubaki K, Konishi M, Isobe T, Murata Y. Antioxidant Activity of β-Glucan. ISRN Pharmaceutics. 2012.

Lattimer JM, Cooper SR, Freeman DW, Lalman DA. Effects of Saccharomyces cerevisiae on in vitro fermentation of a high concentrate or high fiber diet in horses. Proceedings of the 19th Equine Science Society. 2005:168-173.

Loving N. Colic: Updates and Prevention. American Association of Equine Practitioners. Horse Health Fact Sheet. 2016.

Medina B, Girard ID, Jacotot E, Julliand V. Effects of a preparation of Saccharomyces cerevisiae on microbial profiles and fermentation patterns in the large intestines of horses fed a high fiber or high starch diet. Journal of Animal Science. 2002;80:2600-2609

Moore-Colyer, MJS. Gut Health and Dietary Manipulation for Performance Horses: an Overview of (New) Studies Regarding Digestive Aids Available for Horses. 9th European Equine Health and Nutrition Congress. 2019:45-52

National Research Council. Nutrient Requirements of Horses: Sixth Revised Edition. 2007. Washington, DC: The National Academies Press

Ofek I, Beachey EH. Mannose binding and epithelial cell adherence of Escherichia coli. Infectious Immunology. 1978;22:247-254.

Ott EA. Use of mannan oligosaccharides in diets of mares and their suckling foals. Nutritional Biotechnology in the Feed and Food Industries; Proceedings of Alltech’s 18th Annual Symposium. 2002:367-371.

Pagan JD. Effect of yeast culture supplementation on nutrient digestibility in mature horses. Journal of Animal Science. 1990;68(Suppl. 1): 371

Pagan JD, Waldridge BM, Lange J. Dextrose does not affect rate of absorption or retention of electrolytes in idle Thoroughbreds. Journal of Equine Veterinary Science. 2013;33(5):349-350

Paap P, Roberti F. Race horse perform better with beta glucans. All About Feed. 2014;22(6):500-502

Phillips CA, Cavinder CA, Memili E, Rude BJ, Smith T. The effect of direct fed microbials on apparent nutrient digestibility, fecal microbial population, and blood metabolites in the Moderately exercised horse. Journal of Animal Science. 2018;96:85

Respondek R, Goachet AG, Julliand V. Effects of dietary short-chain fructooligosaccharides on the intestinal microflora of horses subjected to a sudden change in diet. Journal of Animal Science. 2008;86:316-323

Roberfroid MB. Health benefits of non-digestible oligosaccharides. Advances in Experimental Medical Biology. 1997;427:211-219.


Schoster A, Weese JS, Guardabassi L. Probiotic Use in Horses – What is the Evidence for Their Clinical Efficacy? Journal of Veterinary Internal Medicine. 2014;28(6):1640-1652

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