Nutrition and Gut Health

What is the Gut Microbiome?

You may recall learning about biomes in biology class. Deserts, grasslands, forests, and tropical rainforests are all examples of biomes. These unique combinations of animals, plants, soil type, temperature, and weather shape an entire community of living organisms and how they interact to create a cohesive unit.

Much like how nature is composed of a series of biomes, your body contains its own set of biomes, called microbiomes. Microbiomes are much like the biomes made of plants and animals that you’re familiar with. But instead of plants and animals, they consist of living organisms too small to see with the human eye. Bacteria, parasites, viruses, and fungi are all vital parts of a healthy, functioning microbiome.

The unique combination of microorganisms (microbiota), and their interaction with each other, play an important role in the human body. In fact, microbiota in the mouth, nose, skin, and gut all affect how your body functions each day.

The gut microbiome is found in your digestive system and consists of millions of microorganisms entirely unique to you. Your DNA, the microbiota you are exposed to as an infant from your mother, your diet, and a host of environmental factors all help determine the makeup of your gut microbiome.

This unique combination affects the exchange of chemical signals and digestion in your gut1. Your gut microbiome also supports the breakdown of toxic food compounds and helps alert the immune system to potentially harmful pathogens2.

Foods for Gut Health

While we don’t have full control over the makeup of our gut biome, we do have some control over the foods we eat. Diet can have a great impact on our gut microbiome and can both help and harm gut function.

Prebiotics and probiotics both play an essential role in maintaining a healthy gut. Think of prebiotics as food for your gut’s microbiota, while probiotics contain living microorganisms that can be introduced to your existing microbiome. When incorporated into a healthy diet, prebiotics and probiotics help maintain a diverse gut microbiome.



Prebiotics are often confused with probiotics, but they play different roles. Prebiotics travel to the colon and provide your microbiome with the fuel it needs to maintain living microorganisms. There are types of prebiotics, all of which do different things when broken down in the microbiome. Some of the many benefits of prebiotics include3:

  • improved immune system function
  • encourage the production of healthy bacteria
  • trigger production of vital hormones, including those that trigger appetite
  • support an anti-inflammatory response
  • maintain regular bowel movements

Many fibrous grains, fruits, and vegetables contain prebiotics that are important for maintaining a healthy gut biome:

  • asparagus
  • onions, leeks, and garlic
  • apples and bananas
  • flaxseed, oats, barley
  • beans and lentils

Note that while prebiotics are healthy for a balanced diet, large amounts can cause gas and bloating, especially in those with IBS or other gastrointestinal irregularities. If you are trying to increase prebiotics in your diet, it may help to gradually introduce these items if you have a sensitive gut.



Prebiotics contain living microorganisms that can help populate your gut with healthy bacteria and yeast. The most common types of probiotics are Lactobacillus and Bifidobacterium. Some also contain saccharomyces boulardii, a type of yeast4.

There is a range of health benefits associated with probiotics. These include vitamin creation, improved digestion, improved medication absorption, enhanced immune response, and a decreased risk of developing certain conditions, including heart disease, bacterial vaginosis, and even cancer5.

Probiotic-containing foods include6:

  • tempeh
  • yogurt
  • kimchi
  • sauerkraut
  • pickles
  • kombucha
  • kefir

Probiotic supplements are also a popular way to increase the amount of healthy bacteria in the gut. While they can be effective at repopulating the gut in those with certain imbalances, it’s important to utilize caution when using probiotic supplements. Because everyone has a unique microbiome, a probiotic that works for one person may not be as effective for another.

If managed incorrectly, utilizing probiotics can potentially worsen gut issues. It’s important to work with your provider if you are taking any probiotic supplements.


Brain-Gut Connection and Diet

The gut microbiome doesn’t stop at the digestive tract. There is mounting research to suggest that there is a connection between the gut and the brain. This connection can be attributed to the enteric nervous system, located in the digestive tract. This system has been nicknamed the “second brain”7.

The brain-gut axis is a communication pathway that allows the brain and the gut to send signals back and forth to each other about digestion and hunger. The gut microbiome also plays a role in the connection. When there is a dysregulation of the brain-gut axis, this can affect your mental health.

Research shows a connection between brain-gut axis dysregulation and depression, anxiety, and irritable bowel syndrome (IBS). Some treatments for these mental health-related disorders now include dietary changes and probiotics as an important piece of treatment.

There is still research to be done to determine the extent of this connection, but we have plenty of evidence to suggest that a healthy, diverse diet full of prebiotics and probiotics can help support a healthy gut, and healthy life.

If you are interested in reading about this topic further, the following book recommendations are great places to start:

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