Leaky Gut and Heartburn, Acid Reflux, and Ulcers

Dr. Doni explains the relationship between heartburn, acid reflux, ulcers, and Leaky Gut, and how reflux medications such as antacids and antibiotics can actually make things worse.

Part 8 of Dr. Doni’s Series on Leaky Gut

In the first three parts of this series we have taken a broad look at Leaky Gut: what it is, how to test for it, and how to treat it. Here are the links if you would like to catch up:

In Parts 4 and 5, we explored the top 10 underlying causes of Irritable Bowel Syndrome (also known as IBS), how they relate to Leaky Gut, how to test for them and possible treatment options:

Then we moved on to how Leaky Gut can affect your health in Parts 6 and 7:

Continuing this theme, in this article I’ll be focusing on a very common digestive complaint: Gastroesophageal Reflux, also known as heartburn or GERD.

leaky gut, intestinal permeability, digestion, digestive system, intestines, inflammation, IBS, stress, healing leaky gut, heartburn, GERD, ulcers, acid reflux, reflux, stomach acid, antacids, antibiotics, dysbiosis, natural healthReflux is what happens when acid from your stomach travels up your esophagus causing irritation, pain and for some people, nausea, belching, shortness of breath, phlegm, coughing, sinus congestion, and/or a sore throat. It is also often associated with IBS. Long term exposure to acid in the esophagus can lead to cancer.1

It’s an unpleasant, uncomfortable, and potentially dangerous condition that is commonly treated by taking antacid medication to reduce the amount of stomach acid. But why is it so common? And what happens after months and years of taking antacids? I will answer these questions shortly, but first let’s review healthy digestion.

How Digestion Works

When you get hungry, the vagal nerve (that, you’ll remember from Part 6, sends messages between your brain and your stomach) releases hormones that tell your stomach that food will be coming soon. Enzymes are produced in your mouth, which mix with the food as you chew, beginning the process of digestion so that you will get all the nutrients from what you eat. When you swallow, the food goes down your esophagus and into your stomach where a muscle called the esophageal sphincter squeezes together to keep the food in your stomach and prevent it from going back up your esophagus. The esophageal sphincter knows to squeeze closed when it is exposed to acid from your stomach and protein from your food.

If there is not enough stomach acid or not enough protein in your food, it won’t close properly and reflux can occur. Certain substances, like peppermint, chocolate, coffee, alcohol, tobacco, and certain medications, will relax the muscle, which can also allow reflux to occur.

Once in the stomach, food and especially protein (such as from meat, poultry, fish, nuts) is digested—or broken down—by stomach acid. Stomach acid is actually hydrochloric acid that is produced by the parietal cells in the stomach in response to histamine which is made by other cells in the stomach when they get the signal from the brain via the vagal nerve that food is on its way. Medications that prevent the production of stomach acid (antacids) do so either by directly neutralizing acid or by blocking the production of acid with PPIs or H2 blockers—these block histamine receptors on the parietal cells so they don’t receive the signal to make stomach acid.

Heartburn – Too Much or Too Little Stomach Acid?

Stomach acid, and the digestion it completes, is essential. Without it, undigested food will ferment in the stomach and bacteria (and even parasites) that would normally be killed by the stomach acid will survive. This would lead to imbalances of bacteria and yeast in the digestive tract (known as dysbiosis) as well as gas and bloating, including the condition known as SIBO (small intestinal bowel overgrowth). See Part 4 of this series for more on both of these.

When most people think of heartburn, they think of having too much acid, but it is also possible to have too little and that can lead to acid reflux as well because, as we have seen, it is the acid that tells the esophageal sphincter to close.2 If there is not enough acid to close the sphincter properly, then what acid there is, is more likely to reflux. Furthermore, treating reflux with antacid medications—which lower the amount of acid produced—further decreases the amount of acid present, decreasing digestion of food, increasing the likelihood of reflux and increasing the likelihood of dysbiosis—a major cause of Leaky Gut.3

How Leaky Gut Causes Heartburn and Vice Versa – The Start of a Vicious Cycle

We know from research that, when we are stressed and cortisol levels increase, GERD (reflux) and stomach ulcers are more likely. Stomach ulcers occur when the hydrochloric acid has eaten away at the stomach lining. We used to think this was because of increased stomach acid, but research now suggests that it is due to decreased protection for the stomach lining and increased susceptibility to the H. Pylori bacteria. Stress also affects digestion overall by directing the nervous system’s attention away from digestion in favor of energizing the muscles that allow us to run from or fight danger (the ‘fight or flight response’). When we are under stress, the cells that line the intestines become depleted which allow tiny gaps to appear between them, resulting in Leaky Gut. Add to this the fact that both intestinal motility and the production of the pancreatic enzymes that aid digestion decrease when we are stressed and we start to see a problem. Reduced digestive enzymes means that the food we eat is not digested properly and reduced intestinal motility means fewer bowel movements. This combination allows bacteria and yeast to grow in areas they shouldn’t, further exacerbating Leaky Gut and eventually adding to the symptoms of nausea, heartburn, and belching.4 Read more about what Leaky Gut is here.

So, what often starts with occasional reflux can easily lead to severe digestive distress after a few months or years of taking antacid medications, antibiotics (to treat H. Pylori, SIBO, and other infections), and stress. Soon, Leaky Gut will have developed, along with the reactions to the foods you eat most often that go hand-in-hand with Leaky Gut. By then, you might notice that skin rashes worsen, headaches increase in frequency, sinus infections won’t go away, and your weight starts sneaking upwards. All of this makes it all the more likely that your immune system will start making auto-antibodies—an immune response against your own cells that we’ll be discussing more next week.

What You Can Do to Prevent Acid Reflux

Here are a few simple things you can do to support your digestion and prevent acid reflux:

  • Take time to eat your food calmly so your digestion gets the right message—to digest, not stress.
  • Eat smaller meals so that you don’t overwhelm your stomach with food.
  • Chew your food well to ensure your food is well digested.
  • Eat a bite of protein at the end of your meal to help tell the esophageal sphincter to close.
  • Breathe. Nice deep breaths support communication via the vagal nerve and ensure your digestion gets the messages it needs to function and heal.

And, if you already have reflux:

  • Avoid alcohol, mint, spicy foods, and caffeine—all of which make reflux more likely.
  • Decrease your sugar and carbohydrate intake. Hold off on breads, pastas, cookies and cakes—all of which make reflux more likely and feed unwanted bacteria and yeast. Fibers can also be an issue, so minimize consumption of fiber, including prebiotics.
  • Heal heartburn with deglycyrrhizinated licorice, an anti-inflammatory herb that is shown to assist the esophagus, stomach and intestinal lining to heal.5 I recommend it as plain DGL powder, or in combination with other healing nutrients and herbs, such as the product Heartburn Tx.*
  • Take pancreatic digestive enzymes with meals to support digestion of food, such as Similase GFCF.
  • If you no longer experience burning but still have gas, bloating, belching, and other signs that food is not digesting well, check with your naturopathic doctor whether you might benefit from taking hydrochloric acid.

Note: If you experience any burning after taking a product that contains betaine HCl, then stop taking it and consult your naturopathic doctor.

If you need more help, I’d like to direct you learn more about the Leaky Gut consultation package I have developed to help you with your digestive issues by getting to the root of the problem. We need to re-establish healthy digestion and get the system working in sync again. The package includes one-on-one consultations with me, tests to understand what your body needs, and support along the way.

Please share your thoughts in the comments section below. And sign up below for my newsletter so you receive my next blog articles right to your inbox.

–Dr. Doni
28th August, 2015


*Please keep in mind that any and all supplements—nutrients, herbs, enzymes, or other—should be used with caution. My recommendation is that you seek the care of a naturopathic doctor (with a doctorate degree from a federally-accredited program) and that you have a primary care physician or practitioner whom you can contact to help you with individual dosing and protocols. If you ever experience negative symptoms after taking a product, stop taking it immediately and contact your doctor right away.


  1. Reza Malekzadeh, et al. Overlapping gastroesophageal reflux disease and irritable bowel syndrome: Increased dysfunctional symptoms. World J Gastroenterol 2010 March 14; 16(10): 1232-1238
  2. Schubert ML. Gastric secretion. Curr Opin Gastroenterol. 2008 Nov;24(6):659-64.
  3. Lombardo L, Foti M, Ruggia O, Chiecchio A. Increased incidence of small intestinal bacterial overgrowth during proton pump inhibitor therapy. Clin Gastroenterol Hepatol. 2010 Jun; 8(6):504-8.
  4. Lee SP, Sung IK, Kim JH, Lee SY, Park HS, Shim CS1. The effect of emotional stress and depression on the prevalence of digestive diseases. J Neurogastroenterol Motil. 2015 Mar 30; 21(2):273-82.
  5. Asl MN1, Hosseinzadeh H. Review of pharmacological effects of Glycyrrhiza sp. and its bioactive compounds. Phytother Res. 2008 Jun; 22(6):709-24.

Image by Richard Stephenson, licensed under CC BY 2.0. Changed from original: Cropped and added text overlays.


  1. Wow! Just posted something like this on my Facebook page Hpylori Help Desk. Stating 2 WAYS to test your stomach acidity. I mentioned heartburn being caused by either too much or too little HCI.
    Thank for the true edification and confirmation Dr. Doni.

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