Gut Microbiome And Mental Health – How They Relate

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By Meghan Stoops, RDN

Reviewed by Juliana Tamayo, MS, RDN - Last Updated

Gut Microbiome And Mental Health

Research is starting to connect the strong relationship between mental health and physical health in humans. Over the last decade, an emphasis has been put on the importance of mental health and how it can impact other aspects of our physical health, including our gut microbiome. But what is our gut microbiome? And how does our mental health play a role in the health and functioning of this body system and vice versa? Let’s take a deeper look.

What Is the Gut Microbiome?

Our body houses a wide variety of different microorganisms, including viruses, fungi, bacteria, and more, that play an essential role in many body functions necessary for our health and wellness. Although these microorganisms are found throughout our body, they are most concentrated in our large intestines, which is referred to as our microbiome. Without these microorganisms, it would be difficult to survive, let alone thrive.

Gut Microbiome

Research has suggested our gut microbiome plays a crucial role in various aspects of human health including digestion, immunity, heart health, brain health, blood sugar management, weight control, and mental health. We begin developing our microbiome in the womb and it diversifies as we grow. The more diverse the microbiome the better for overall health.

Our microbiome is strongly associated with our dietary habits, starting in the womb, and extending post-birth through breastfeeding and oral diet. The key star players for gut health begin with a healthy diet that includes a consistent intake of probiotic and prebiotic food sources. Reducing or eliminating processed foods can also make a significant impact on gut health as these foods increase inflammation in the body which can lead to chronic conditions that may be detrimental to our gut microbiome.

How Does Gut Health Impact Mental Health?

It may be difficult at first to see the possible connection between gut health and mental health without discussing the gut-brain axis. The term gut-brain axis was created by researchers to explain the communication processes between our brain and our gut. Surprisingly, there are many ways our brain and gut communicate with one another.

gut health and mental health

Our brain is responsible for telling our body what to do. It does this through neurons. These are special signal cells that act as messengers. Our gut contains millions of these neurons that are directly connected to our brain through different nerves, such as the vagus nerve, which can send signals in both directions. A common example of this communication is when your gut transmits a signal through your vagus nerve that you are hungry.

Our gut and brain also communicate through neurotransmitters. These are chemicals most often produced by the brain that control feeling and emotion. A popular neurotransmitter is serotonin, the feel-good neurotransmitter, that is also partially produced by our gut. Our gut microbes are also responsible for producing the neurotransmitter gamma-aminobutyric acid (GABA), which is associated with feelings of anxiety.

The microorganisms in our gut can produce other compounds that affect our brain, such as short-chain fatty acids (SCFA) which are produced from the digestion of fibrous foods. SCFA can affect the way we feel in several ways, including reducing our appetite.

Lastly, our gut microbes are sensitive to inflammation. The microorganisms in our gut play a key role in our immune function. When our immune system is working overtime, it can trigger inflammation and increase your risk for certain cognitive conditions, such as depression and Alzheimer’s disease.

How to Improve your Gut Health

As researchers continue to find new evidence linking the gut microbiome to various aspects of overall health, an emphasis on improving our gut health has taken effect. But how exactly do we improve our gut health?

improve gut health

The first area to address when looking to improve your gut microbiome is your diet. Next would be supplementation for those who are unable to provide adequate probiotic and prebiotic-rich foods in their diet alone.


The foods we consume are our body’s main source for creating a healthy environment that supports a diverse microbial population. As mentioned earlier, the more diverse your microbiome, the better for your health. The main dietary sources to promote healthy and hearty gut flora are probiotics and prebiotics.

Probiotics are live microorganisms that help to contribute to the beneficial flora in our microbiome. Probiotic food sources include fermented foods such as yogurt, kefir, kimchi, sauerkraut, miso, and tempeh. Prebiotics are sources of plant fibers that help to encourage the growth of beneficial bacteria in the gut. Common sources of prebiotics include apples, artichokes, asparagus, bananas, oats, dandelion greens, and garlic. 

Other ways to support your gut microbiome with diet aside from including probiotics and prebiotics are to eat a variety of different foods, specifically whole foods. Avoid heavily processed foods and artificial sugars as these can increase inflammation in the body which is detrimental to the microorganisms in your gut. Lastly, try to avoid taking antibiotics if possible as these also disrupt the flora in your gut and make it more challenging to have a healthy and diverse population of microbes.


Aside from dietary adjustments, you can also help to support your gut with supplements. There are supplemental forms of probiotics and prebiotics specially designed for those who have a limited diet or who are challenged with getting adequate amounts of these foods in their diet to support their gut. These supplements are intended to be used in conjunction with a healthy diet, not to replace it.

gut supplement

If you do choose to take a probiotic or prebiotic supplement, always be sure to choose a product that was created by a trustworthy manufacturer. Ideally, this product will be third-party tested for quality. If you are choosing a probiotic supplement, pay attention to the colony-forming units (CFU) in the product as this number should be in the billions to be effective. This is the number of healthy microorganisms per serving. 

Some top prebiotic supplements:

Some top probiotic supplements:

Some top options that include both prebiotics and probiotics:

Conclusion: Gut Microbiome and Mental Health

We are now able to recognize that the importance of what we put in our body and how the organisms in our gut react far surpass what we believed in the past. Our microbiome is linked to so many different aspects of our physical and mental health, it is crucial to make sure we are taking care of these organisms and providing them an environment where they can thrive so we can too. In the future, managing the health of our gut may be the first line of defense in the treatment of many mental health conditions. Now that we know how important it is to have a healthy gut, let’s start taking care of it.

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Meghan Stoops, RDN

Meghan Stoops is a Registered Dietitian and licensed Nutritionist with a bachelor’s in Dietetics from San Diego State University. Meghan developed an interest in dietetics early on through her own personal struggles with nutrition misinformation. She began doing her own research, which sparked her passion for nutrition and it’s impact on our physical and mental health. Today, she takes take a non-diet, all-foods-fit approach to nutrition, and is devoted to teaching others that eating healthy does not mean restriction or sacrifice.