The Equine Microbiome


Bad bacteria

What with all of the products out there to help “support” your horse’s gastrointestinal system, I thought it might be fun to share some thoughts and research with my friend Dr. Carolyn Arnold.  Dr. Arnold is an Associate Professor at Texas A&M University, in College Station, Texas, where she specializes in soft tissue surgery.

In 2014, Dr. Arnold became interested in trying to understand why some horses developed colitis (inflammation of the colon) and diarrhea (which usually goes along with colitis) after they had a surgery.  She wondered, “Was it the surgery?  Non-steroidal anti-inflammatory medication?  Antibiotics?”  These questions led her to pursue a post-graduate degree investigating the equine microbiome.

“What’s a microbiome?” you say.  The microbiome is made up of all of the microorganisms that live in a particular environment.  Dr. Arnold is particularly interested in the microbiome of the horse’s gastrointestinal tract:  you know, colon, small intestines, stomach, and such.  The horse’s body depends on all of these microorganisms to live a healthy life.  They protect the horse against invading bacteria, they are involved in the immune system that helps keep horses from getting sick, they break down food to release energy for the horse to run and buck and spook on, and they even produce many of the vitamins that the horse needs (which is one reason why vitamin supplementation in horses is mostly pointless).  Understanding the equine microbiome is critically important for understanding the horse’s health, and for understanding what we can and cannot do for (and to) the horse.

Bad bacteria

Dr. Arnold starting her research by going back through the literature on horses to see what veterinary science thought it knew.  Turns out, not much, or at least, not enough.  Even 10 years ago, people would get manure from a couple of horses and do the sorts of things that microbiologists love to do:  culture the manure and try to identify the bugs in it.  That was all well and good, but there was a serious limitation to this approach:  it only really measures the bacteria in the hindgut, at the (quite literal) end of the horse’s gastrointestinal tract.  There’s a whole foregut at the front part of the intestinal tract of the horse that essentially wasn’t being measured it all.  And whereas food breakdown, water absorption, and vitamin production (among other things) occurs in the hindgut, the foregut is where the food that the horse eat first starts being digested.

Dr. Arnold started about looking at the bacteria in the horse’s intestinal tract in a different way.  She’s relied on RNA sequencing instead of actually growing bacteria.    RNA sequencing uses part of the bacteria to identify it, rather than relying on growing the bacteria.  It turns out that this is really important for identifying gut bacteria because so much of the gut bacteria can’t live in the presence of oxygen; they’re anaerobic.  So, for starters, Dr. Arnold found out that there were a whole lot more species of bacteria – bugs, if you will – than we had thought.

Good bacteria

The big question in Dr. Arnold’s mind was, “Do horses with disease of their gastrointestinal (GI) tract have different bugs than healthy horses?”  In people, that’s been shown to be the case.  That is, people with GI disease – Crohn’s Disease, Inflammatory Bowel Disease, and the like – have a different microbiome from healthy people.

Before getting into what’s abnormal, however, Dr. Arnold first had to go about trying to establish what was normal in the horse’s GI tract.  Importantly, she had to try to determine if what was normal in one horse was normal for most all horses, and, if not, what things could cause changes.  A big task indeed. Undaunted by the challenge, Dr. Arnold went about trying to find out if different populations of horses have different microbiomes.  If things like age, breed, sex, and diet made huge differences in the microbiome, it would be hard to make recommendations across the species.

As it turns out, the microbiome of the Quarter horse in Texas is actually quite similar to the microbiome of the Warmblood in Connecticut.  Otherwise stated, for about 90% of horses, in different seasons, on different diets, and in different locations, there seems to be something of a normal range for the bacteria in the horse’s GI tract.

It also turns out that certain things can rather predictably alter the equine microbiome.  For example:

Nutrition.  When horses eat large amounts of grain in their diet (e.g., racehorses), their microbiome changes.  Veterinarians have known that large amounts of grain are associated with all sorts of diseases – laminitis, colic, etc. – but large amounts of grain also change the bacterial population.  It doesn’t seem to matter much whether horses live on forage alone (hay and pasture), they get a low fiber concentrate (sweet feed:  5 – 7% crude fiber), a medium fiber concentrate (10 – 15% crude fiber), or a high fiber concentrate (18 – 33% crude fiber – most feeds advertised as “low starch” fit this description).  As long as a horse gets adequate forage, giving a horse some grain doesn’t seem to affect the microbiome.  It’s at high concentrate levels – such as are fed to racehorses – the microbiome changes.

NOTE:  You can find the amount of crude fiber on the label of your horse’s feed (assuming that he’s not just on forage, which is just fine for most horses).  Fiber is inversely related to starch – the more fiber, the less starch. And low starch is certainly desirable for many horses.

While changes in the horse’s microbiome probably also changes some of the physiologic processes of the horse, but it’s too early to say if this change directly causes disease.  In many other species, it’s been shown that the microbiome is slightly sensitive to things like, diet, season, and acute changes in diet, as well, however, these changes aren’t necessarily associated with disease.  Regardless, it’s food for thought and future research, to be sure.

Antibiotic use.  Antibiotics kill bacteria.  The gut is full of bacteria.  Antibiotics can affect the microbiome.  That’s easy to understand – maybe less easy to understand is why antibiotic-induced diarrhea isn’t more of a routine problem, although to be sure, different antibiotics have different effects on different bugs.

Disease.  It is known that with intestinal disease, e.g., colitis, there are BIG changes in the microbiome. It’s been shown in at least one study that the microbiome of horses that colic is different from the microbiome of horses that don’t colic, but it’s too early to say that a change in the microbiome will always cause a horse to colic.  It’s going to be an area of a lot of research, for sure.

To make things even more complicated, all equine microbiome changes are not created equally.  So, for example, horses with diarrhea caused by Salmonella bacteria appear to have a different microbiome from horses with diarrhea caused by antibiotics.  If that’s the case, it might be possible to develop a sort of microbiome index to see if it’s possible to tell what might have caused the changes.  According to Dr. Arnold, we might even have such a thing in a year or so.


Well, certainly, at least if you believe everything you read.  Protecting the microbiome is pretty much the entire premise of giving horses things to “support” their digestive tract:  prebiotics and probiotics and the like.  However, the fact is that giving a pre- or probiotic doesn’t magically make a horse’s GI tract safe, secure, and efficient.  For one thing, the relatively few bacteria that are in equine probiotic products don’t really make up much of the bacteria that live in the horse’s gut.  It’s at least possible that they may provide some benefit (that’s still to be determined), but they absolutely certainly do not “normalize” the equine GI tract.  There’s a long way to go before we get to having a product designed to restore the equine microbiome.

Then there’s the problem with the equine stomach.  The horse’s stomach is, among other things, a vat of acid.  Acid is one of the worst things you can run into if you’re a bacteria, and there’s a lot of question about how much, if any, bacteria can survive the stomach is you squirt some in a horse’s mouth.

Another part of the problem is that probiotics are not drugs, and they aren’t regulated as drugs.  That is to say that you really have very little idea what you’re giving when you’re giving a horse a probiotic.  There’s also problem with content –  the products may not have the bacteria said to be in the product in the product, the bacteria in the product may not be alive, and the cell count (the colony forming units, or CFU) may not be what they say.

In addition, there’s also the whole question of dose.  There’s a tremendous variety in how many CFU are in equine products.  In humans, products may have as much as 900 billion CFU’s – and humans are about 10% of the size of most horses.  In horses, the doses are usually much, much smaller.  Even if a product were to be effective, a dose of 2 billion CFU (or even 25 billion) isn’t like to go very far in a horse.

Probiotics in foals have not turned out well.  In fact, most studies in foals show that probiotics actually make foals worse.  If you think about it, that makes some sense.  A newborn foal doesn’t have the same microbiome as an adult horse.  Foals transition from drinking Mom’s milk and eating Mom’s poop to eating Mom’s food, and it takes a while for their microbiome to be like an adult’s microbiome.  Treating a foal with adult horse probiotics doesn’t make a ton of sense, no matter what else might be wrong with them.


Good news!  A probiotic isn’t likely to hurt your horse.  That’s a pretty low bar for any therapy, of course.

Bad news!  There’s really not enough evidence to support their widespread use.

Good news!  There has been one study that suggested that freeze-dried bacteria given to horses can shorten the duration of hospitalization, but, well, that’s one study.

Bad news!  There are conflicting studies.

Good news!  It turns out that in the process of studying the equine microbiome, Dr. Arnold has found that most people feed their horses pretty well.

Better news!  If you’re fretting a lot about how you’re feeding your horse, it’s probably worth fretting less.


In medicine, as in law, things should be considered innocent until proven guilty.  That is, a product or therapy – probiotic, prebiotic, or anything else, really – should be considered innocent of having any effect on the horse until proven guilty of having an effect on the horse.  When it comes to the equine microbiome, we don’t really know enough about what’s normal to go about making any strong recommendations or having any firm conclusions about what to do when things are abnormal.  Happily, horses seem to do pretty well on their own, but there’s certainly a lot more to learn.  Thanks to researchers like Dr. Arnold, we’re getting there.

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