Most horse owners have heard of microbiomes, but they might not understand the wide role these communities of organisms play in equine health. In this podcast, Dr. Simon Daniels of the Royal Agriculture University in the United Kingdom talks to us about the equine gut microbiome.

(Editor’s note: The content of this podcast is the expert’s approach to the topic. Please consult with your practitioner if you have questions.)

What Is a Microbiome?

“There are microbiomes everywhere,” stated Daniels. This includes on the skin and in the gut, mouth, and respiratory system, to name a few locations.

While scientists knew there were micro-organisms in the horse’s cecum back in the late 1800s, it wasn’t until the late 20th century and early 21st century that the equine gut microbiome became a research focus.

Daniels explained that in the equine gut (mostly the hindgut, but also the stomach and small intestine), there is a natural array of bacteria, fungi, and protozoa that makes up the microbiome. “We actually almost think about them like a virtual organ,” Daniels said. “They’re like an extra part of the horse.”

The Equine Gut Microbiome

Daniels said the equine microbiome is “like this extra organ that a big part of its role is involved in turning all that lovely fiber in the diet into energy. But actually, it plays an even bigger part that we’re only really starting to now understand. It can be linked to health and disease. We think it’s linked to behavior.

“When we talk about the microbiome, typically we’re talking about all of the bacteria, fungi, protozoa, everything that you find within the horse’s hindgut,” he continued. “But quite often the microbiome studies focus pretty much only on the bacteria rather than the other elements. This is simply because of the different ways that we measure bacteria, fungi, and protozoa in microbiome studies.”

The Microbiome Is Sensitive to Change

In the feral horse, forage is trickling into the gut almost constantly, said Daniels. He said the microbiome doesn’t cope well with quick changes in the diet, which has been proven in many research studies. Quick changes to complementary feeds and even to forage can lead to colic and other issues.

Daniels said this goes back to basic equine management. Making feeding changes gradually allows the “bugs” of the microbiome to adjust to the new rations.

Daniels recommended changing forages or complementary feeds over a period of a couple of weeks. “There are some bacteria in the gut that change, but they are doing a similar job when the diet changes to those that were there before,” he explained. “But, if the new bacteria that take over [after a feeding change] put out a different metabolite, that seems to be where we get problems.”

“We’re also starting to understand broader health and behavior concepts…that seem to be driven by signals [from the microbiome] up to the brain,” said Daniels. The microbiome “can give signals for more depressive states or happier states, and that can actually link to behavioral responses.”

The current understanding of how the microbiome affects the whole horse is just the tip of the iceberg, he said. “There’s a huge amount under the water yet we haven’t managed to unpick.”

Prebiotics and Probiotics

Antibiotics and other factors can cause changes in the horse’s microbiome. Daniels explained how horse owners can help re-stabilize the gut in these instances.

“There are lots of studies on the use of prebiotics and probiotics,” said Daniels. “Prebiotics especially help to feed the healthy bacteria and other organisms in the microbiome. Different studies have very different feelings about probiotics. But, even if they don’t always fully colonize in the gut, they provide food for those bacteria. So, certainly the use of pre- and probiotics seems to have some help in stabilizing after an event such as an antimicrobial.”

The same could be true when giving anthelmintics.

Daniels relayed research findings from the Horse Microbiome Group in the UK. Researchers followed a set of Thoroughbred foals into their racing careers. They found if foals had antimicrobials early in life—often for respiratory illnesses—they seemed to be less successful as racehorses. Daniels said that could be traced to a reduced diversity in their microbiomes as adults.

Stress and the Microbiome

One area Daniels thinks deserves more research is how the microbiome might be associated with weight loss in senior horses.

He also discussed leaky gut syndrome in humans and horses. This condition can cause substances to leach out of the gut and enter the animal’s body. “Serotonin, the feel-good hormone, can come from the gut,” said Daniels.

He said horses on high-starch, low-fiber diets can display more reactive behaviors. Other horses that are stressed can be more reserved in their behavior.

Daniels said if the diet is right and the gut is happy, the horse probably will be happier. “But, if the diet’s not quite right, then potentially you’re seeing some of those behavioral circumstances. Again, it’s an area we really need to explore because it may give us another sort of indication as to where we can try and improve the health and welfare of the horse.”

Tips for a Happy Microbiome

Daniels said senior horses should have the vast majority of their diets as fiber. “That becomes more difficult when we have older horses that are a little more dentally challenged. Then it’s about what fiber options we have. Are there things that we can soak?”

Make sure feed and forage transitions are slow and steady, he stressed. If you see inconsistency in the horse’s manure, consider a prebiotic or probiotic. “In some horses it’ll work really well, and some not so much,” said Daniels. “But, it’s worth trying those different approaches.”

About Dr. Simon Daniels

Simon Daniels, PhD, PgCert, R. Anim. Sci., SFHEA, BSc (Hons), is an Associate Professor of Equine Science at the School of Equine Management and Science, Royal Agriculture University (RAU), in the United Kingdom. He is the program leader for BSc (Hons) Equine Science and Business and BSc (Hons) Bloodstock and Equine Performance Management. Daniels also oversees all the equine provision at the RAU.

Daniels has been involved with horses since childhood. After completion of his undergraduate degree, he spent time in industry working as a nutritionist at an animal feed company specializing in equine nutrition. He then took a position at the University of Liverpool in the School of Veterinary Medicine working with an industry partner to design and implement a parasitology diagnostic laboratory service.

This brought about the opportunity to undertake a PhD in the efficacy of equine anthelmintics and their effects on intestinal health. This was completed at the University of Surrey School of Veterinary Medicine. Completion of the diagnostic parasitology project with the University of Liverpool led to his move back to full time academia.

In 2014, he joined the RAU within Equine Management and Science. His main areas of interest remain within health of the equine gastrointestinal tract. For further information visit https://dr-simon-daniels.co.uk/.

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  • Kimberly S. Brown and Jewell

    Kimberly S. Brown is an award-winning writer and publisher. She founded My Senior Horse for Equine Network and Linda Mars in her retirement, and now she is an editor of the brand. Brown previously had spent 10 years at Equine Network. Prior to that she worked for three years in equine nutrition after she retired from nearly 30 years working at The Blood-Horse. Brown spent the last 15 years of her time at that organization creating and developing the award-winning The Horse and TheHorse.com.

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