Equine Microbiome Update: Study Reviews Research
Throughout the 100 feet of intestines packed as winding passageways inside your horse’s abdomen, life runs abundant, in abundant forms. Entire communities of bacteria, fungi, and protozoa share this microcosm, known as the gut microbiome, where they interact with your horse—and with each other. Worthy of their own science fiction movie, these millions of independent, living organisms have an entire world of their own within the equine gut’s lining, with “good guys,” “bad guys,” and the ever-constant risk of some group taking up too much power and destroying their universe. It’s a fascinating but highly complex story—and it’s told by science.

As researchers move toward a better understanding of the equine gut microbiome, one scientist has sought to unite the more than 150 studies exploring this somewhat obscure part of the horse’s body. The objective of such a globally encompassing review was to “assimilate our current knowledge on equine microbiome studies,” and in particular to focus on the various effects of factors that could influence gastrointestinal microbiota in horses, said veterinarian and nutritionist Anna Garber, PhD, of the School of Veterinary Medicine at the University of Glasgow, in the U.K.

Understanding Good and Bad Gut Bacteria

Understanding the gut microbiome and how different factors positively or negatively affect it would be easier if we understood what truly constitutes “good” and “bad” bacteria. But it’s not that cut and dry, said Garber. Much depends on delicate balances as well as on context, making the evaluation of factors particularly challenging.

“It’s difficult to divide what is good and what is bad,” Garber said. “It’s not always clear what can be considered negative changes in the gut microbiome of the horse.”

A few generalities do, however, exist, she said. For example, bacteria that produce high levels of lactic acid—such as Streptococcus and Lactobacillus—are considered bad because they’re associated with increased lactic acid production in the gut, which “often leads to colic,” said Garber. “And even if it’s not manifest colic, it can be subclinical (showing no signs), which is also not good for the horse.”

Meanwhile, Lachnospiraceae and Ruminococcaceae bacteria are usually among the good guys because they help break down plant material, processing the nutrients and converting them into energy. Lachnospiraceae also produces butyric acid, which aids immune function and gut wall integrity, Garber said.

Despite these generalities, much affects what we consider “good” or “bad,” said Garber. “It’s really difficult to make global conclusions,” she said.

The Top Gut Microbiome-Affecting Factors

Garber’s review led her to identify several primary factors that can affect the equine microbiome’s composition—for better or worse.

  • Diet: Pasture grass, hay, and concentrated feeds each promote different environments in the gut, which are more or less favorable for certain kinds of microorganisms. Starches from concentrated feeds can ferment in the hindgut, making it more acidic. Acidic environments are challenging for certain kinds of good bacteria that help break down plant cells and can lead to digestive issues. Supplements (probiotics and prebiotics) seem to cause changes in the microbiome, but researchers don’t always agree on what’s happening or whether the supplements are effective. Fasting can cause a drop in certain kinds of good bacteria, as well.
  • Exercise: Intense exercise, regular exercise, light exercise, or no exercise—all these situations can influence digestibility and digestion rates, which can alter the microbiome.
  • Obesity and metabolic issues: Researchers note clear differences in the microbiome makeup between obese and nonobese horses. In particular, obese horses and easy keepers seem to have greater diversity of organisms. “Obese horses would usually have a more diverse microbiome, because their gastrointestinal tract might be better adapted to extract energy from the feed,” Garber said. But it’s hard to say whether the microbiome changes are due to metabolic changes or the obesity itself. Plus, there’s the “chicken-and-egg” conundrum: Do the horses have obesity/metabolic issues because of the microbiome, or is it the other way around?
  • Time and place: Microbiomes change in horses according to geographic location and season. It seems that “microbial communities of the equine gut are highly dynamic and responsive to environmental changes,” Garber said.
  • Medications: Antibiotics attack both good and bad gut bacteria, she said. The good kind includes those that can hydrolyze cellulose in the plants horses eat. It can take days or weeks for horses’ microbiomes to normalize after some kinds of antibiotic treatment, she said. Non-steroidal anti-inflammatories also tend to affect the number of good bacteria, even though they’re frequently prescribed to control colic pain. Deworming products can reduce populations of useful bacteria, as well, she said. They can also affect the production of mucin, gut proteins that promote a good nutritional environment for bacteria. Other drugs that can reduce bacteria numbers and diversity include anesthetics.
  • Breed, age, sex, gestational status: Researchers note a variety of differences in the gut microbiome related to horse-specific factors, Garber said. Gut makeup differs according to a horse’s breed and sex and whether a mare is pregnant, not pregnant, or nursing. All horses are born without a microbiome and then develop one over the first few months of life.
  • Gastrointestinal health: Diarrhea and colitis are associated with significant changes in some bacteria ratios more than others, leading to infection, said Garber. Meanwhile, colicking horses experience microbiome shifts that might be detectable in their feces before they show signs of pain.
  • Laminitis: Study results suggest a strong link between laminitis and microbiome changes, specifically alterations in the presence of lactic-acid producing Streptococci and Lactobacilli, which might be involved in the development of the disease itself.
  • Equine grass sickness: This disease appears to be associated with specific microbiome changes, such as decreased Firmicutes phylum and increased Bacteroidetes and Veillonella.
  • Stress: Researchers have detected various changes in the microbiome of horses before and after being transported, but the results aren’t consistent across studies. Scientists seem equally divided about how weaning affects the microbiome, with some studies showing major changes and others showing very few.

Individual Factors? Not in the Real World

A downside to these 150-plus studies is none of them successfully focus on a single factor affecting the microbiome, said Garber. The researchers never fully isolate one element from everything else. It’s “not really possible,” she said. Horses are so individualized, with so many different characteristics, experiences, and influences, that getting an entire study group of horses that have identical situations except for one single factor isn’t realistic. But in the end, she said, it might not matter much anyway.

“Probably the most interesting finding from this review is basically that all factors affect gut microbiota, and you can’t really isolate one factor,” Garber said. “It’s always a complex that you’re evaluating. This isn’t a constraint, though, because in the real-life scenario, this is what horses encounter. I don’t think there is a need to try to focus on only one thing and reduce the influence of other factors (in research), even if that’s ideal to know how one factor affects the microbiome.”

Change Might Be OK, if Gradual

Although science still hasn’t been able to home in on what the ideal equine gut microbiome looks like, one message seems clear: Slow change is better change.

“As a vet and a nutritionist, I really have to say that, okay, different factors affect the microbiome, and yes, that’s normal,” Garber said. “Our role, though, is to make those changes gradual. The microbiome is adaptive, and it can adjust. It just needs time to do it.”

That means introducing new foods and management conditions progressively, rather than abruptly, said Garber. “Progressive change is less stressful for the animal and less stressful for his microbiome, as well.”