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Short Chain Fatty Acids, Immune Health, and Your Thyroid.

Is your thyroid disorder or other immune issue from low levels of short chain fatty acids in the gut, like butyrate? Here’s how to know…

In this video, I talk all about short chain fatty acids and their role in the gut, immune system, and thyroid conditions. If you’re struggling with chronic immune-inflammatory conditions, thyroiditis, Grave’s disease, Hashimotos, arthritis, chronic food reactivity or food sensitivities; or if you’ve done multiple gut protocols, take lots of probiotics, and still have chronic immune inflammatory issues and don’t feel well, you want to listen to this one.

Video Transcript

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Today we’re talking about short-chain fatty acids. Many of you may never have heard of short-chain fatty acids, but if you’re struggling with chronic immune-inflammatory conditions, thyroiditis, Grave’s disease, Hashimotos, arthritis, chronic food reactivity or food sensitivities; or if you’ve done multiple gut protocols, take lots of probiotics, and still have chronic immune inflammatory issues and don’t feel well, you want to listen to this thyroid Thursday. 

So let’s talk about what these things are. You have bacteria that live in your GI tract. They’re called commensal bacteria. Think about commensal bacteria as the bacteria, as maybe the neighbors, the people that live in your neighborhood. They should be there, but you also don’t want too much of ’em, you don’t want too few of ’em. You want a nice balance of the commensal bacteria. 

When we eat, especially soluble and insoluble type fibers from our diet, the bacteria take those soluble and insoluble fibers. They ferment them and produce these things called short-chain fatty acids. And there’s a couple of ’em, but Butyrate is the one that gets most of the love and attention.

Okay, now what’s the importance of these things? Well, they do a lot to help maintain health, balance, and homeostasis in the GI tract.

They are critically important for helping regulate the immune system and helping maintain what we call the gut’s “tight junctions” or your intestinal integrity. Those are the two most important things that you might be familiar with, especially if you have some type of immune-based condition or autoimmune condition or chronic inflammatory condition. 

You’ve probably heard the term “leaky gut” before. And if you’ve had leaky gut and you haven’t evaluated and addressed or discussed short-chain fatty acids with whoever’s helping you, that may be a reason why you might return pretty quickly to having food sensitivities and leaky gut issues after doing some type of functional medicine GI support formula. 


So what do these short-chain fatty acids do? They help regulate what are called the T regulatory cells. 

When the immune system gets activated, T cells get activated, and once the immune system’s activated, we need to calm it back down again. One of the cells that’s really in charge of maintaining the balance in the T-cell system and kind of calming down the immune system once it gets turned on are your T regulatory cells, and the short-chain fatty acids help regulate these T-reg cells. 

So if you don’t have appropriate short-chain fatty acids, there’s a high probability you’re going to start to develop autoimmune inflammatory conditions, both in the gut and outside of the gut.

They help maintain GI homeostasis and the balance between these different systems.


So there’s a lot of stuff going on in the GI tract, and something has to help regulate the balance between these systems. So it is the short-chain fatty acids that help maintain the balance between the intestinal cells, the immune system, the commensal bacteria (again, that’s the bacteria that should be in the GI tract), and all the regulatory mechanisms that help run the GI system.

So too much or too little short-chain fatty acids can be a problem. How do you know if you have too much or too little? 

Well, you have to measure if you really want to know. And there are functional GI tests out there that do measure short-chain fatty acids, and there are some that don’t. I used to use a test in the past that didn’t measure them, and now over the last five plus six, seven years, I think I’ve only been running tests that actually have them because of how important it is to know where those short-chain fatty acids are.

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How do we get these short-chain fatty acids? We have to have the appropriate bacteria, and then we have to have the proper nutrition.

We need fiber for the bacteria to ferment, and then they will produce the short-chain fatty acids that help regulate the immune system and help maintain the integrity of your intestinal barrier. 

So as I said, too much or too little can both be a problem, but typically what we see is too little short-chain fatty acids. 

And this may be the result of somebody’s diet. It may be the result of stress impacting the gut flora. It may be the result of antibiotic use, it may be the result of other factors that have changed the gut flora. 

Could it be things like glyphosate that are potentially changing the gut flora? Maybe. That could be why somebody going on a gluten-free diet sees a benefit because, hey, if I’m eating less wheat and gluten, there’s potentially less glyphosate coming into the system, less damage to the commensal bacteria, and then they can produce those commensal bacteria can produce more short-chain fatty acids, and that can help make them have less inflammation, less immune-based issues


So what are the potential issues that can occur from too little short-chain fatty acids?

If you have decreased short-chain fatty acids, you’re going to have increased intestinal permeability or a leaky gut issue. And for those who don’t know what that is, think of your intestinal lining like a screen in your window. It’s got little teeny tiny holes to let the air in but keep the bugs out. Intestinal permeability is just that. That screen has now bigger holes. If I stick my fist through that screen, I’ve just created bigger holes, so there’s more permeability.

That might sound good, well, then I can get more air in. But you can also get more bugs from outside into your home, which can then start to create chaos in the GI tract. 

If we have higher levels of intestinal permeability, more undigested food can cross the barrier. That poorly digested food can then trigger immune and potentially autoimmune conditions, as well as food sensitivities or food intolerances.

If we have more permeability, then bacteria and yeast can cross the barrier and get into the body and start to trigger systemic immune inflammatory conditions. If there’s more permeability, the toxins from those organisms continue to cross the barrier and create problems. 

70% of the immune system’s on the other side of that GI barrier. And if you have too much stuff crossing the barrier that shouldn’t, you’re going to really ramp up that immune system. And that can be one of the big factors that triggers immune-based, inflammatory based disorders. 

If you have decreased short-chain fatty acids, that leads to increased intestinal permeability. That means more food peptides are crossing the barrier, more organisms and toxins are crossing the barrier, and this drives GI inflammation and systemic inflammation that can drive thyroiditis, which then causes primary hypothyroidism and Hashimoto’s.

So what do we do about it? 

One, if you’re a person who doesn’t eat much soluble or insoluble fiber, try adding those to your diet. You should be focused on a whole food-based diet primarily. 

But if you don’t eat some of these fibers, could you purchase fiber supplementation? Absolutely, you can do that. It may be a good short-term strategy until you can really incorporate these things into your diet. But long-term, the best solution is to just make sure you incorporate some of those things in your diet. 

If you add some of these fiber components to your diet, whether it’s food or supplementation and you don’t feel good, then there may already be an imbalance of the bacteria and some of those bacteria may be over fermenting some of those fibers.

And if it doesn’t feel good, you want to reduce those and reach out to a functional medicine practitioner to help you understand what’s really going on and what’s the right solution. 

My recommendation would be to make sure that you’re getting a functional GI test that then evaluates for short-chain fatty acids. Right now, I like the Gut Zoomer as my kind of go-to test for assessing GI function and GI physiology. Other physicians may have other tests they prefer, but make sure it measures those short-chain fatty acids. 

Then the next question is, what do you do? 

Some people suggest, well, just take butyrate if your butyrate’s low. But that’s like a bandaid. That’s a good short-term solution to help regulate the immune system to help maintain the junctions. 

But you have to address the complexity of what’s going on, and that’s where you should work with a functional medicine practitioner to understand what’s wrong and how to raise those short-chain fatty acids naturally instead of just relying on something like butyrate.

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Hi, I’m Dr. Eric Balcavage, owner and founder of Rejuvagen. If you’re struggling with health issues or have questions, let’s chat. You can schedule a 15-minute call with me to get started.