Depression, Anxiety, Stress & Sleeplessness — The Microbiome

by Dr. David Minkoff September 27, 2023 6 min read

Depression, Anxiety, Stress & Sleeplessness — The Microbiome

Our body's ability to relax, de-stress, recover, and sleep deeply is heavily determined by one area of our body overlooked more often than almost any other — our Microbiome.

This colony of trillions of bacteria living in our large intestine helps produce the calming, relaxing, cortisol-lowering, and sleeping-giving neurotransmitters GABA and serotonin.

These bacteria have more to do with our overall health, calmness of mind, nerve function, ability to sleep, ability to burn fat and build muscle, and even our hormones than you might think.

This colony, made up of about 500 different species of bacteria, is called the Microbiome.

But these bacteria, while being fully separate from us, act as if they were an organ unto themselves within our bodies. And what they do, amongst each other and in coordination with the cells in the lining of our colon, is truly extraordinary.

While we’ve only scratched the surface as far as what we know about how these bacteria operate and interact, not just with one another, but with our own cells and nervous system, we do know a few key things:

First, there's no aspect of our health or bodily functions they don’t play a part in.

In fact, they’re so important they have been found to play a role in nearly every human disorder: They affect our sleep, our ability to relax or start up, our weight, our hormones, our energy levels, and even our mood.

Second, we will find in almost every case that if we have someone with a generally healthy microbiome, we have a generally healthy person. And if we have someone with an unhealthy microbiome, we have an unhealthy person with physical conditions, out of balance hormones, low energy, and high stress.

Third, the microbiome profiles of individuals suffering from acute depression and anxiety are quite different, in very exact ways, from individuals not suffering from this.

We can now spot key bacteria in the microbiome, and byproducts that they create, which are elevated in severely depressed individuals while being in normal ranges in non-depressed persons.

And lastly, the bacteria in our microbiome are inextricably linked to our nervous system, our brain, the ability for messages to pass up and down our nerves, and our mental alertness.  

Our body would not function without them, and to the degree they’re suppressed or deficient, our body doesn’t.

And to understand how this works we need to look at the chemicals that allow for nerve and brain function, known as neurotransmitters.


Neurotransmitters are communication particles between nerve cells, or neurons. Neurons send and receive communications to and from your brain.

There are approximately 86 billion neurons in the human nervous system, from the brain, to the spinal cord, and stemming out throughout the body to form a very complicated network. And the way they communicate is through neurotransmitters.

If one nerve cell wants to pass on a message to another nerve cell, the particle they use to communicate is a neurotransmitter.

Let’s look at this. We have a neuron, which basically carries an electrical charge, and a neurotransmitter, which carries a chemical message.

The neurons don’t touch one another. Instead, they have tiny gaps between them called synapses. If an electrical charge comes into a neuron, this neuron puts out a neurotransmitter which then takes this charge, reaches out across the synapse, the gap between neurons, and connects to the next neuron, passing on the message.

The message is then turned back into an electrical charge in the second neuron, which puts out its own neurotransmitters, and these pass the signal on to the next neuron in line, etc.

But it’s fast. In the time it took you to see the period at the end of this sentence, the above cycle took place in your body a few billion times. And your body and mind couldn’t function properly if it was anything less.

To give you an easily experienced example of how these actually affect us, think of a time you were out in the sun too long on a hot day, sweating, and how tired and lethargic you felt.

You lost electrolytes through your sweat, another key ingredient that allows these electrical impulses to slow. So you have less of them now and you feel it. When you take some electrolytes, or even some salt under your tongue, it’s amazing how fast energy and alertness come back.

It’s the same with neurotransmitters, only there isn’t something to drink or take which immediately provides more that quickly. Instead, they rely on our microbiome to help produce them.

Now, there are thousands of different types of neurons, some for motor control (movement), some for sensory perception (sight, smell, touch, etc) and some that pass signals between the first two types.

Then there are many kinds of neurotransmitters, about 60 that we know of. And they have a vast array of functions amongst the thousands of types of neurons.

You may have heard of some.


Dopamine, which regulates mood and muscle movement. It’s mainly in the brain and a lack of it brings on mental fog, depression, and slowed reaction time.

GABA, a neurotransmitter that calms over-excited nerves. A lack of it can cause bad moods, anxiety, and even seizures. And too much GABA can cause daytime sleepiness and lessened nerve activity.

This is because GABA is the major inhibiting neurotransmitter of the nervous system and decreased levels are associated with depression, anxiety, and sleeplessness.

If you don’t have enough GABA, you’re going to have trouble relaxing and falling asleep. If you have too much then you’ll have a hard time staying awake.

Then there’s Serotonin, which helps regulate mood, body temperature, and appetite. Serotonin is what you could call the “feel good” neurotransmitter. When we have more of this we generally feel happier, and when we have less we can feel depressed or anxious.

Also, when we have more of this we have a more controlled appetite for food. But with too little serotonin we can get more food cravings. This is in part because lowered serotonin and GABA also bring on raised cortisol, and vice versa.

Serotonin also plays a large roll in both immune cell activation and, when lessened, the generation and perpetuation of inflammation in the gut.

Altered levels of serotonin have even been linked to Irritable Bowel Syndrome, cardiovascular disease, and osteoporosis due to its affects on our hormones. It can even alter your behavior.

There are many more, each with exact functions and interactions with one another necessary to a properly running nervous system and body.

But neurotransmitters aren’t all created by the body. Much of them are actually created in the gut either directly by the bacteria there (the microbiome), or with the bacteria’s help.

They come about through an interaction of the bacteria with cells on the walls of our colon called neuroendocrine cells, or are directly created by the bacteria themselves and then taken up by the cells into the nerves.

Actually, most serotonin is produced in the gut, about 95%.

It’s made in the neuroendocrine cells in the lining of your colon through an interaction with the bacteria there.

And GABA is produced directly by bacteria in our microbiome, which is then shuttled into the nerves to be used by the neurons.

But what happens when we start playing around with these bacteria, knowingly or unknowingly?

According to a research paper from Caltech, researcher Jessica Yano studied mice with normal gut bacteria and mice without gut bacteria (the bacteria was removed).

The mice without gut bacteria had 60% less serotonin than the mice with gut bacteria.

Then, when the mice’s microbiome was recolonized with bacteria, their serotonin levels went back up.

In this research they found 20 species of spore-forming bacteria that elevated serotonin levels through interaction with the neuroendocrine cells in the lining of the colon.

These bacteria are very important and, if we have lower levels due to poor diet or antibiotics, we need to both take probiotics to help recolonize this region.

You would be surprised at the difference it makes.

In the next article we’ll cover what causes disruptions in the microbiome. But for now I’ll leave you with this.

The bacteria that help you, that you need for neurotransmitter production and lessened cortisol levels, are fed mainly by essential amino acids that make their way to the colon, and nutrients found in many plant foods.

These give the bacteria what they need to thrive and produce neurotransmitters.

This is actually why we feel calmer and sleepier after eating turkey. It contains the essential amino acid tryptophan which feeds key GABA-producing bacteria.

It’s also why many people feel calmer when taking PerfectAmino and eating a higher protein diet that also includes greens and no processed sugars.

I hope this helps.

And, if you haven't seen the Gut Health Protocol & 30-Day Challenge, I highly recommend you check it out! It's very possibly the most important program we have for overall health.

Just use the code GUTHEALTH for 10% off the Gut Health Collection.

And make sure to join our PerfectAmino VIP Group if you haven’t already, where you can ask all of your questions and we can help you with anything you need.

*These statements have not been evaluated by the Food and Drug Administration. These products are not intended to diagnose, treat, cure, or prevent any disease.