You're a bag of bugs with 3 brains. How the gut-brain connection impacts mental health

Updated: Apr 4

Man laughing while eating a salad that is good for his gut health and mental health

If you're like me, you are always looking for more ways to improve your mental health. Diet is no doubt one of them.

Your gut health directly impacts your mental health. This is because your gut contains a "brain" of sorts - a conglomerate of neurons referred to as the Enteric Nervous System. This nervous system interacts directly with your brain, and your brain interacts with it. This is known as the "gut-brain connection". In addition to this, your heart contains around 40,000 neurons, making it your 3rd "brain". As if this weren't strange enough, your gut is loaded with hundreds of trillions of microorganisms - bacteria, fungi, parasites, etc. - that are central to your physical and mental health. This is known as your gut microbiome.

So, in a way, you are not all that human. You are a "bag of bugs" with 3 brains!

Why is this useful to you? Because the interaction between these 3 "brains" and the health and balance of your gut microbiome has a tremendous impact on your mental health. While we won't address the heart-brain in this article, we will talk about how your gut health impacts your mental health and how you can improve the health and balance of your gut microbiome to boost your mental well-being.

My personal experience with the gut-brain connection

I've struggled with perfectionism and anxiety pretty much my entire life. It's a heck of a lot better now than it once was, but nonetheless I'm still walking my journey just like you. During that journey, I've learned about the connection between the gut and the brain - in particular the gut microbiome and how it impacts mental health. Knowing about this connection and understanding the diet and lifestyle changes I needed to make has helped a great deal with the anxiety, depression, and OCD I've struggle with, and I believe it can help you too.

If you want to cut right to the chase and get some practical advice for diet, such as foods to eat and not to eat for mental health, you can take a look at this article. I recommend trying to limit or cut out processed sugar, dairy, and/or gluten if you suffer from mental illness, as these are highly inflammatory foods that can have a big impact on mental well-being. I say this because I've heard stories of people whose mental health has improved from removing these foods from their diet. I've also experienced drastic changes from doing so myself.

But of course this is completely up to you. I know diet changes are difficult and anything but simple to make. If you want to make changes, but it feels overwhelming, you could try cutting something out for a few weeks and see if it makes a difference for you. If doing something that small overwhelms you, I totally get it! Don't take on everything at once. For now, how about just learning about how gut health impacts mental health? Nothing wrong with learning, right?

What you eat affects your mental health

You probably know about genetic predispositions that contribute to mental illness. But what if there are other biological factors affecting your mental health that you don’t know about?

What if there were simple changes you could make to your biology through what you eat that could increase your quality of mental health significantly?

Read on to learn about what the gut microbiome is, how it affects mental health, and what you can do to strengthen it.

You're a bag of bugs with 3 brains

Do you ever feel a little strange? Well that's because you are! You are not human. Not entirely at least. You're made up of trillions of microorganisms that all contribute to the way you think.

Human beings are filled to the brim with bacteria, fungi, viruses, parasites and other microorganisms. Together these are referred to as the "microbiome", and their number far exceeds the number of human cells in your body.

Despite what you may have been taught about these little critters, many of them are actually crucial to your health. Some of them even play a central role in creating hormones and neurotransmitters for you.

What's perhaps even stranger is the number of genes in your body made up by these little bugs. As it turns out, your human genes are far outnumbered by your microbial genes. You have around 18,000-23,000 human genes and around 46,000,000 microbial genes. That means that the genes of bacteria, viruses, fungi, and parasites in your body outnumber your human genes about 2,000 to 1.

We once believed that all psychology was from the neck up. As it turns out, your gut (small and large intestines and other organs such as your liver and kidneys) play an important role too.

Fairly recent science shows that human beings have three brains:

The brain, heart, and gut all contain neurons. Your brain contains about 100 billion neurons - give or take a few million; your heart contains around 40,000 neurons; and your gut contains over 100 million neurons. These neurons are spread throughout the organs in your gut, making up what is referred to as the Enteric Nervous System.

So, as it turns out, you actually can “think with your stomach.”

The gut microbiome and its impact on mental health

A study published in 2018 by Sherwin et al. showed that our gut microbiome - the trillions of bacteria, fungi, etc. in our small and large intestines - impacts the following functions of mental health:


Your brain’s ability to learn, focus, develop memories and social skills, and more.


Your brain’s capacity for change and forming new neural connections throughout life. Without this, you could not form new habits, beliefs, and behaviors.


These are your body’s chemical messengers. They play a big role in brain function, particularly neurotransmitters like dopamine, serotonin, GABA, and oxytocin. These impact your sense of purpose, happiness, peace, and connection to others.

And that's only to mention a few of these powerful little chemical signals. You have over 100 different neurotransmitters from what we know so far!


Your brain has the ability to produce new brain cells. This is referred to as "neurogenesis". This neat little process is important for solving problems, producing new memories, and much more.

Behavioral phenotypes

Behavioral phenotypes are the cognitive processes and social interaction styles that are determined through genetics. Bear in mind that we now know, with the development of research on epigenetics, that we can change the way our genes express themselves through changes in our environment and behavior.

Whew… There are a lot of ways that the bacteria in our gut affect our brain. Pretty incredible, right?

The gut microbiome and mental illness

The brain and gut communicate via the vagus nerve - the connection between the brain and the Enteric Nervous System (or your "2nd brain" located in your gut). Trillions of intestinal bacteria make up your gut microbiome, and these critters communicate with and inform the cells in your gut, which in turn inform the cells in your brain (gosh, no wonder I feel crazy sometimes). These bacteria and the gut-brain communication affect your brain function, including your mood, behavior, and level of motivation.

If your body is lacking good bacteria and a healthy, balanced gut microbiome, this can impact your mental health.

“As reviewed in the study of Butler et al., alterations in microbiota [(bacteria)] composition have been reported in major depressive disorder, bipolar affective disorder, anxiety disorders, schizophrenia and psychotic disorders, neurodegenerative disorders, and autism spectrum disorder.” (Jane A. Foster Ph.D.)

Mental illnesses such as addiction, anxiety, and depression are highly complex. All parts of your being play a role in your ability to manage these challenges. You need to care for yourself spiritually, mentally, and socially in order to improve your mental health. You also need to care for your nutrition.

Don't think that you ever need to be perfect. You may always struggle with things like perfectionism or anxiety - I know I do - but at least you can feel better and suffer less. And that's the goal of all this I think.

So, how can you improve your gut health, balance your gut microbiome, and thus raise your energy levels and sense of peace and well-being? Let me tell you a few things that could help.

Improve Mental Health with Prebiotic & Probiotic Foods

While I still have a lot to learn, I try to take to heart the quote from Hippocrates, “Let food be thy medicine, and medicine be thy food.” Hence why I eat nothing but vegetables, nuts, and seeds all day. Okay, so I don't do that. I'm certainly not perfect, but there are many foods I eat to improve my gut health, and thereby my mental health. It doesn't fix everything, but it does help.

Probiotic foods

Probiotic foods contain live, active cultures (good bacteria). When you consume these cultures, they enter your body and make a home for themselves temporarily (creepy, huh?).

These are foods such as:

Organic fruits and vegetables grown in rich, healthy soil also have microbiomes of their own. So does raw honey.

Prebiotic foods

Prebiotic foods contain different types of fiber that feed the good bacteria in your gut. The bacteria feed on this fiber and multiply. This is one of the reasons why eating fruits and vegetables (especially cruciferous vegetables) is so important. If you do not get enough of these foods then certain beneficial bacterial species can grow sparse or even die off.

Prebiotic foods include:

  • Vegetables such as onions, shallots, leeks, asparagus, cabbage, broccoli, cauliflower, radish, and kale

  • Fruits such as bananas, apples, grapefruit, and watermelon

  • Nuts

  • Seeds

  • Garlic

  • And more

Remember that some bacteria (such as Lactobacilli and Bifidobacteria species) help create neurotransmitters like serotonin and dopamine. While they are not the end-all-be-all, they can contribute to your mood and sense of well-being, so it is important to get good probiotic and prebiotic foods in your diet if you want to improve your mental health.

But as I'm telling you this, I also don't want you to forget how important things like prayer, meditation, reading inspiring books, exercise, building good relationships, serving others, and living a purposeful life are. Diet is just a part of caring for your mental health.

Sleep, stress, exercise, and the microbiome

Diet makes a difference in the composition of your gut microbiome. But it's not the only thing that does. Things like sleep, stress, and exercise also play a role.


If you want a healthy microbiome, you need to sleep! It is also extremely important to try to be on a regular sleeping schedule. Cause guess what? Because the bacteria in your gut are alive, not only do they eat, but they sleep too!

Having a regular sleeping schedule is helpful to you and the beneficial bacteria in your gut. This is due to your circadian rhythm. Your circadian rhythm is a type of '"internal clock"' that functions based on your sleeping schedule. If your sleep is erratic or lacking, your physical and mental health will probably suffer - but your little bacteria buddies will suffer too.

You see, your microbiota sleep when you do; they have circadian rhythms of their own. So sleeping on a regular schedule can impact your mental health in more ways than one!

But hey, if you're a crazy recovering perfectionist like I am, you know how overwhelmed you can get trying to be perfect. So I will add that your sleeping schedule does not need to be perfect.

Sometimes that are more important things that sleeping, like family, friends, or staying up late to help someone in physical or mental need. And heck, on occasion you just gotta' stay up for fun, and that's okay too!

Work on keeping a semi-regular schedule during the week - waking up and going to sleep close to the same time. But act according to your level of ability and your specific circumstances. Don't stress about it. Your body is resilient and it can survive some irregularity when needed.


The health of your gut microbiome has an impact on your mental health. But what about the other way around? How does the stress you experience impact your gut microbiota (bacteria)?

Stress does impact the microbiome. The funny thing is, while stress impacts the composition of the gut microbiome, this in turn affects the brain due to the gut-brain connection.

So, the key is to stress a lot about making sure you're never stressed, right?

Okay, that won't help.

Things like prayer, meditation, service to others, gratitude, and breathing techniques can help to lower your stress. Incorporate a few of these into your life and make your little gut-buddies happy. Never try to make more than one change at once, and remember that baby steps are key. Give yourself time and practice self-compassion.


Exercise also impacts the gut microbiome (gosh, what doesn't affect the microbiome?). Getting regular exercise increases the concentration of short-chain fatty acid, such as butyrate, that are produced by the gut microbiota. This can lead to better gut and brain health.

To learn more

To learn more ways to improve your mental health, subscribe to my blog at the bottom of this page, or go to my home page at

To learn more about the gut-brain connection, check out my article The 4 Ways the Gut and Brain Connect.

Feel free to contact me with any questions here. I'm here to help you as a friend however I can. If for nothing else than to just listen!

Thanks for reading!

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