by Emily Dickson Collaborator

Is My Horse’s Digestive System Disrupted?

Is My Horse’s Digestive System Disrupted?
An Inside Look at the Equine Gut Microbiome

Key Takeaways You’ll Get

  1. With so much focus on the exterior of our equine athletes, it’s easy to forget about what makes them run. And like a car you haven’t maintained except by washing and filling up the fuel tank, you don’t necessarily know something’s going wrong with your horse’s hindgut until he’s in crisis—with diarrhea, colic, or other problems.

  2. We unintentionally cause imbalances in our horses’ hindgut microbes by how we feed them. We increase their calories and carbs to try to keep weight on them, for instance, and end up doing the equivalent of flooding the carburetor—overwhelming those good microbes.

Besides being able to smell your horse’s stinky manure from two stalls away, it’s now possible to confirm if your horse’s microbiome needs stabilizing, and to correct it.

Watch Dr. Rob Franklin and Dr. Keith Latson explain The Equine Gut Microbiome

How Do I Know if my Horse’s Digestive Tract is Disturbed? 

Your horse’s manure is shapeless and super-stinky. His weight and coat are just a little “off” compared to normal. Yet you’re feeding him by the book—forage first, then concentrates and supplements to meet other nutrient needs based on his age, activity level, and condition. His appetite is good, his attitude fine, and his under-saddle work routine, if not a little dull. But, wow … that pile of horse poop is foul-smelling. Something isn’t quite right, but is this just how your horse is, or should you be concerned? What’s going on? 

A horse’s gut health is a bit like a car’s performance. You can carry on for quite a while with a mild issue, not realizing there’s a problem lurking until you’re left on the side of the road somewhere. In the horse’s case, what’s brewing escalates to diarrhea, colic, or other illnesses that are disruptive at best and deadly at worst.

And “brewing” isn’t too far off in describing what goes on in the equine digestive system. Last time, we talked about the importance of properly maintaining the microbiome—the rich ecosystem of microbes living in the horse’s digestive tract, particularly the ones responsible for fermenting food in the hindgut, which comprises the GI tract components after the small intestine (cecum, large intestine, etc.). 

“The horse has evolved over lots of time and it has to have this symbiotic relationship with these bacteria, protozoa and fungi, to help it break down these indigestible sources of energy that they ingest,” including the cellulose that makes up the tough parts of grass and hay, says Dr. Rob Franklin, an equine internal medicine specialist and co-founder of FullBucket, a veterinary-strength supplement business based in Weatherford, Texas.

How do I figure out “normal” to create a happy, healthy gut environment for my horse? 

Bad Fuel and Stinky Stalls

As horse owners, how do we judge “normal?” We tend to assess the outside of the horse, just like car owners might just consider the exterior of their cars, says Robo Hendrickson, also FullBucket’s co-founder and director of marketing. “Very little do they know about the engine and transmission and the things that make it run.” 

Indeed, we fill up the tank and expect our horses to run—literally and figuratively. Dr. Keith Latson, an equine surgeon and FullBucket’s third co-founder and director of operations, emphasizes that our intentions are good, but how we “fuel” them is the problem.

 “What type of gas do we put in it?” he says. “We give a little sweet feed and some crimped oats. We have all these choices, and oftentimes those choices are made based on a performance horse that can’t hold its weight. ‘Well, let’s give it more sweet feed,’ (we say), because more calories, more starch, more energy, means more bulk, right? Now, we continue training … and are creating a situation in the gut where the good bacteria are not happy because they’re getting too much sugar, they’re not getting enough forage or fiber.”



By adding extra starch (easily digestible carbs) to your horse’s diet, you immediately expand a certain population in the gut—Lactobacillus—which the gut does need to break down these carbs. But an overgrowth of these bacteria drops the GI tract’s pH (makes it more acidic). And if that weren’t enough, that bacterial bash can’t digest all the starch so, instead of it getting absorbed in the small intestine, it dumps into the cecum. “Then these horses get these sour guts, they get intestinal ulcers, they get diarrhea, they feel like crud, they don’t want to perform,” says Franklin. 

“And these oftentimes are the horses that you can smell two stalls away,” adds Latson, describing the loose, light-colored manure these horses produce.

DNA Tests for Belly Bugs??

Forty years ago, this stinky stall told the vet and horse owner that something wasn’t right—and it still does—but researchers have developed exciting new ways to figure out exactly what imbalances are at play so they can correct them.

Franklin returns to the car analogy. “If you think about an axle breaking, there was a point where that axle was getting weak and probably still handling fine, but then, ‘Boom!’ When the axle breaks, the horse has diarrhea. We used to have to wait for that diarrhea or soft, smelly pile to show up in the stall, but now, because we can measure the microbiome and we can see what’s happening in there, we can see that crack in the axle before the whole thing snaps—the same way they can evaluate your genome and predict your predisposition towards X, Y, Z disease.”

You know the story from the many human DNA test kits marketed online, on television, and in social media: Understanding your health condition tendencies means you won’t be held hostage by your genetics; in many cases you can make overall health and lifestyle changes to reduce the risk of diseases developing. 

“You’re not just waiting for nature to take its course; now you can be assertive,” Franklin adds. “We’ve got the same opportunity … we don’t have to wait for (horses) to develop these problems, we can go in there, diagnose there’s a disturbance, make an adjustment and, now, hopefully prevent problems” that are often to blame for colics and other GI disturbances (think horses’ responses to weather or feed change, turnout buddy change, or pasture change).

“The blinders have come off,” says Franklin. “We have the ability to see into the intestinal tract and predict these problems before they occur and do something about it.”


What Can I Do to Promote Gut Health For My Horses?

If something’s amiss with your horse’s manure, attitude, condition, or performance—even if he seems just a little “off,” or that manure smells to high heaven—have your vet out to the farm. He or she will take a complete history and conduct a thorough physical examination, using what they see, feel, hear, and—yes—smell. 

They’ll move on to bloodwork, stallside tests (to confirm infection, for example), and sometimes advanced imaging, they might not come up with anything, says Franklin. “Now, these tough problems, these chronic, nagging, why-is-he-doing-this type of problems, now we’re going to have the ability to do a microbiome study and to see: Is the microbiome disrupted? Is there a problem with the genetics in the microbiome that’s translating into this subtle, chronic disease state that this horse has?”

Veterinarians are on the precipice of being able to dive down and identify every microbe active in the horse’s hindgut, says Franklin.

Until these tools are ready to use, the FullBucket team recommends using the right pre- and probiotics. Prebiotics are the fertilizer that allows healthy bacteria to survive and thrive and the equine microbiome to reestablish itself and be healthy. Probiotics are live microbes that help improve digestion and supply nutritional benefits.

“Every horse that’s domesticated, that’s living on anything other than a natural, wide-open pasture needs to be on prebiotics and probiotics,” says Franklin, that are encapsulated and of the variety that the horse needs in his gut.

“We (as veterinarians) are doing everything we can within our power to allow those horses to perform as well as possible,” adds Latson. “But what’s reasonable for the horse and how much can they really take? They can take a lot before the axle breaks, but it really becomes about our stewardship of the horse. As we’re treating with the probiotics and the prebiotics, we’re really setting them up for success.”

Keeping the Hindgut Healthy with FullBucket


FullBucket is the only supplement company totally focused on digestive health.

We have a complete line of all-natural digestive products to help control and prevent GI distress that leads to severe problems such as diarrhea, colic, colitis and ulcers.

Athletic Formula - For the equine athlete under intense stress of training, travel and performance.

Probiotics - 3 levels for Prevention when under common stresses, Extended Care for horses that have had colic, colitis or ulcers and Urgent Care when horses are showing signs such as loose stool, diarrhea or weight loss.


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