Decomplexicating Equine Nutrition Part 03 of 12 – Gut Microbes

So far we have covered the definition of grazers as an animal that eats cellulose. We have discussed the similarities between carbohydrates (glucose, starch, cellulose, glycogen), fats (triglycerides, short chain fatty acids, ketones) and amino acids (the building blocks of protein). Each of these has the atoms Carbon, Hydrogen and Oxygen and the way they are put together into molecules determines whether they become a carbohydrate, fat or protein. In this article, we will be looking at the microbes in our gut and their relationship to the different molecule construction.

Who Eats Our Food?

The concept of gut microbes will either mesmerize you or will completely turn you off to further discussions on feeding anything. It took me a bit of convincing but now that my paradigm has shifted, I live by this concept. Simply put, we do NOT feed ourselves or our horses. We feed the bacteria living inside the gastrointestinal tract and THEY feed us and our horses. This is the part that has been missing in so many discussions on nutrition and has led to more confusion. It is the missing link. Feeding the body is a two-step process involving the gut microbes.

Now the concept of comfort food is not the food that comforts us but the food that comforts the gut microbes that in turn makes our horses healthy and happy. And grains are NOT comfort foods for horses.

The words to describe the colonies of microbes that inhabit the gut are the “microbiome” and the “microbiota.” There are also microbes on the skin (this causes the armpit odor and skin infections when wounded) as well as a cloud of microbes around us (our breath). This total collection is called the holo-biome and the number of total bacteria inside us, on us and around us is 8 times larger than the number of cells in our body. 90% of our genetic makeup is from this holo-biome.

Advancing science has enabled us to look at the bacteria in our feces and in our mouths identifying the individuals by name. Swabbing the mouth has identified 700 individual species of bacteria. Think of it as a neighborhood with the Smith family, the Jones family, the Adams family and many others. Within one family there are many individuals like Papa Smith, Mama Smith, Little Smith 1, Little Smith 2, Uncle Smith, Aunt Smith and all of their children. In a study done recently at the Texas A&M vet school, it was found that one dose of a non-steroidal anti-inflammatory drug commonly given to horses wiped out an entire family of bacteria. The same is true with antibiotics, anti-ulcer medication and anti-parasite medications. After they are killed, either opportunistic bacteria take over or if the drugs are stopped the original family returns.

There is a company now asking for a pea-sized sample of feces and it will tell you what diseases your horse is prone to. No one has been able to sample gut material from specific sites in living beings yet, but I will tell you a fascinating story. When potent antibiotics first came out in humans back in the 1970’s many patients developed life-threatening colitis (inflammation of the colon). To save these patients a “honey pot” was passed around to healthy medical students to collect their normal feces. This was mixed with water and the patients were given an enema of this fresh feces mix. It stopped the colitis instantly and saved lives because, in essence, they were given a good gut microbe transfusion.

The importance of normal gut bacteria cannot be overemphasized. Feces from fat mice were fed to thin mice who then became fat. Feces from thin mice were fed to fat mice who then became thin. It is the neighborhood of gut bacteria that feeds the body. Once the neighborhood goes bad there is not much to stop the disease processes that come from it nor the fat that develops. But with healthy gut bacteria, the body becomes healthy. This is being proven over and over again in human medicine but in the horse world, we are very slow to realize this relationship.

In the first article, I stated that stopping what we are feeding the horse is more important than adding something new to gain an effect. This is because when a horse feeds on what it has fed on for millions of years the good gut bacteria thrive and they feed the horse correctly. In 1973 horses were still fed a lot of pasture and given hay to survive the winter. Now the number of different types of grains and supplements is staggering. Anecdotal stories of various seeds (grains) and oils and herbs abound without even a tip of the hat to what the horse really should be eating. If we all realized that the horse can produce everything that it needs to survive and thrive when the gut bacteria are fed what they need to survive and thrive then feeding the horse becomes very simple. This includes vitamins produced by good bacteria.

Unfortunately, the horse owner has been blasted with misinformation on what a horse should be fed and these ingredients are causing the destruction of the good bacteria and the overpopulation of the bad bacteria. Additionally, most horses are limited in what they can eat due to confinement and overgrazing. This in turn is affecting the gut lining (leakage with invasion of foreign proteins, immune system compromise, ulceration, hormonal disruption and an overall unthriftiness and structural demise).

An emu at a horse farm in FL –  Just a break in the dialog to rest your brain 🙂

In my discussions with horse owners, I ask what they are feeding the horse. The starting point for almost everyone is describing the grains and supplements rather than the amount of pasture and amount and types of hay. Digging deeper, the answers given include the name of a product but when asked for the ingredients of the feed, the owner doesn’t know. Worse, after reading the ingredients the owner still is unsure of what they mean. Almost every horse feed I look at now includes byproducts of the grain industry such as wheat middlings, oat hulls, soybean hulls, distillers’ grain byproducts, rice bran and sugar beet pulp. All of these at the minimum are inflammatory due to plant defense proteins built into them. And if there are whole grains such as corn, oats, barley and such, these are also sources of starch. There is nothing that will cause fat production and inflammation more rapidly in horses or humans than starches fed year round coupled with inflammatory plant proteins (more on these later.)

Remember the last article where I described the constant feeding of sugar taxes the insulin system, burdens the mitochondria, adds body fat and prevents the use of body fat as a fuel source of the preferred fuel called ketones? This is bad enough but remember that bacteria are also living things requiring food. This is the definition of prebiotics which is the foods that feed these good bacteria. Unfortunately when fed incorrectly the “good” bacteria needed for cellulose digestion die while the smaller colonies of sugar-eating bacteria expand and overgrow in the horse’s gut. This in turn causes inflammation and even ulceration of the colon leading to behavioral issues including bucking and girthiness. It also contributes to many if not all colonic causes of colic.

Many horse owners have described the benefits of removing grain and other sources of added sugar (sugar cubes, carrots, apples, red mineral salt licks and other minor sources). These include ease of grooming and saddling the horse, calmer energy, quieter and more productive rides, and elimination of colic and anhydrosis (non-sweating) among other things.

There often is a complaint in older horses that they look worse after the elimination of grain. Like taking the clothes off and seeing what a person really looks like, once the fat comes off the horse the owner now sees how much muscle has been lost. This is from gluconeogenesis where existing muscle protein is turned into glucose for survival. Why does the horse need glucose from muscle when he is being fed starch in the grains? Simply put, the cells are becoming insulin resistant and the glucose isn’t getting to the cells. The brain sees a lack of glucose and orders gluconeogenesis because it thinks it is starving to death even though the body has abundant fat. Additionally, any gut microbes digesting the cellulose to make short-chain fatty acids have been greatly reduced in numbers while the neighborhood is being overrun with sugar-eating microbes.

Add to this nutritional mess any nonsteroidal anti-inflammatory, anti-ulcer medicine, anthelmintic, or anti-biotic and the microbiome balance just gets worse.


  1. Feeding our horses is a two-step process. We feed the microbes living in the gastrointestinal tract and they in turn feed the horse.
  2. If the good microbes are fed correctly the way they have been fed for millions of years then they will feed the horse with everything they need to live a healthy life.
  3. If the good microbes are fed incorrectly then they will starve and other opportunistic bad gut microbes take over feeding the horse things the horse can not remain healthy on.
  4. The dead bacteria create inflammation of the gut lining and along with plant proteins, the gut starts to leak bad things into the body disrupting hormone communication (insulin resistance for example) and immune function (autoimmune disease for example), and gut ulceration.
  5. Year-round intake of glucose-laden food bypasses the normal lean time of the year causing mitochondrial fatigue and destruction, insulin resistance and muscle resorption (gluconeogenesis).

These last two points are teasers of what will be coming in the next few articles. I hope you will return for more.

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  1. Oh boy, knowledge is power, also knowledge leads to “OMGosh am I a good microbe farmer?” I needed to fertilize and weed kill my pasture today. I now have a furrow between my eyes wondering if the weed kill is also killing gut flora? Tomorrow starts a 5-7 day rain system moving through. Keeping the horses off the pasture for 18 hours. Gives the spray a chance to dry and absorb over night. Rain should start around 3:AM. Horses usually have access to 12 acres 20 hours a day, mopey faces in the barn. Also Knowledge helps you make small adjustment for improvement, even if it isn’t perfect. Sandspurs or weed kill. I chose weed kill. sorry Flora!

    1. This is often a difficult decision especially when our pastures are limited in size. Because of the limited nature of the grasses the normal defense mechanisms of the grasses are removed, hence the weed invasions. Nobody wants to use chemicals these days and would rather go “natural” yet there is nothing “natural” about fences and seeding pastures with a limited flora. The same goes for parasite control, diet, exercise etc. We all make the difficult decisions you made, but then after choosing a weed killer, they add sugar in grains, fly control, and unneeded medications. Yikes! In my mind, choosing the battles in horse care, politics, relationships is all about compromise. All we can do is the best we can 🙂

      1. Compromise… you said it Doc T!

        3 years ago, my Mare managed to get a sand spur in her eye, as you know eyes do not heal well in the heat of the summer. Lucky for us, it went well, it was exhausting to medicate her eye every 3 hours day and night, for 3 weeks.

        I weed kill 1 time a year. Because of all the knowledge you share, my small adjustment was to keep them off the pasture until after the first rain fall. Next year I was thinking I should give them Wormer, at the same time I weed kill. Thus disrupting the gut, one less time per year.
        I worm every 4 months or 3 times a year plus weed kill, so that is 4 known times a yr, of disrupting the Flora. Sounds like a lot, and it makes me feel like they will never truly have a healthy gut.

        This leads me to ask, what is your opinion on feeding a probiotic after you knowingly disrupt the gut?

        1. My view on probiotics is evolving. I never really believed in them but would eat a yogurt to settle an upset stomach. Currently there is evidence that the addition of foreign cultures on a regular basis into an individual’s gut microbiota actually can overrun the normal gut flora.

          According to some human functional doctors, using prescription strength probiotics encapsulated to avoid the killing effect of the stomach acid may be beneficial in humans. On the other hand, a company called Viome that tests the flora of human manure states that they never find any bacteria that have been introduced as a probiotic. They say probiotics are useless because they are all killed.

          Who is right? I’m not sure but I know for certain that if they don’t know the answer in human medicine then there certainly is no basis for giving probiotics to horses – because there is no research. It is just marketing once again. I would love to see some good research on this but it probably won’t happen as the word “good” precludes any agenda driven research.

  2. Hi,

    I have two horses that have been fed commercial feeds for years and yerasthen straight oats for about a month in Dec 17/Jan 18 and now on complete forage (Feb/Mar 2018) (bermuda hay and timothy/alfalfa pellets). How long does it take to restore the gut microbes?

    I switched all supplemental feed to pellets when I learned my 18 year old horse had EORTH…and after reading your website about EORTH, I made the switch. My second horse has been challenged with IR for last 5-7 years. He has not foundered but is heavy with atypical fat pads. Local vet scored him 9 last two years. He is on Rx for thyroid replacement which for a 14 months now with no significant change in BCS. Since on all forage, he is starting to present better plus I have made it a priority to work him moderately for 20 minutes every day that I can. Since 3/12/2018, when I started tracking his moderate exercise, I have exercised him 75% of the days.

    So now, I am wondering how long before the microbes are restored and IF i need to do anything beyond switching to all forage?

    Thank you. Lynne

    1. Every horse has a unique genetic code depending on his or her ancestry. Add to this the sugar content of the hay / pasture and it becomes hard to say exactly when the gut microbes are restored. A rule of thumb would be 6 weeks if all is well but this can change with different hay or the introduction of spring pasture. What I can say for sure is that if you feed your horse anything other than hay and pasture then the gut microbes will never return to a normal population.

  3. Excellent article — after reading the previous articles and the references you’ve made to protein, I’m seeing the bigger picture about what is best for my horse.

  4. Hi Doc T. I’m reading this series with interest and I wonder how the food value of hay is changed by soak it. I’m following my vet’s advice to soak the grass hay I am feeding for at least an hour to reduce sugars for a horse that had laminitis triggered by equine metabolic syndrome. I would like to know your thoughts. Keep up the good work!

    1. soaking hay in hot water for 30 minutes will dramatically reduce the sugar content to less than half. cold water takes a little longer with the same results.

  5. I have a Sr horse here (age is undetermined) but close to 30. Over the past 2 summers when put back onto hay he got the squirts. Then it became the normal state of his being. He is healthy and weight is good, teeth are good, they are checked every 6 months, he has cushings and is medicated accordingly. I tried your no grain approach for 3 weeks as you suggested.
    The only sweet he got was a small piece of apple for the pill. His manure looks good and solid. It is hard to tell if he still has the squirts as prior manure is frozen on his tail and I can’t really determine if there is new material on it. Overall though, I would say things look good. I have a 29 year old gelding, and two 17 year old horses as well. The others don’t have issues with their manure. All get the same food, lots of hay in hay nets, and twice a day a 1/2 bucket of soaked alfalfa/timothy cubes, optimal for mineral supplement (hay in Ontario Canada was terrible this year), a scoop of pure yeast and ground flax mixed. Free service loose white stock salt in buckets. Mine live outside 24/7/365 and all do well on that easy diet. Thanks for your articles.

  6. When the weather turns frigid here in PA we start to feed haylage. Since when the temps get above 40° it starts to ferment, I have to believe the good bacteria in my horses gut are over joyed at this time of winter. Although my horses look like a bunch of guys standing around at the bar on Friday night…. LOL