How Acid Reflux, Fatigue & Depression Are Tied Together

by Dr. David Minkoff April 30, 2023 5 min read

How Acid Reflux, Fatigue & Depression Are Tied Together

We covered the connection between low thyroid, depression and exhaustion in this article.

But there is another factor that can bring on depression and low energy from an entirely different sector: digestion and the microbiome.

When our digestive ability is weak, we don’t get all of the nutrition from foods we eat. This is because food, including proteins and minerals, must be fully broken down by stomach acid in order for our body to be able to use it.

In fact, poor digestion of protein is one of the largest causes of muscle loss as we age: our digestive system isn’t working as well as it was when we were younger, and so not enough protein is being broken down for our body to use.

But it’s not just our cells that need this nutrition.

Specific bacteria in our colon are responsible, in whole or in part, for the creation of the neurotransmitters serotonin and GABA, the happy, calming neurotransmitters.

When these bacteria don’t get the food they need, they don’t produce these neurotransmitters, and we can start to feel more anxious or depressed.

Our energy levels go down, our stress levels go up, and our body is less able to repair itself, leaving micro-injuries unattended to and causing inflammation and cortisol levels to rise.

But not only do most people in America today have lower than normal digestion, over 20% of Americans take some form of acid blocker or neutralizer to help calm acid reflux.

And this is making things worse.

This is because acid reflux isn’t caused by too much stomach acid — it’s caused by too little.

Let’s see how this works.


When we eat, our stomach secretes digestive acid and enzymes.

This is necessary to:

  • Break down our food into a form our cells can use (if protein isn’t broken down into individual amino acids, your body can’t use these to make new protein)
  • Break down minerals like calcium and magnesium, which are necessary for strong bones and a relaxed nervous system, so they can be used
  • And to kill off harmful bacteria, viruses, fungi, and parasites coming in through food and water, so they don’t get into our intestine and take root.

All of these are very important.

But here’s the problem:

There is something called the PH scale, which goes from 1-15, with 1 being the most acidic and 15 being the least acidic.

The stomach secretes acids until it hits a ph of about 1 or 2 — very acidic.

Hitting this point signals that the food and minerals are broken down enough to be used, and so are ready to move on into the small intestine, which opens to let them in.

However, if the stomach doesn’t reach this level, then the food can stay in the stomach longer and go rancid.

When it goes rancid it can start to bubble up and hit the esophagus.

While the stomach is made to withstand a very acidic environment, the esophagus is not, so it burns.

But, to stop the acid reflux, instead of raising acid levels to what the stomach needs to properly function, many of us take acid neutralizers, which act to make the stomach even less acidic.

Or even acid blockers, which poison the body’s ability to produce stomach acid, making it much less acidic than it needs to be.

This is addressing the symptom on a short-term basis, while making things worse in the long-term.

Most people today have poor digestion.

This is due to the amount of processed foods and sugars we eat, and too little protein, which results in less stomach acid being produced and released.

We need to make the stomach more acidic so it fully digests our foods, so we get all of the nutrition, and so that it doesn’t stay in our stomach as long, but moves through without having a chance to cause acid reflux or heartburn.

But there’s something else that happens here, and it’s why heart burn and stress, anxiety, and even depression, are so closely related.


The key neurotransmitters that keep our mood higher and allow us to be more relaxed, are produced directly by, or in conjunction with, key bacteria in our colon.

When these bacteria have the foods that they need to thrive, they make the neurotransmitters that we need.

And these bacteria live on essential amino acids.

This is so much the case that the essential amino acid Lysine is the base of both GABA and Serotonin, and without that amino acid existing in quantity in the colon, these bacteria can’t make enough of the neurotransmitters we need.

This affects our nervous systems, which runs on neurotransmitters, our brain, our ability to think or to relax.

It affects our mood and our sleep and our recovery ability.

And it’s directly associated with depression and anxiety.

We need to raise our digestive ability and get the bacteria in our colon the essential amino acids they need to produce the neurotransmitters we need.

When we do that, it’s amazing what happens.

I hope this helps.


If we have Acid Reflux, Heartburn or GERD then we have lower levels of stomach acid. Period.

So first, we need to get off any acid blockers, antacids, and even soda water, which also lessens acidity. If you are on any antacid medications prescribed by your doctor, make sure to consult them when doing this.

We then need to start taking Digestive Enzymes to provide the Stomach Acid and Enzymes the stomach needs to fully break down food and kill off bacteria and parasites coming in. Because if we have one of the above situations, then we already know we don’t have enough.

To address the harmful bacteria already present in our small intestine we then have Gut Defense which helps to not only eliminate these harmful bacteria, but break down the protective films they create and hide behind which shield them from our immune system.

Next, Probiotics help to replenish the key bacteria that help produce our serotonin and GABA, helping to us to relax, balance cortisol levels and lower stress levels.

And finally, we need to get more protein. Taking the Digestive Enzymes helps to ensure the protein we do eat is fully broken down. But even more, our body makes it's own stomach acid and digestive enzymes out of the essential amino acids from protein. If our protein levels stay low, we'll be taking digestive enzymes indefinitely to make up for low levels being naturally produced.

This is one place PerfectAmino becomes very important. It not only provides the amino acids needed to synthesize protein and produce more enzymes and stomach acid, but it also helps to heal the cells injured by the effects of low stomach acid.

Even more, it is the essential amino acids that these serotonin and GABA producing bacteria feed on. PerfectAmino helps ensure they are getting the amino acids they need for this. I hope this helps.

To learn more and take control of your gut health, check out the Gut Health Series and 30-Day Challenge. It's quite effective.

And if you haven't already, make sure you join our PerfectAmino VIP Group, where you can ask all your health & fitness questions.

I hope this helps.

*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.