The Basics of Gut Microbiome in Horses and Humans

In discussions about the human or equine gut, some important terms such as gut microbiome and microbiota are often used interchangeably; however, there are differences. Like humans, all animals have a diverse and unique set of microorganisms “living” in the gut or intestinal tract including bacteria, fungi, parasites, viruses and other “bugs.” Taken as a whole, these microorganisms inhabit a defined space in the gut which is known as microbiota and is specific identifier to the individual such as fingerprints or eyeballs, for example. They are a community of microorganisms with unique characteristics that literally share our body space.

The genetic material that makes up microbiota is the microbiome or the corresponding DNA. The Microbiome is technically the DNA of microbiota. Most research to date is based on human data. We have limited research on horses but the same principles apply.

The number of genes in all the microbes in one person's microbiome is 200 times the number of genes in the human genome. And it might weigh up to five pounds. So, in a horse, it might weigh up to 50 pounds of microscopic bugs. That's a lot of bugs helping to run the entire mechanism. It's not just in the gut. It is everywhere within the body and it affects our physiology, metabolism, nutrition and immune functions.

We only started studying microbiome since the early 2000s. The more we learn, the more we realize that we actually are a bunch of bugs! The rest of us is water. And then there are a few structures holding it all together. But essentially we are a microbiome.

We also have metabolites which are any substances produced during metabolism or digestion or other chemical reactions in the body.   The metabolites are present in the cell and we require them for the normal growth and function of every cell. The metabolites are byproducts of our microbiome at work.

You may have heard the media and advertisers using the terms “prebiotics” and “probiotics.”  Prebiotics are compounds that support the growth and activity of the beneficial microbes that are living in our gut. Prebiotics tend to act as food for probiotics. They get fermented or processed by them. Prebiotics are fiber (such as beans, whole grains and vegetables). But not all fiber is prebiotic. In other words, not all fiber is liked by the microbiome. Some fibers are desirable and some are not desirable, such as genetically modified products. But currently most of our prebiotics are fiber and also can be herbs.

Probiotics are living microorganisms found in food, (such as yogurt or in the organic dirt on a carrot) that are in an active state when they arrive at their location in the intestine. They directly impact the intestinal track itself, how it works to digest, absorb and process food. .

Probiotics have a direct effect on the immune system and on the intestinal microflora that's already there. Probiotics may or may not actively colonize and live in the gut. We may have to feed them on a regular basis in order to have them present because they aren't going to “set up shop.”

But they will reproduce, do what they are intended for, and pass on through. But they do not generally live actively in the gut.

A new term we are hearing more about is postbiotics. These are  basically the compounds produced by the prebiotics and probiotics. Healthy examples of these residuals include amino acids, vitamin B and vitamin K and others that support or help maintain good bacteria or “good bugs” in the body.


Thursby E, Juge N. Introduction to the human gut microbiota. Biochem J. 2017;474(11):1823-1836. Published 2017 May 16. doi:10.1042/BCJ20160510

Kauter, A., Epping, L., Semmler, T. et al. The gut microbiome of horses: current research on equine enteral microbiota and future perspectives. anim microbiome 1, 14 (2019).

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