Our gut — and the millions of microbes that live there — plays a key role in our health and how we feel
There are millions of microscopic organisms living in our guts. And the more scientists study those microbes, the more they learn about their importance to human health.
Anna Seekatz, an assistant professor and microbiologist in the Clemson University Department of Biological Sciences, researches interactions within the gut microbiome. Seekatz explains what the gut microbiome is, why it is important that it is balanced, and what we can do to ensure our gut microbiome is as healthy as it can be.
What is the gut microbiome?
The gut microbiome refers to the ecosystem of microbes in your digestive system, primarily the large intestine. There are millions of bacteria, viruses, fungi and parasites living in your gut. Each of us has a unique microbiome that starts forming as soon as we are born, either through delivery or breastfeeding. By the time children are about 2 years old, their gut microbiome resembles an adult’s.
How does it affect human health?
When most people think of the gut microbiome, they think of digestion. And it does play a major role there, helping break down food the body can’t digest as well as producing products that we physiologically need. One example is short-chain fatty acids, or butyrate, a fermentation product that is only produced by certain bacteria in the gut. Butyrate has been shown to be anti-inflammatory, and it serves as an energy source for your colonocytes, which are epithelial cells that line the colon.
How does the gut microbiome play a role in other bodily functions?
Gut microbes have been shown to prime the immune system. Having certain types of bacteria present at the right life stage is likely important because it trains your immune system to act properly. There is evidence that when you are not exposed to certain types of bacteria (or, exposed to more harmful organisms instead) during this window of immune development, you might be more at risk for certain autoimmune diseases during adulthood.
The gut microbiome is important for providing colonization resistance, or the ability of the body’s natural microbial community to protect itself against harmful microorganisms. A diversity of microbes prevents a pathogen from taking over. If that balance is altered through the use of antibiotics or another perturbation, colonization resistance could be lost and allow a harmful or pathogenic bacterium to grow out of control and cause disease.
There’s also convincing evidence that the gut microbiome can affect the nervous system through the gut-brain axis, which is a network of nerves that runs through the digestive tract.
How can you nourish your gut microbiome?
One of the best ways to support your gut microbiome is by eating a range of fresh vegetables and fruits, which contain plenty of fiber and serve as a food source for good bacteria. Limit foods high in sugar and saturated fats, items that favor less helpful microbes.

Did you know?
Anna Seekatz is part of a group of researchers working to find better treatments for diseases caused by deadly pathogens. The Eukaryotic Pathogens Innovation Center (EPIC) at Clemson over the past decade has received more than $50 million in federal funding to study parasitic and fungal pathogens.