Leaky Gut, Gut Health & Auto-Immune Conditions

by Dr. David Minkoff August 16, 2023 6 min read

Leaky Gut, Gut Health & Auto-Immune Conditions

Disclaimer: This article is purely informational and makes no claims as to treatment or cure from any supplement or program BodyHealth may offer. If you or someone you know has an autoimmune condition we recommend you see a doctor trained in functional medicine to help you locate the cause of the disease or condition and recommend a solution for it.

This is the second article in the Autoimmune Series.

In the last article we covered what autoimmune conditions are and what they’re actually doing in the body. But in this article we’re going to cover how they come about.

What actually causes them.

And it starts in the gut, our first defense against illness.


Your digestive system has two main functions:
  • To fully break down the food you eat into a form your body can absorb and use.
  • And to kill off or remove harmful bacteria, viruses, fungi, parasites, and toxins coming in through food and water so they can’t harm you.

It does this in two main ways.

When you eat, your stomach releases digestive enzymes and stomach acid.

Now, when someone has acid reflux or heartburn, this isn’t because of too much stomach acid, quite the reverse. It’s due to too little.

You see, the digestive enzymes and stomach acid are released to help break down your food.

They don’t break it down all the way, but most of the way.

And the stomach acid kills off, for the most part, any harmful bacteria, viruses, fungi or parasites coming in — foreign invaders.

This stomach acid has to get very acidic to break down all this food and kill these harmful invaders, to a 1 or 2 on the ph scale — very acidic.

When it hits this level that’s the signal to release this food into the small intestine where it will be digested further and then released through the liver into the blood stream.

If the stomach doesn’t get this acidic, then the food stays in there longer, for hours even, and goes rancid. When this happens it can start to bubble up and hit your esophagus, which can’t handle any acid.

This is heartburn and acid reflux, too little stomach acid, not too much.

But also, when it doesn’t get acidic enough, it doesn’t kill off all the foreign invaders, allowing them into the small intestine where they shouldn’t be.

Once inside the small intestine the food particles are broken down even more. Fats and carbs are broken down into their smallest forms, and proteins, which were mostly broken down in the stomach, finish this process, being broken down into the individual amino acids that made them up.

These then brush up against the inner lining of the small intestine, which determines they are nutrients, and opens up small holes, called tight junctions, to let them through to the liver and then into the bloodstream to the cells.

But that’s food.

Then there are any foreign invaders that weren’t killed off in the stomach. And these mustn’t get through the tight junctions to the bloodstream.

But your body has a system for these. You’ve heard that 80% of your immune system is in your gut. This is where.

Your small intestine has three walls.

There is the inner wall, which sees nutrients and lets them through. Then there is the outer wall, which is made of blood vessels which take the nutrients to the liver.

And then there is a middle wall. And this is made of immune tissue.

When food comes in, immune cells are released from this middle wall to scout for foreign invaders.

And when they find them, they kill them.

Or at least, that’s how it’s supposed to work.


If your stomach was in good shape, and was very acidic, it would be killing most foreign invaders so your immune cells wouldn’t have too much to attack.

But if it’s not, if it’s letting many foreign invaders through to the small intestine where they can grow and thrive, then your immune cells could get overloaded, trying to handle them all, but unable to.

That's one thing. 

But there is also something else here.

We have toxins coming in as well: glyphosate, the herbicide on most crops, heavy metals, plastics, and other toxins.

In today’s world it’s amazing how many of these come in through our food and water.

And, between these and the foreign invaders, over time they can start to damage the inner lining of our intestine.

That inner lining is made to prevent them from getting through so the immune cells can kill them.

But when there are too many harmful bacteria to address, as well as toxins, the immune system can’t keep up. And these foreign invaders and toxins start harming the inner lining of the small intestine, causing something called leaky gut.

Leaky gut is exactly what it sounds like, tiny holes in the intestine that let things through that shouldn’t be let through — including these foreign invaders and toxins.

It's literally the tight junctions that open up to let nutrients through, now being held open to let harmful things through as well.

And that’s where the real trouble starts.

And where Autoimmune Conditions start.


These harmful toxins and bacteria, released through the tiny holes in our small intestine, can now go anywhere in the body and start stacking up.

And they can start causing autoimmune conditions.

As covered in this article, autoimmune conditions form because of corruptions to protein tags on our cells.

Our immune system operates by looking for things that are “not us,” (harmful bacteria, viruses, fungi, parasites) and attacking them.

And it does so by seeing that their protein tags are not the same as the ones on our cells.

But these harmful bacteria and toxins released into our blood stream, piling up, can both corrupt the protein tags on our own cells, or stack up on them, in either case making our own cells appear to be “not us.”

And so our immune cells start to attack our own cells thinking they are “not us,” but a foreign invader.

And that’s what autoimmune conditions are. Us attacking us.

This can affect our kidneys (Lupus), thyroid (Hashimoto’s), joints (Rheumatoid Arthritis), muscles or nerves (Fibromyalgia), skin and much more.

Each of these come from, along with the harm the bacteria and toxins are doing directly to our cells, our own immune cells that are supposed to protect us… attacking us.

It may take years for our gut to get into this shape, and more for these foreign invaders and toxins to build up in our body, corrupting the protein tags on our cells so that our immune system starts to think our own cells are foreign invaders to be attacked.

But it happens. And it’s especially happening with our children who are now growing up with toxic loads over 50 times higher than we had many decades ago.

And with low levels of proteins in our diets, necessary to produce stomach acid, and high-sugar foods that feed the harmful bacteria that get in, so they can take root in our intestine and thrive, we now have children getting conditions we used to only see in the elderly.

This is because during the first many years of life is when our children’s digestive tract and immune system are forming.

For many of us, we didn’t have near the toxic load, or sugars, coming in when we were younger as kids do today.

So for many of us, if this happens to us at all, it’s when we’re much older. Our immune systems are already formed, we grew up, for the most part, fairly healthy.

But our children are having their intestinal tract ruined while it and their immune system are still forming.

And due to this, while it can take years, we start seeing these conditions in them when they’re 12, 15 or 20.

But this is why.

And this is also why it’s so important to not only keep harmful toxins out of our bodies — and remove them when they get in — but to also keep protein levels high and sugar levels low. Or at least keep out processed sugars which these bacteria seem to love the most.

If we can do that, our children can grow up healthy with immune systems that fight for them, not against them.

Because the gut truly is the key to health in the body.

Alright, now that we’ve explained what autoimmune conditions are, and what causes them, in the next article we’re going to dive into what to do to reverse them.

Because it can be done. We see it every day in our clinic.

*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.