The Gut Microbiome Explained

The Gut Microbiome Explained

"Most of the microorganisms in our guts have a symbiotic relationship with us, their hosts. That means we both benefit from the relationship. We provide them with food and shelter, and they provide important services for our bodies. These helpful microbes also help to keep potentially harmful ones in check.

Your gut microbiome interacts with many of your body systems and assists with many body functions.


Beneficial microbes in your gut help to train your immune system to tell them apart from the unhelpful, pathogenic types. Your gut is your largest immune system organ, containing up to 80% of your body’s immune cells. These cells help to clear out the many pathogens that pass through it every day.

Gut microbes can affect your nervous system through the gut-brain axis — the network of nerves, neurons and neurotransmitters that runs through your GI tract. Certain bacteria actually produce or stimulate the production of neurotransmitters (like serotonin) that send chemical signals to your brain.

What environmental factors affect your gut microbiome?

Just like a garden, your gut microbiome is affected by the nutrients and pollutants, pests and weeds it’s exposed to. The diversity of plants and their different seasons or life cycles also affect it. In your gut, this means your diet, chemical exposures, disease-causing organisms and bowel movement regularity.

Diet

The variety of microorganisms in your gut microbiome requires a variety of plant fibers to thrive. Different organisms prefer different whole foods. In turn, they produce short-chain fatty acids and other byproducts that nourish your gut and lower the pH inside, which favors the more beneficial microbes.

On the other hand, a diet high in sugar and saturated fats tends to favor the less helpful types of microorganisms. Processed foods not only lack fiber and micronutrients (vitamins and minerals) but also tend to come with many additives and preservatives, which can be harmful to your microbiome.

What can I do to take care of my gut microbiome?

A healthy diet and lifestyle encourages a healthy gut microbiome.

For example:

Improve your gut health naturally with a diverse and plant-rich diet. Aim for a variety of whole foods like whole grains, vegetables and fruits. These offer plenty of dietary fiber for your gut microbes as well as micronutrients for you. These foods also reduce inflammation in your gut, which affects the environment inside. Processed and convenience foods do the opposite.
Try probiotics and prebiotics. You can get probiotics and prebiotics in supplement form, or from foods. Probiotics are helpful microbes that you can ingest, through supplements or fermented foods, that’ll take up residence in your colon. Your healthcare provider can help you pick the best probiotic for you. Prebiotics are the dietary fibers that feed your helpful gut bacteria."

Source: Cleveland Clinic

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Updated March 11, 2025