woman holding abdomen

Enzymes, Short-Chain Fatty Acids (SCFA’s) and Gut Health in SIBO, Mast Cell Activation Syndrome and Histamine Intolerance

The majority of people with Mast Cell Activation Syndrome and Histamine Intolerance have gut issues.

In my practice, I work with Mast Cell Activation and Histamine Intolerance. And about 90% of the people I see have gut problems.

Why is this?

  1. One of the major histamine degrading enzymes (DAO) is made in the gut. DAO production goes way down if there is gut inflammation.
  2. There are a huge number of mast cells in the gut. Gut inflammation means more mast cell activation. And mast cell activation means more histamine release (as well as hundreds of other inflammatory mast cell mediators.)
  3. 95% of people in the Mast Cell 360 clinic have Mold Toxicity. Mold toxins wreak havoc on the gut. This is because they get dumped into the gut to get eliminated.

All three of these greatly affect Mast Cell Activation Syndrome and Histamine Intolerance.

So, working on gut issues is one of the first steps in recovering your health.

It’s usually step #3 for the private clients in my practice. (#1 is supporting the nervous system and #2 is calming the mast cells.)

Working on my gut has made a HUGE difference in my own health.

I had gut issues as a child. I now know that those issues stemmed from mold toxicity. Of course, I didn’t know that then.

And as a young adult, my gut issues got even worse after I got dysentery when traveling abroad. This is a common gut infection for travelers. It’s caused by bacteria or an amoeba.

So my gut was out of whack for years…literally years.

I was burping a lot after meals. Food sat heavy in my stomach. I felt tired and brain-fogged after eating. I had heartburn all the time.

But I finally got my gut in great shape. Taking digestive enzymes was one of the major things that made a huge difference.

Then something awful happened.

If you’ve been following me, you’ve probably heard this part. I was using a hydrogen water machine as a part of a case study.

My machine broke and sat for a few months with moisture inside it. I sent it off to the company for repairs.

I was told the machine had been fully sanitized and treated for bacteria and mold.

It hadn’t.

And before I knew that, I drank the water for two days. I quickly developed a lot of new gut problems – diarrhea, bloating, gas, etc.

I lost my ability to tolerate FODMAPs. And when I tested my gut, I had significant bacteria and candida infections.

So I was dealing with both SIBO (small intestinal bacterial overgrowth) and SIFO (small intestinal fungal overgrowth).

I had to repair my gut…again.

But the things I tried in the past weren’t working this time. I was really frustrated!

That’s when I reached out to my good friend and gut genius, Steve Wright.

Steve knows more about complicated gut issues than almost any other practitioner I’ve met. In fact, he’s the founder of Health Gut, one of the largest online gut websites.

And he’s always on the cutting-edge of the gut world.

Steve reminded me to go back to basics – start with increasing digestive supports.

I was so grateful for what Steve shared with me. I know a lot about gut health, but my case was complicated.

Sometimes I have to reach out to cutting-edge experts like Steve to get new ideas. I LOVE learning this kind of new stuff. And I love being able to share it with you!

In this post, I’ll go over what I learned from Steve — including after tons of trial and error, the top digestive supports in our Mast Cell 360 Functional Gut Health Lineup. These are: enzymes, stomach acid support, and short-chain fatty acids.

I know if you’re reading this you or a loved one probably has a complicated health case, too. And like I said earlier, about 90% of the clients I see have gut issues. Most commonly these issues present as constipation and diarrhea. So let’s start there.

Constipation and Diarrhea – What to Know if You Have Mast Cell Activation or Histamine Intolerance

Constipation and diarrhea are frequent symptoms in Mast Cell Activation Syndrome and Histamine Intolerance.

Most people tend to have one or the other. However, you could switch back and forth between them.

This can be due to any number of things. It could be from:

No matter what the cause, constipation and diarrhea tell you that your gut is crying out for help.

If a change in diet hasn’t helped enough, it may be helpful to use extra gut supports, too. That’s where gut-supporting supplements can come in.

Especially things like:

  • Digestive Enzymes
  • Betaine HCL
  • Butyrate

We’ll start out by talking about digestive enzymes. What are they? And why are they important for Mast Cell Activation Syndrome or Histamine Intolerance?

Digestive Enzymes – What to Know if You Have Mast Cell Activation or Histamine Intolerance

To begin with, what are enzymes in general? Enzymes are proteins in the body that speed up processes. Not just a little. A LOT. Anywhere from 100 million to 10 billion times.

Why can speeding up processes be beneficial?

In the digestive process, if you have slow motility, food can be sitting around in the gut longer than it should…and that can create an environment for bacteria to thrive.

Speeding up that process can allow your body to properly digest your food. And eliminate waste regularly. Together, this keeps food matter moving. When things are moving, they aren’t creating that perfect environment for bacteria.

Digestive enzymes can be helpful for Mast Cell Activation or Histamine Intolerance, too. This happens in a couple ways.

  1. There are tons of mast cells in the entire gut – from end to end.
  2. A lot of the nervous system is found in the gut.

And if you’ve been reading much here at Mast Cell 360, you know that the nervous system and mast cells are really arm in arm.

An upset gut = an upset nervous system and upset Mast Cells

And that can aggravate Mast Cell Activation Syndrome or Histamine Intolerance.

So, digestive enzymes can help Mast Cell Activation and Histamine Intolerance by starting digestion off right — by improving the stomach’s ability to break down food.

Better digestion = happier gut.

Happier gut = happier nervous system & happier mast cells

And digestive enzymes can help in another way: they can help you get more nutrition out of what you eat.

And nutrition is so important for healing.

If your gut is inflamed or damaged, you’re not going to absorb nutrients as well. And if you happen to have SIBO, you’ve got bacteria just waiting to eat what you don’t absorb. That can keep your body from using nutrients beneficially.

With SIBO, bacteria are living in the small intestine — where they aren’t supposed to be. The small intestine is where you absorb nutrients from the gut into your bloodstream. And if there are hungry bacteria there, you might not get to benefit from those nutrients.

That’s where digestive enzymes come in. They improve your ability to break down food and absorb nutrients. And that means bacteria can’t multiply by feeding on undigested food.

So we’ve talked about how digestive enzymes can be helpful when dealing with gut issues.

Next we’ll look at another of my top recommended digestive supports — the one that supports stomach acid.

Stomach Acid Supports: Betaine HCL and Pepsin – What to Know if You Have Mast Cell Activation or Histamine Intolerance

What is Betaine HCL? HCL stands for hydrochloric acid. It’s what’s produced in your stomach as stomach acid.

Betaine HCL is basically a supplemental form of stomach acid.

And Pepsin is a protease (breaks down protein) produced by the stomach.

They are usually found together in supplements because Betaine HCL is needed to activate pepsin. And pepsin digests protein.

A Betaine HCL with pepsin supplement can help boost your stomach acid levels.

But why would you need to do that?

It turns out, a lot of people have low stomach acid.

  • Steven Sandberg-Lewis (ND) has found that 75% of his patients who have acid reflux (GERD) also show low stomach acid.
  • Jonathan Wright (MD) has found that 90% of the patients in his clinic have low stomach acid.

Having indigestion or acid reflux isn’t necessarily from having too much stomach acid. It’s more likely to be caused by too little stomach acid.

In one study, 31.5% of men and women over 60 (nearly 1 out of 3) suffered from low stomach acid.

If your stomach acid levels are low, you’re not going to break down proteins in foods very well. And larger food molecules will get into the small intestine.

That’s not good.

Partially digested food particles in the small intestine can contribute to Small Intestinal Bacterial Overgrowth (SIBO). And inflammation in the gut.

And we know an inflamed gut can set off mast cells. You can learn more about the Mast Cell – SIBO connection by reading this article.

Betaine HCL has been shown in studies to restore stomach acid. That can greatly improve your ability to break down food.

I’ll mention this again later, but here’s something very important about betaine HCL.

This is an acid. You don’t want it to come into direct contact with your skin – either your hands or your mouth.

DO NOT SPRINKLE IN FOOD OR WATER – If you need to start slow, wear gloves and empty part of the contents into an empty regular veggie capsule like this one: 

And do not use Betaine HCL if you have an ulcer, h. pylori infection, or heartburn.

So it’s important to restore stomach acid and get rid of SIBO. And betaine HCL can be one way to help with that.

Next, let’s look at another of my top recommended digestive supports – short-chain fatty acids (SCFAs).

Short-Chain Fatty Acids (SCFAs) – What to Know if You Have Mast Cell Activation or Histamine Intolerance

Findings have shown that short-chain fatty acids (SCFAs) are important in maintaining gut and immune health.

Some different names of SCFAs are:

  • Butyrate
  • Acetate
  • Propionate
  • Pentanoic acid
  • Hexanoic acid

Butyrate is the most important and most beneficial of the SCFAs. The majority of it is produced in the colon. It helps provide energy to 60-70% of the cells there.

SCFAs are important for Mast Cell Activation Syndrome and Histamine Intolerance because they help lower inflammation. And they help keep the gut healthy.

Butyrate in particular is known to help improve these aspects of the gut:

  • Tight junctions (to heal or avoid leaky gut)
  • Mucus layers to help avoid leaky gut
  • Increase good bacteria numbers
  • Getting rid of pathogens
  • Keeping oxygen levels low in the colon (making the colon better for good bacteria and helps reduce bad bacteria)

All of these things are important for healing your gut…and getting your immune system back in balance.

If you don’t have enough butyrate, you may have trouble with those things listed above.

And those things could cause digestive problems and unpleasant symptoms like constipation or diarrhea.

So now you know why those top three digestive supports can help. But how do you choose the right support supplements? We’ll cover that next.

How to Choose Gut Support Supplements – What to Know if You Have Mast Cell Activation or Histamine Intolerance

But first, It’s important you know that this blog post is for informational and educational purposes. It’s not meant to treat any health condition or to be prescriptive for anyone. 

Anyone can react to anything. Before you start new supplements, please make sure you’re working with a healthcare practitioner who can help you with this.

So, how do you choose gut support supplements?

We’ll go over what to look for in each supplement category below:

Digestive Enzyme Supplements

For digestive enzyme supplements, this is what you should look for:

  • Full pH coverage – Systemic Effective range of pH 1.7 to 11.0
  • Both pancreatic and brush border enzymes
  • Activated with mineral cofactors (Enzymes are “activated” by cofactors. Basically, cofactors are helpers. They are usually vitamins or minerals. They help get the enzymes energized to work.)
  • Strong, concentrated enzymes
  • Pharmaceutical grade status
  • NSF certification (highest 3rd party standard in supplements)
  • Systemic absorption (functioning as both digestive AND systemic enzymes)
  • High quality raw ingredients
  • Lack of additives like magnesium stearate, silica, artificial colors or flavors
  • Avoidance of allergens – milk, casein, eggs, fish, shellfish, soy, wheat, gluten, tree nuts, peanuts, yeast, or rice

Betaine HCL Supplements

For Betaine HCL supplements, look for:

  • At least 1 gram per serving
  • Includes at least 15 mg pepsin per capsule
  • High-quality raw ingredients
  • Lack of additives like silica, artificial colors, or flavors
  • Free of GMOs

Again, Betaine HCL is an acid, so you don’t want it to come into direct contact with your skin – either your hands or your mouth.

DO NOT SPRINKLE IN FOOD OR WATER – If you need to start slow, wear gloves and empty part of the contents into an empty regular veggie capsule like this one: https://amzn.to/3xmITOz

And do not use Betaine HCL if you have an ulcer, h. pylori infection, or heartburn.

SCFA Supplements

For a short-chain fatty acid (SFCA) supplement, you’re mostly looking for butyrate. Check for:

  • Type of butyrate: you want tributyrin rather than butyrate salts
  • Delivery system: enteric softgel, which makes it through the stomach acid and into the gut
  • Between 300 to 4,500 mg of butyrate a day
  • Lack of additives like magnesium stearate, silica, artificial colors or flavors
  • Easy to use and lack of smell
  • Free of GMOs

There are other supplements which can be helpful, too. We’ll take a look at those next. After that, I’ll share the Mast Cell 360 Functional Gut Lineup. That includes the brands of supplements that have worked for me and many of my clients.

And I can tell you I’ve tried a lot of supplements. Most of them didn’t work at all. These sit in what I call my supplement graveyard. Maybe you have one of your own!

I’ve learned a lot with all this trial and error. I want to help you learn from my mistakes and wins.

But first let’s get an overview of those other supplements I mentioned — DGL, ginger, and intrinsic factor.

DGL, Ginger, and Intrinsic Factor – Importance for Mast Cell Activation or Histamine Intolerance

DGL is a form of the herb licorice. Licorice can raise blood pressure when taken over time. But DGL has the part that raises blood pressure removed.

And fortunately, the safer DGL form of licorice has a lot of gut and mast cell supporting properties.

For example, compounds in licorice (and the safer DGL extract) have been shown in research to support the lining of the GI tract. This happens by lowering inflammation-producing cytokines that trigger mast cells.

Those cytokines can trigger a lot of mast cell inflammation. So, these studies are telling us that DGL can support mast cell calming by reducing inflammatory cytokines.

When looking for DGL Supplements, look for:

  • High quality raw ingredients
  • Lack of additives (Magnesium stearate, silica, artificial colors or flavors)
  • Free of GMOs

Ginger has also been shown in studies to be a great mast cell stabilizer. And it can lower histamine levels. It’s been shown in research to have H2 antihistamine properties.

For Ginger Supplements, look for:

  • Organic, high quality raw ingredients
  • Lack of additives
  • Free of GMOs

Intrinsic factor is a protein that’s made in the cells of the stomach. It’s important for the absorption of vitamin B12.

Gut inflammation can cause an intrinsic factor deficiency. Then you can’t absorb vitamin B12.

That’s why low B12 is so common with gut issues.

Supplementing with intrinsic factor can help get those B12 levels back up while the gut heals.

For Intrinsic Factor Supplements, look for:

  • at least 7.5 mg per capsule
  • High quality raw ingredients
  • Lack of additives like silica, artificial colors or flavors
  • Free of GMOs

Next let’s look at how you might be able to avoid adding to the supplement graveyard. After all, there are a lot of brands out there. How do you know what to get? How do you know whether you’ll be able to tolerate them?

That’s exactly what we’ll cover next.

The Mast Cell 360 Functional Gut Lineup – What to Know if You Have Mast Cell Activation or Histamine Intolerance

Over my time in practice, I’ve put together what I call the Mast Cell 360 Functional Gut Lineup.

These are supplements I’ve found to work for clients with Mast Cell Activation or Histamine Intolerance. And good news!

Here’s the Lineup:

The Mast Cell 360 Functional Gut Lineup:

And here’s why I’ve found those products to be excellent digestive supports.

HCL Guard by HealthyGut

This is the best HCL supplement I’ve found. It’s a holistic, professional grade stomach support. This formula goes beyond the traditional HCL supplement you’ll find. There’s actually nothing else like this on the market currently. Here’s why:

  • Includes intrinsic factor – important for absorbing and protecting vitamin B12
  • Strong dose of pepsin – 3000 to 1 strength
  • Powerful motility (gut flow) support
  • Contains DGL, a Chinese licorice that soothes the gut lining
  • Great stomach acid support – 550mg betaine HCL per capsule
  • Free of fillers, flow agents, and other additives
  • Non-GMO
  • Free of gluten and major allergens
  • Manufactured in USA

This supplement has been so helpful for me and many of my clients. But I want to tell you one more time:

This is an acid, so you don’t want it to come into direct contact with your skin – either your hands or your mouth.

DO NOT SPRINKLE IN FOOD OR WATER – If you need to start slow, wear gloves and empty part of the contents into an empty regular veggie capsule like this one: https://amzn.to/3xmITOz

And do not use any Betaine HCL products if you have an ulcer, gastritis, stomach cancer, or against your health practitioners recommendations.

If you have salicylate sensitivity or a lot of supplement sensitivities, though, check out the recommendations further below.

>>>>>Get HCL Guard+ – Top stomach acid support


HoloZyme by healthy gut

This is my top digestive enzyme support. This is because it contains the needed mineral cofactors to make those enzymes work properly (activation).

There are no fillers in this. But it does have a little kelp as part of the mineral cofactors. It also has a little bit of Magnesium citrate.

I normally say to avoid citrates. But in this, the citrates are used up by the activation process. So, I haven’t found it to be a problem very often.

There also isn’t anything else on the market like this product, because:

  • Blend of both pancreatic and brush border enzymes
  • Activation the right amount (470 mg per 2 servings) ideal mineral cofactors
  • Activation blend that’s precision tuned to our Activ-Blend dual 4x concentrated enzymes
  • Pharmaceutical grade status with NSF certification (highest 3rd party standard in supplements)
  • High quality raw ingredients
  • Lack of additives like magnesium stearate, silica, artificial colors or flavors
  • Avoidance of allergens like: milk, casein, eggs, fish, shellfish, soy, wheat, gluten, tree nuts, peanuts, yeast, or rice
  • Manufactured in USA

Rarely, I have a small number of clients who have trouble with this one. Usually it is because of significant nervous system dysregulation and sensitivities to every supplement. Or it is metal toxicity (minerals can displace metals).

Keep reading for some alternatives if you’re in either category.

>>>>>$15 off HoloZyme – Top digestive enzyme support

Tributyrin-X by healthy gut

This butyrate supplement is the latest technology out there. It’s easy to absorb and easy to take. Keep in mind that you don’t want to open this capsule, though!

Butyrate naturally tastes and smells very strong. So, it’s not one you can start with just a drop. You have to start with a whole capsule.

  • This supplement is 99.9% pure liquid tributyrin
  • Tributyrin is the most effective type of butyrate
  • Has an enteric coated gel cap – so it goes safely through the stomach
  • Non-GMO
  • Gluten-free and lactose-free
  • No fillers, stearates, silicon dioxide, or charcoal
  • No smells or burps
  • Easy to swallow gel caps
  • 30 day serving, providing up to 1,500mg per day
  • Manufactured in USA

Learn more about Tributyrin-X™ by reading this article: The Best POST-biotic Butyrate for Mast Cell and Histamine Supports

These are some of the best digestive supplements I’ve seen. And they’ve been the only ones that really helped my gut.

But, there isn’t any single supplement that works for everyone with Mast Cell Activation Syndrome and Histamine Intolerance. Specifically, if you have salicylate intolerance you may be able to take the HCL Guard+.

And if you are super sensitive to supplements, you may not be able to take combo formulas.

In that case, I have a different lineup of supplements that I use. I’ll share what that is next.

>>>>>$15 off Tributyrin-X™ – Top SCFA Support

Digestive Supports if You Have Salicylate Intolerance – What to Know if You Have Mast Cell Activation or Histamine Intolerance

If you have salicylate intolerance, you might not do as well with the HCL Guard+. That’s because the ginger and DGL are higher salicylate.

In that case, you may want to try Betaine HCL+Pepsin as a “stand alone” product first. Without the ginger and DGL.

So, with salicylate intolerance, here’s a good combination of supplements to consider instead…

Functional Gut Lineup for Salicylate Intolerance:

Now, if you’re super sensitive and can’t do combo supplements, you can try a slightly different combination.

Functional Gut Lineup for the Super Sensitive:

  • Pure Encapsulations Liquid Butyrate (not as effective as the Tributyrin-X™ but may be an option if you can tolerate the lemon oil because you can open the bottle and start with one drop)

This combo keeps the Betaine HCL with Pepsin to support good stomach acid and protein digestion.

But instead of HoloZyme, it uses a simpler formula for pancreatic enzymes.

And instead of the Tributyrin-X™, it uses a Liquid Butyrate supplement that allows you to start with a drop and titrate slowly.

Just keep in mind that the Liquid Butyrate isn’t as effective as Tributyrin-X™. And it also has lemon oil in it. Sometimes citrus isn’t well tolerated by those with Histamine Intolerance.

That’s a lot of information we covered! Remember, you can always come back to it a little at a time.

Regaining your health takes time and patience. You may need to go back over an article a few times, and that’s ok. As always, remember to take a deep breath and be gentle with yourself.

If you’re interested in learning about other supplements that could help, check out my Master Class: The Top 8 Mast Cell Supporting Supplements. Just click on the first link below.

If you’re dealing with gut symptoms, you may also need a nervous system tune-up. After all, the gut and brain are very much connected.

You can sign up for my Master Class: Nervous System Reboot by clicking the link below.

*Some links in this website are affiliate links, which means Mast Cell 360 may make a very small commission if you purchase through the link. It never costs you any more to purchase through the links, and we try to find the best deals we can. We only recommend products that we love and use personally or use in the Mast Cell 360 practice. Any commissions help support the newsletter, website, and ongoing research so Mast Cell 360 can continue to offer you free tips, recipes, and info. Thank you for your support!

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  1. Joanna

    Thank you for the great article! I always wonder, when to take butyrate, is it best on empty stomach or with food? Should I take it together with my probiotics? Thanks

    1. Suz, Mast Cell 360 Team

      Hi Joanna,
      In her interview with Steve Wright from Healthy Gut, Beth said she takes these supports before a meal, about ten minutes or so before. Steve said that it is ok to experiment to see what works for you. He suggested making a few notes as you experiment to help you find what might be the best course of action for you personally. You can see that interview here if you are interested:


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