Key Points:

  • SIBO is often found in patients with complex chronic illnesses, and may be a root cause of their gut symptoms. Patients diagnosed with Lyme disease, mold toxicity, mast cell activation syndrome, and dysautonomia may be at a high risk of developing SIBO over time.
  • SIBO often co-exists with SIFO (small intestinal fungal overgrowth). While testing is not currently available for SIFO, patients should be treated for both if clinical evaluation calls for it.
  • Some initial treatment strategies for SIBO include the low FODMAP diet, probiotics, and herbal antimicrobials.

If you’ve been diagnosed with a chronic illness, then unexplained symptoms might feel like just another part of your average Tuesday (or any day of the week for that matter).

Maybe you’re even so tired of keeping track of everything that’s wrong with your body, you ignore new symptoms of bloating, gas, and chronic diarrhea or constipation until they become all-consuming.

I know it feels overwhelming sometimes — but you shouldn’t ignore these signs! Stressful GI symptoms like these can be a big indication of SIBO — small intestinal bacterial overgrowth.

SIBO is a complication I often see in my patients with Lyme disease, Mast Cell Activation Syndrome (MCAS), dysautonomia (dysfunction of the autonomic nervous system), mold toxicity, and other complex chronic illnesses.

There are many potential causes and manifestations of SIBO, which is why I recommend working with a healthcare professional to treat and diagnose it. Some root causes may include food poisoning, medications (like antibiotics), an underlying chronic illness, or abdominal surgery. But I’ll share more about that later.

SIBO occurs when the careful balance of healthy bacteria in your small intestine is disturbed. Bad bacteria take over, causing malabsorption and symptoms like gas, cramping, constipation, bloating, and chronic diarrhea.

If you suffer from a complex chronic illness and suspect SIBO is behind your GI symptoms, I’m here to help with diagnosis and the treatment plan that’s helped my patients heal their gut.


Table of Contents:

  • What Is Small Intestinal Bacterial Overgrowth (SIBO)?
  • How Does SIBO Develop?
  • Types of SIBO
  • Symptoms of SIBO
  • Complex Chronic Illnesses Associated with SIBO
  • How Do You Test for and Diagnose SIBO?
  • Other Complications Associated with SIBO
  • Strategies to Help You Heal from SIBO
  • The Bottom Line


What Is Small Intestinal Bacterial Overgrowth (SIBO)?

Small intestinal bacterial overgrowth (SIBO) is characterized by excessive bacteria in the small intestine.

A healthy gut requires some bacteria species throughout the gut (aka, probiotics), but too much of the wrong bacteria can throw off your gut and cause uncomfortable GI symptoms. Patients with SIBO typically experience issues like diarrhea, constipation, gas, bloating, nausea and malabsorption. Since there is an abundance of mast cells in the intestines, including the small bowel, SIBO can be a significant trigger and driver of MCAS.


How Does SIBO Develop?

Often, SIBO is the result of a sluggish digestive tract (slow gut motility). When food and waste get stuck or stay too long in the small intestine, it creates a breeding ground for unhelpful bacteria. Other common causes include things like:

  • Low stomach acid, particularly from medications like proton pump inhibitors
  • Antibiotic use
  • A history of abdominal surgery, especially gastric bypass
  • A dysfunctional immune system.

SIBO may also occur after a significant disruption to the GI system, such as food poisoning. Some people can point to a short-term gastrological illness where their gut was “never quite the same” after they recovered, eventually leading to full-blown SIBO.


Types of SIBO

The bad bacteria that’s found its home in your small intestine produces a type of gas. This gas determines which type of SIBO you may have — and helps your doctor determine the proper treatment.

Type of SIBOTypical SymptomsTreatment
Methane-Dominant SIBO (now known as Intestinal Methanogen Overgrowth (IMO)Bloating, gas, constipation, heartburn/acid reflux, malabsorption.Antibiotics, biocidin, low FODMAP diet, root cause treatment for chronic illness.
Hydrogen-DominantBloating, gas, diarrhea, malabsorption, and dehydration.Antibiotics, probiotics, low FODMAP diet, root cause treatment for chronic illness.
Hydrogen Sulfide SIBODiarrhea, abdominal cramping, malabsorption, nausea, bloating. (Often mistaken for hydrogen-dominant SIBO)Low sulfur diet, low FODMAP diet, antibiotics, root cause treatment for chronic illness.


Hydrogen-Dominant SIBO

Good news — this is the most common type of SIBO, and it’s typically easier to treat. Antibiotics may be first line defense along with other interventions like dietary changes.

With hydrogen-dominant SIBO, you may experience fast-moving stools. The root cause of this could be a variety of things like:

  • Increased bile salts
  • Fermented carbohydrates in the gut
  • Damaged gut mucosa.

As a result of these issues, diarrhea and malabsorption are commonly experienced by patients with hydrogen-dominant SIBO.


Methane-Dominant SIBO

Many practitioners find that methane-dominant SIBO or Intestinal Methanogen Overgrowth (IMO), is harder to treat for several reasons, so it may need more aggressive treatment. Several antibiotics may be recommended along with probiotics, herbal antibiotics like biocidin,* and motility agents.

Generally speaking, methane-dominant SIBO includes symptoms of constipation, bloating, gas, and sometimes heartburn, but these symptoms may overlap with other forms of SIBO as well. While hydrogen-dominant and hydrogen sulfide SIBO are typically associated with too-fast motility, methane-dominant SIBO often (but not always) has the opposite problem: too-slow motility, aka chronic constipation.


Hydrogen Sulfide SIBO

We are still learning about hydrogen sulfide SIBO since it was discovered only recently. However, diagnosis and treatment for hydrogen sulfide SIBO are similar to the other types. The only different recommendation may be the use of a low-sulfur diet in select cases.

*Important note: For patients with biotoxin illness (mold, Lyme, etc.), biocidin should be used with care. It can cause a Herxheimer reaction and begin the die-off process before the body is ready. This reaction results in flu-like symptoms that can last from hours to days.


Symptoms of SIBO

Not sure if you have SIBO? If you suffer from any kind of unexplainable digestive distress, it’s worth checking into. Here are common symptoms I see in patients with SIBO:

  • Constipation
  • Bloating
  • Food allergies or intolerances
  • Vitamin deficiencies (from malabsorption)
  • Abdominal pain
  • Brain fog
  • Confusion/memory lapses
  • Frequent nausea
  • Fatigue
  • Diarrhea
  • Heartburn
  • Abdominal cramping
  • Dehydration


Complex Chronic Illnesses Associated with SIBO

Your body is brilliant — it doesn’t fall apart for no reason. I find that there’s usually a root cause behind SIBO beyond less-than-ideal diet and lifestyle choices (although that doesn’t typically help either).

For example, chronic stress from illness wears away at the healthy bacteria in your gut, leading to a microbiome imbalance. SIBO can also result from poor diet along with environmental factors like chronic infections and mold/toxin exposure.

If you suffer from any of these illnesses, you may be more at risk for developing SIBO:

  • Mast cell activation syndrome (MCAS)
  • Dysautonomia
  • Tick-borne infections
  • Mold toxicity.


How Do You Test for and Diagnose SIBO?

The Breath Test

This is a simple test that can be done at home. It gives a great baseline diagnosis for SIBO, although it can produce false negatives occasionally. However, a skilled clinician will also take your symptoms and medical history into account to make an accurate SIBO diagnosis.

Breath tests usually measure hydrogen and methane gas. However, there is a new test that can not only measure those two but can also measure hydrogen sulfide, which is steadily gaining recognition in the medical community as an important form of SIBO.

The test is done on a fasted (empty) stomach in the morning. You will be instructed to ingest a type of sugar, either lactulose or glucose, and you will then breathe into a tube to capture the gas. Collections are best done over three hours for more accurate results, but some tests are designed for only two hours, which isn’t always enough time to detect the gasses.

These tests can be obtained from medical practitioners who routinely test for SIBO. Make sure to ask your practitioner about the test they recommend and how long the collection period lasts to get your best results.


Other Complications Associated with SIBO

Decreased Bile Acid Secretion and Gallbladder Dysfunction

Have an overburdened liver? Liver and gallbladder issues are common for people with immune system dysfunction. When the liver is overtaxed with pathogens, biotoxins, or chemicals, its detoxification power gets backed up and can reduce bile secretion.

Bile secretion is extremely important for optimal digestion. It also acts as an antimicrobial substance for bad bacteria in the gut — particularly, the small intestine.

Low bile secretion can often be one of the leading causes of SIBO, especially in MCAS patients and those with other gut-related diseases.


Small Intestinal Fungal Overgrowth (SIFO)

The symptoms of Small Intestinal Fungal Overgrowth (SIFO) are similar to those of SIBO. This is why it’s so important to run the right tests and work with a knowledgeable practitioner. SIFO is an overgrowth of a variety of fungal organisms, and can be caused by antibiotic use, steroids, other immunosuppressants, and even mold toxicity.


Difficulties with Nutrient Absorption

Patients with chronic SIBO often suffer from malabsorption — due to diarrhea, decreased ability to digest fats, and other complications, including eating less because of their symptoms.

When a patient comes to me with SIBO, I always test for nutrient deficiencies, too. The most common deficiency I see is Vitamin B12 deficiency, because B12 is absorbed in the small intestines and the bad bacteria interfere with this process. In addition, some fat-soluble vitamins (A, D and E) are also commonly low.

These deficiencies are often at the root cause of unexplained symptoms, and it’s important to get patients feeling back to normal with much-needed vitamins and minerals.


Strategies to Help You Heal from SIBO

If you think you may be struggling with SIBO, there is hope. With the right treatment, your gut will be able to rebalance and handle food again without pain or discomfort — but it does take time. Here are some strategies I use to help my clients recover from SIBO.


The Low FODMAP Diet

The low FODMAP diet eliminates fermentable short-chain carbohydrates to ease digestive discomfort and give the microbiome time to recover. Think of it as removing irritants from the gut lining. The low FODMAP diet has also been shown to lead to improvements in the microbiome, which in turn can improve the health of the GI tract, reduce inflammation, control the activation of mast cells, and decrease histamine. All good things!

The low FODMAP diet, however, may not be right for everyone, especially those with intestinal methanogen overgrowth. According to recent research, a low FODMAP diet does not seem to reduce methane or methanogens but can reduce hydrogen.

The diet should be used on a case-by-case basis and may be combined with other elimination diets, like the low histamine or low salicylate diets. In general, eliminating sugar is probably most important and is my recommendation across the board with all conditions that I treat.



Give your microbiome the boost it needs to heal from SIBO. Probiotics can help to increase good bacteria in the gut — and chase out the bad bacteria.

I usually recommend a variety of different types of probiotics in the treatment of SIBO. One example is a probiotic blend with both lactobacillus and bifidobacteria combined with a spore probiotic. Sometimes the addition of Saccharomyces boulardii can also be helpful, especially if SIFO is present.

If probiotics are not tolerated well initially, antibiotic or antimicrobial treatment might be needed first before trying to recolonize the microbiome.



The right dose and type of antibiotics can help remove the bad bacteria from your small intestine. In general, antibiotics seem to be most helpful for hydrogen-dominant SIBO.

When using antibiotics to treat SIBO, just ensure that you also take probiotics to protect against candida overgrowth and other opportunistic pathogens. Antibiotics should be used with caution (due to microbiome disruption), in addition to herbal remedies and a healthy diet for optimal results.


Herbal Antimicrobials

There are a variety of herbs and herbal blends that can be used to treat SIBO and SIFO. The protocol should be individualized but some examples of herbs I use include: Berberine, Black Cumin Seed Oil, Artemisia, Oregano Blend, Neem, and Biocidin.

Herbs should be taken under the guidance of a healthcare provider who can help you evaluate your symptoms and determine which treatment is best for you.


Improve Motility

Some patients treated for SIBO will find that their motility improves with the above interventions. However, some patients will require specific prokinetic treatment due to persistent constipation or inability to clear SIBO, with pharmacological, nutraceutical or lifestyle change.

In general, movement of the body, such as exercise or walking, will encourage movement of food and waste through the intestinal tract. There are also specific medications like prucalopride (brand name Motegrity) that act to stimulate gut motility. There are also herbal products that are somewhat weaker in action but still have some prokinetic activity like digestive bitters and aloe.


The Bottom Line on SIBO

For patients with complex chronic illnesses, SIBO can be difficult to treat — but it’s not impossible. I believe in a multi-pronged approach to treating SIBO including:

  • Diet
  • Stress reduction
  • Antimicrobial herbs and/or antibiotics
  • Probiotics
  • Stabilizing mast cells
  • Continuing to look for the root cause.

That’s why it’s best to work with your practitioner to help find the right path for you and treat the root cause of SIBO.

It’s all about taking the next right step for your health — you can do this!

Book a Consultation at the AIM Center



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