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Small Intestinal Bacterial Overgrowth (SIBO) — What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

When you have issues with Mast Cell Activation Syndrome or Histamine Intolerance, one of the most common root causes can be gut issues. And these issues can sneak up on you from anywhere!

But especially if you have mold toxicity. Because mold toxins (mycotoxins) really upset the balance in the gut.

Here is one of the worst things that happened to my gut.

I had just gotten my hydrogen water machine back from being repaired. It had helped me a lot previously.

So, I was so excited to start using it again.

But I noticed a few hours after drinking the water that my stomach felt “off.” I started having some discomfort. Then I started having pain. But I wasn’t sure what was going on.

I thought maybe I had eaten the wrong thing. Or caught a tummy bug.

The next day, I developed significant loose stools, gas, and bloating.

It was so bad that I knew something was definitely wrong.

I started to notice that every time I drank water from the machine, my gut was feeling worse and worse.

So, I stopped drinking water from the machine after only two days of having it back.

But the pain, bloating, gas, and diarrhea kept getting worse and worse.

And the things that usually helped my GI tract weren’t making it any better this time.

Then I noticed every time I ate I got worse.

Especially, when I was eating healthy, low histamine foods. Like apples, Brussels sprouts, and broccoli.

I had just ½ an apple. And my tummy blew up like I was 7 months pregnant. I literally looked like I had a basketball under my shirt.

It was actually getting very embarrassing – I didn’t want to be around anyone.

It was at that point that I realized… “Oh my gosh, I’ve got SIBO.” SIBO means Small Intestinal Bacterial Overgrowth.

I started thinking about what had changed in my routine. Then I remembered…the hydrogen water machine.

So, I tested the water. And it came back full of bacteria and yeast. When I sent it in for repair, the company told me it would be thoroughly sanitized.

But obviously that hadn’t happened.

The bacteria from the water ended up giving me SIBO – Small Intestinal Bacterial Overgrowth.

This is why I want to share some information on how SIBO relates to Mast Cell Activation Syndrome and Histamine Intolerance. Because a LOT of us are dealing with this.

And I see it daily in the practice. Especially for those with  issues.

But this is a very complicated area. So this post will be covering the basics and the starting steps.

We’ll start with what can cause SIBO.

Causes for Small Intestinal Bacterial Overgrowth (SIBO) and What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

This post is for informational and educational purposes only. It is not meant to replace medical advice. Please work with your medical provider on any medical issues. This post is not here to treat, diagnose, or cure any disease or condition, nor is it prescriptive for any person.

Small Intestinal Bacterial Overgrowth is basically either a high amount of bacteria living in the small intestine. Or an imbalance of bad bacteria in the small intestines.

There are quite a number of possible causes behind SIBO. And keep in mind that you could have multiple causes if you have SIBO.

Just a few of those possible causes include:

  • Antibiotics – kills off helpful bacteria and causes imbalances
  • High sugar/carb intake – feeds harmful bacteria and causes imbalances
  • Stress – affects movement of food through intestines — undigested food and waste products in the digestive tract create a breeding ground for bacteria
  • Mold Toxins – #1 cause in the people I work with, disrupts balance of gut bacteria
  • Low stomach acid – Hydrochloric Acid (HCL), called stomach acid, is very important for the digestion of food – undigested food and waste products create a breeding ground for bacteria
  • Low digestive enzymes – food doesn’t get properly digested — slow passage of food in the digestive tract creates a breeding ground for bacteria
  • Certain medications – Like Protein Pump Inhibitors (PPIs) for acid reflux, decrease in stomach acid can increase SIBO.
  • Loss of motility – constipation — again, slow passage of food and waste products = perfect environment for bacteria to grow
  • Vagal nerve issues – this nerve goes from the neck to the gut.   Any problems with it can affect motility of small & large intestine + stomach emptying
  • Certain surgeries – like appendix removal or having your colon taken out — surgeries like these can slow passage of food and waste products in the digestive tract = breeding ground for bacteria
  • Age – SIBO risk increases as you get older. This is because you make less stomach acid that breaks down food.
  • Drinking contaminated water – this could be like from swallowing water from a river or lake, drinking from an open bottle, water that hasn’t been treated (like in Mexico) or even a contaminated water filter or water machine – like what happened to me

So those are some of the causes of SIBO. And if you received my MastCell 360 Guide, you know that infections are one of the common root causes of mast cell issues.

Small Intestinal Bacterial Overgrowth is one of those possible infections.

SIBO can trigger our mast cells. It does that by setting off inflammation in the gut.

That amps up the immune system. And then mast cells are activated. They become unstable, which causes them to release histamine.

Now we’ve covered what SIBO is and what can cause it. Next up: symptoms of SIBO.

Symptoms of Small Intestinal Bacterial Overgrowth (SIBO) -- What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

What are some symptoms of Small Intestinal Bacterial Overgrowth? Since SIBO is an issue in the gut, a lot of the symptoms are digestive-related. But not all of them.

Here’s a list of possible symptoms of SIBO:

  • Bloating
  • A distended belly
  • Intestinal pain or discomfort (cramps)
  • Gas/flatulence
  • Heartburn
  • Acid reflux
  • Belching
  • Diarrhea
  • Constipation
  • Low energy
  • Absorption problems – causing nutrient deficiencies (especially Iron, B12, and vitamin D)
  • Weight loss

And bone loss – osteoporosis or osteopenia – can be related to SIBO too. This is because with gut inflammation from SIBO, you might get mineral loss.

But sometimes SIBO doesn’t cause any symptoms at all. Or, the symptoms may be misinterpreted.

And there are 3 major types of SIBO. Let’s look at those next.

Hydrogen vs. Methane vs. Hydrogen Sulfide Small Intestinal Bacterial Overgrowth (SIBO) – What to know when you have Mast Cell Activation Syndrome or Histamine Intolerance

SIBO is all about imbalance of bacteria. But is it always the same type of bacteria? No.

There are actually different types of bacteria that can over grow in the small intestine.

Depending on the type, you can get different symptoms. This is why there are different types of SIBO. Because different bacteria species produce different types of gases when they eat their food.

The three main types of SIBO are named after the types of gases produced.

Those gasses are:

  • Hydrogen
  • Methane
  • Hydrogen Sulfide

Hydrogen SIBO – has mostly hydrogen-producing bacteria. This type of SIBO more often causes diarrhea. But not always.

Methane SIBO – has mostly methane-producing bacteria. This type of SIBO more often causes constipation. But again, not always.

Hydrogen Sulfide SIBO – in this kind of SIBO, your gas can smell like rotten eggs. It’s VERY noticeable. This type of SIBO tends to cause diarrhea. There isn’t as much research on this type of SIBO. And testing for it is just becoming available. But if you have this type, you likely will have issues with high sulfur foods or hydrogen water.

So, other than symptoms, how can you know for sure which type of SIBO you have?

Or, how do you know if you have SIBO at all? We’ll go over testing options in the next couple of sections.

Testing for Small Intestinal Bacterial Overgrowth (SIBO) – What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

Another reminder: This post is for informational and educational purposes only. It is not meant to replace medical advice. Please work with your medical provider on any medical issues. This post is not here to treat, diagnose, or cure any disease or condition, nor is it prescriptive for any person. 

There are a few tests that can help determine if you have SIBO. You’ll want to talk with your healthcare practitioner if you think you have SIBO. Your healthcare practitioner can help you know if one of these tests might be right for you. Here are a few of the common tests.

1. Breath Testing:

Testing for SIBO is usually done using Breath Testing.

Breath Tests are widely available and non-invasive. That’s a plus. But you have to drink a type of sugar (like lactulose syrup) that triggers more bacterial growth and activity. That’s a negative. Breath testing is also limited in the types of bacteria it can detect.

And SIBO breath testing has been shown in research studies to have about a 50% rate of false positives. So that’s definitely a negative.

It’s very important to follow the test prep instructions exactly as they are written. And it’s important to do that with your medical practitioner’s guidance.

2. Organic Acid Testing

The Organic Acid Test can offer some insight into the gut and potentially SIBO.

There is a test called the Microbial Organic Acids Test. It tests organic acids that are produced by the bacteria you have. That can give some clues of overgrowth.

Great Plains Labs offers a great Microbial Organic Acids Test. It has some good markers for both bacteria and gut fungal species.

The one main drawback with this test is that you can’t tell where the bacteria or fungi are located. They could be overgrown in either the large or small intestine.

But, at least you’ll know whether the levels are high. That can be helpful in figuring out what’s going on.

So, the mOAT may be a good test to start with.

Here is a sample of the Great Plains Labs Microbial Organic Acids Test:

GPL Sample Toxin Report

Another thing to think about testing is mold toxins. Mold can actually be keeping you from getting rid of the SIBO.

In fact, mold toxins are one of the BIGGEST reasons I see SIBO protocols fail for people over and over.

This is because mold toxins get dumped into the gut. And then no matter what you do to heal your gut, the mold toxins cause more damage.

And mold toxicity has truly become a hidden epidemic. About 95% of people I see in the clinic have mold toxins affecting their gut (and the rest of their bodies).

3. Mold Toxins Testing  

If you keep trying gut or SIBO protocols…and you aren’t getting better…then it’s usually time to check for mold toxins.

Urine testing can let you know what level of mold toxins are being eliminated from the body. But there isn’t one panel that covers all the mold markers. So, I use two. They complement each other:

Certain States are “Direct Access” – and give you better pricing:  Alaska, Arizona, Arkansas, Delaware, District of Columbia, Indiana, Iowa, Kansas, Louisiana, Minnesota, Mississippi, Missouri, Montana, Nebraska, New Mexico, North Carolina, North Dakota, Ohio, Oklahoma, South Dakota, Texas, Utah, Vermont, Virginia, Washington, West Virginia, Wisconsin

International or in a Direct Access State?

>>>>>Order the RealTime Mycotoxin Panel here

In the US but not a Direct Access State?

>>>>>Order the RealTime Mycotoxin Panel here

If you can get both, then this one will show some other molds in addition: The Great Plains Mycotoxin test (or this link for Canadians)

Be sure to read about these tests and get the provocation information here.

But why is mold testing important if you think you have SIBO? I’ll go over that next.

Mold Toxins and Small Intestinal Bacterial Overgrowth (SIBO) - What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

Mold Toxins can worsen SIBO. They do this by continually disrupting the gut bacteria. This is because the mold toxins get dumped into the gut. And then they can cause a lot of problems.

Mold toxins affect our immune balance in the whole body.

Particularly, mold toxins affect the body’s ability to keep bacteria levels in the gut in check. (And they really increase mast cell activation at the same time.)

When this happens, normal bacteria in the gut can overgrow. Or bad bacteria can grow out of control.

I have seen people try to get rid of SIBO for years with little luck. It was most often because the mycotoxins weren’t addressed first. 

If you haven’t read my series on mold yet, these are the best articles to start with:

But, here’s the good news!

SIBO is usually much easier to address once mycotoxins are out of your system. But you’ll definitely need help from your healthcare practitioner.

It’s hard to heal from mold or SIBO if you are doing it yourself.

So what steps can you take if you do have SIBO? A low histamine diet can help. It can help to lower your inflammation. And it can allow your gut to heal.

I’ll go over key foods to think about adding in the next section.

Low Histamine Eating for Supporting the Gut in Small Intestinal Bacterial Overgrowth (SIBO) - What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

Eating low histamine can help keep your gut inflammation levels in check. Here are some food ideas that could help support your gut if you have SIBO.

  • Eating low FODMAP short term may help – FODMAP is an acronym for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols.These are all types of carbohydrates in food. And they can trigger SIBO. That’s why you might have to avoid them just while you’re addressing SIBO.Once you have addressed SIBO, you can start adding them back in. Learn more about FODMAPs and the SIBO connection in this post.
  • Ginger – Ginger is known to work as a prokinetic. That means it helps food move through the intestines. This is important so the food doesn’t stick around to feed bad bacteria. Ginger also lowers inflammation. And it stabilizes mast cells.
  • Radishes – They are low FODMAP, and low histamine. (They are high salicylate, so avoid if you have salicylate issues) Radishes can give you fiber to help feed the gut’s helpful bacteria…without feeding harmful bacterial or fungal infections.
  • Lemon (if tolerated) – Lemon juice can help protect the liver. That’s important in gut function. Lemons also contain limonene. Which also was shown in studies to be able to help lower inflammation in the gut.
  • Meat Broth (Not bone broth) – It has nutrients (amino acids) needed to heal your gut lining. Meat broth is lower histamine. Bone broth is higher histamine so you’ll want to avoid it. Here’s info on making a low histamine meat broth.
  • Spacing meals out – 4-5 hours between meals, if possible. If possible, it can help if it’s possible to go 10-12 hours overnight. (of course, don’t do this if you are diabetic or have adrenal fatigue)

The reason why this is important has to do with what’s called the Migrating Motor Complex (MMC). This nerve complex makes a clean sweep of your gut after you eat. Your MMC needs time between meals to work properly. And if the MMC isn’t allowed to do its job, SIBO will often not go away.

So, a low histamine diet can be helpful. And if possible, spacing your meals out can really help too.

But what if you’re already eating a low histamine, low FODMAP diet? And what if you’re already spacing your meals out?

Then keep reading.

In the following section I’ll give you supplement ideas and lifestyle tips to consider. You can discuss these with your healthcare practitioner.

Lifestyle and Supplement Ideas that May Help with Addressing Small Intestinal Bacterial Overgrowth (SIBO) - What to Know When You Have Mast Cell Activation Syndrome or Histamine Intolerance

Again, this post is for informational and educational purposes only. It is not meant to replace medical advice. Please work with your medical provider on any medical issues. This post is not here to treat, diagnose, or cure any disease or condition, nor is it prescriptive for any person.

This is a general starter approach I’ve seen help many of the people I work with.

SIBO is complex, though. And often has numerous factors. And each of those factors need to be addressed. This is rarely something people can DIY. This has to be customized for each person.

So, what I’m going to share with you now are some possible options to start with. You can use this information to start a discussion with your healthcare practitioner. Together, you can work with your practitioner to find the right options for you.

We’ll get into more advanced steps in a future SIBO Part II blog post on more advanced steps.

Support the Nervous System

This is critical because your nervous system, immune system, hormone system, and stress levels are all connected. In fact, they aren’t separate! So if you work on the nervous system you are automatically working on your gut.

SIBO is impacted by all of those: nervous system, immune system, hormone system. You need your parasympathetic (“rest and digest”) system to work well if you want to get rid of SIBO.

The vagus nerve is also involved here. The vagus nerve is a long nerve that goes from the top of your neck through your whole gut. The vagus nerve affects motility – the movement of food through the gut. If the vagus nerve isn’t working well, you’ll be more likely to have SIBO.

You can learn more about supporting your nervous system and Vagal nerve here: The Mast Cell Nervous System Reboot

Fix Gut Motility
movement through the gut)

  • Enough water – This is critical. I’m often surprised how many people I talk to who aren’t drinking enough water. Here’s an easy way to calculate how much water you should be getting. Take your body weight in lbs and divide that in half. That number, in ounces, is how much water you should be drinking. Here’s an example. If you weigh 150 lbs, 150 divided by 2 is 75. That means you’d want to drink 75 ounces of water, herbal tea, etc/day. (Caffeinated drinks and alcohol don’t count toward that total. They can actually dehydrate you.
  • Magnesium Oxide – Magnesium helps relax spasms and allows easy movement through the gut. It works as a natural laxative. It’s not well absorbed. But it can help with constipation.

Calm Mast Cells In The Gut

  • Follow a low histamine diet (plus low oxalate or low salicylate if you need to).
  • Perilla Seed Extract is an option that has mast cell calming effects, when tolerated. I like to take it 30 minutes before a meal.
  • Quercetin has also been shown to be very mast cell supporting, when tolerated. The form Alpha-Glycosyl-Isoquercitrin is the most well absorbed. This means less is needed. I like to take this 30 minutes before meals too.
  • Medications – Some people may find they need to talk with their medical practitioner about trying some medications. This can include things like Cromolyn Sodium and/or H2 blockers like Pepcid.
It’s very important to onboard new things slowly. Especially if you’re sensitive.

You can learn a lot more about these supplements and several others here:

Supplements MasterClass Button

Digestive Enzyme Support

    • Holozyme – Best digestive enzyme support on the market right now. They are fast acting and clinically proven. They are also free of fillers and non-GMO.HoloZymes
    • Or you can try Pancreatic enzymes


Short Chain Fatty Acids

  • Tributyrin-X – This is the best butyrate supplement on the market. It provides those short chain fatty acids (SCFAs) that might be low with SIBO.Tributyrin


It actually feeds good bacteria. It is really good if you’re eating low FODMAP. And you can’t do all the fiber.

It helps to normalize gut function. While also supporting mast cells.

It can help balance constipation or diarrhea for people. But if you try this, DON’T open the capsule to start slow on this one. Butyrate naturally has a very, very strong smell.

Address Mold Toxins, If Present

It starts with supporting your nervous system. Then you prepare your body by supporting your elimination systems. This is at least a 3 to 6 month process. Again, you can read the whole program here.

Remember, these things take time. So don’t forget to take a deep breath and be gentle with yourself.

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  1. Svdmeere

    Can you maybe comment on hydrogen water therapy to combat SIBO/MCAS? (I read it can help with SIBO) If the hydrogen water had helped you in the past, why did you not resort to it again, by eg. getting hydrogen from tablets / bottles (instead of your infected machine) ?

    1. Suz, Mast Cell 360 Team

      I had gotten hydrogen SIBO, and the hydrogen tablets made it worse for me, so I couldn’t use hydrogen water anymore. Maybe we’ll do a blog post on it sometime in the future – it’s a very long topic. I don’t think it helps with most SIBO, though. –Beth

  2. Sharon

    Hi Beth, Have you looked into Integrative Peptides KPV to reduce Mast Cells. Seems like a more hidden product out there, many don’t know about? Seems great in theory don’t if the product is worth it.

    1. Suz, Mast Cell 360 Team

      Hi Sharon,
      There are hundreds of types of peptides. Many sensitive people don’t tolerate them until after root causes are addressed. Some do ok, though. It’s really case by case.

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