by Robo Hendrickson

Your Horse's Gut Health: It's all about the microbiome

Your Horse's Gut Health: It's all about the microbiome

Key Takeaways You'll get

1) The microbial ecosystem, aka the microbiome, in your horse’s hindgut plays a crucial role in determining how your horse responds to common daily stressors. 

2) The hindgut is where the magic happens: The millions of microbes living there break down your horse's feed, extracting nutrients and releasing energy-containing fatty acids.

3) If you protect and keep the microbiome healthy, everything else falls in line. Taking care of your horse's gut health is the most important management decision you can make. 

Watch Dr. Rob Franklin and Dr. Keith Latson explain your Horse's Gut Health

What is a microbiome, and why should I care about the one in my horse’s gut? 

“I keep hearing about my horse’s microbiome, but I have no idea what it means.”

These days it’s nearly impossible to turn on our televisions, scroll Facebook or Instagram, walk through a grocery store, or even open our email without encountering a message about our gut microbiome and how important it is. 

We know it has something to do with the “bugs,” or microbes, in our gut. 

And we might be familiar with the “good bugs” in our gut from talking with our physicians, how certain foods are helpful for those bugs and others aren’t, and how antibiotics can knock them all down. 

But our understanding might be a little murkier when we’re talking about our horses, who have about four times the length of intestine that we do and consume vastly different diets. 

So, what exactly is the equine microbiome and why is it crucial to care for it?

A Crucial Ecosystem

The word microbiome need not be intimidating. Just think of it as an ecosystem of microorganisms living in a location on or in the body. Your microbiomes—whether you’re talking about the one in your gut, your lungs, or on your skin surface, for instance—are going to be much more like your neighbor’s microbiome than your horse’s. But even within one species there is considerable microbiome variation. 

“We know that horses are different based on where they live, what they eat, what they do, and on how old they are, but there are a ton of similarities between them, up to about 90 percent across the board,” says Dr. Rob Franklin, an equine internal medicine specialist and co-founder of FullBucket, a veterinary-strength supplement business based in Weatherford, Texas. 

Franklin and his co-founders Dr. Keith Latson and Robo Hendrickson, have a passion for educating the veterinarian and horse owner on the horse’s microbiome and how we can optimize it for health.

“The intestinal microbiome is really the broadest term that we can use to define all of the microbes and their genes (what they are programmed to do) in the intestinal tract,” says Franklin, who’s also FullBucket’s director of development and giving programs. 

He notes that the microbial population is a veritable “who’s who” of bacteria, protozoa, fungi, and viruses. 

“These things aren’t just in there inertly living, they’re doing stuff: They’re digesting food, they’re signaling different parts of the immune system, they’re dealing with pathogens,” which is a fancy word for disease-causing organisms.

Indeed, the sum of these bugs is making things happen and governing how the horse responds to situations such as stress from trailering, exposure to infectious agents at a horse show, or time spent under general anesthesia—situations that can cause gastrointestinal issues such as colic or diarrhea. 

This is a big shift in thinking for equine internists and surgeons alike, says Latson, an equine surgeon and FullBucket’s director of operations. 

“To think that all of the situations that we’ve treated symptomatically over the years—whether it’s inflammation or infection, diarrhea, any of those things— could directly contribute or be contributed to by the microbiome is mind-blowing.”

What’s changed the veterinarian’s understanding of the microbiome’s importance? 

Scientists have mapped various species’ genomes over the past few decades and shown how factors in individuals’ lives “turn on” or “turn off” different genes in the body, in different situations, leading to variations in everything from what color eyes they have to how they respond to different environmental toxins or pathogens. 

“Well, the same thing is happening now with the microbiome,” says Franklin. 

For example, when once vets might have merely speculated about a mysterious colic’s cause—attributing it to a change in weather, feed, stall neighbor, or pasture, for instance, says Latson—they now know such events do cause measurable stress on and shifts in the population of microorganisms in the hindgut, their overall balance, and how they interact with each other. 

Essentially, these events turn genes on and off, and the gut responds with symptoms like inflammation, stasis, and ulcers and other pathology.

While things can be easily upended, and you can try to avoid those situations best you can, the FullBucket team says you can be proactive about stabilizing and then maintaining the gut microbiome so it is ready for any such insults. 

“What we’re doing in the feed trough has tremendous effect for the overall health of the patient,” Franklin says. 

“This is something that applies across all horses, across all animals, across all cases, and I think the opportunity to really harness that as we go forward is exciting,” he adds.

Know Your Horse’s Gut

To wrap your head around how to channel the strength of a healthy microbiome, you must understand the horse’s GI tract, especially the hindgut—a word you might have read or heard your vet say but whose meaning, like the microbiome, is a bit mysterious. 

Besides the odd assortment of critters—rhinos, rodents, rabbits, and koala bears—horses are the only animals out there that are hindgut fermenters. 

We humans are primarily enzymatic digesters, which means enzymes in the GI tract unlock the simple sugars, proteins, and fats in our diets and the small intestine absorbs them into the bloodstream to use as energy. 

Our horses have some enzymatic action going on, too, but fermentation is really the focus for horses’ guts. In fact, it’s necessary to all animals that subsist on a high-fiber diet, says Franklin. 

“They have to digest things that are not easy to digest, and the way they do that is with bacteria that can help them break down these indigestible fibers.”

But let’s not get ahead of ourselves. 

The hindgut, as its name declares, is toward the end of the tract. 

Ahead of it lies the 8-foot-long esophagus, the 2-gallon stomach, and the 70-foot small intestine. Horses’ stomachs, like rabbits’, are designed to deal with small amounts of food throughout the day—acids and enzymes there liquefy the ingesta and kick off protein digestion, respectively. 

The resulting material enters the small intestine, where pancreatic enzymes digest and absorb sugar, starch, protein, fat, fat-soluble vitamins, calcium, and phosphorus. 

Everything left over gets broken down by all the bugs in the hindgut, which includes the 4-foot cecum (akin to our appendix, but ours is 3-4 centimeters) the 12-foot large intestine, and everything beyond until the ingesta exits as manure. 

The cecum “is like a sock that food just percolates in,” says Franklin, after which it shoots into the massive U-shaped 20-gallon large intestine with its big, sweeping turns. 

There, the bacteria, fungi, and protozoa (tiny multicellular organisms) break down the remaining ingesta, extract all the nutrients, and release all the energy-containing fatty acids they can through the intestinal wall and into the bloodstream. 

(Note: Humans do a little bit of fermenting in the colon, too, but don’t get that much energy from it.) 

What’s left travels through another 10-12 feet of small colon, where water gets absorbed and fecal balls form. 

Hindgut fermentation is why horses do well on increased levels of forage to keep warm and maintain body condition during the winter. 

“They have this great bounty of microbes, they can break it down,” Franklin explains. 

“All that magic is happening in that back part, the hindgut,” Franklin adds, noting that it’s problematic if we don’t manage it right. “Colic and diarrhea, they’re major, major problems for us as veterinarians and they all occur when that system is not operating properly.”

What Can I Do?

Now that we know disease is a downstream effect of microbiome-related problems, it puts veterinarians, who often serve as “firefighters” in their daily practice, says Latson, in a better position to stave off issues altogether. 

Here’s How: 

FullBucket, in conjunction with a field of independent researchers, are building a gut microbiome library using fecal samples from thousands of horses. 

As the libraries build, population scientists and epidemiologists—who investigate the reasons why disease occurs within populations (in this case, horses)—and their computers can determine what specific variations in the microbiome create risk for certain health problems.

“Now we’re starting to talk about preventative medicine, not reactive medicine,” Latson says. "That’s exciting.”

“The scientific community has realized they’re pioneers on the front end of a huge discovery and it’s ratcheting up the ladder of importance in the industry very quickly,” says Hendrickson, who is also FullBucket’s director of marketing, noting that some studies even show that caring for the microbiome could remove the need for antibiotics in some cases.

Aiming for hindgut health and balance used to involve a whole lot of art along with science, but as microbiome research progresses, innovators in the horse industry like the FullBucket team, are equipping veterinarians with the correct prebiotic and probiotic supplements to effect real change in their patients. 

“These aren’t just extra vitamins so you can shave a tenth of a second off your run or so that your horse’s coat looks a little bit prettier at the show,” says Franklin. 

“No, we’re talking about big-picture health. We know that if we protect and keep the microbiome healthy, everything else falls in line- including competition and winning.” 

“Horse owners need to remember that what they’re putting into their horse’s feed bucket could be the most important choice they make today,” adds Hendrickson.

Gut Health for Horses: The FullBucket Solution

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

Our complete line of all-natural digestive products helps control and prevent GI distress and other severe problems such as 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 recently 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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