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Demystifying SIBO for Functional Medicine Practitioners

Digestive and gut issues are common symptoms patients seek guidance for in the U.S., but what's at the root of gastrointestinal distress? 

Though SIBO is underdiagnosed, some research estimates that up to 80% of those diagnosed with irritable bowel syndrome (IBS) also have SIBO. 

SIBO, or Small Intestinal Bacterial Overgrowth, is a condition characterized by the overgrowth of bacteria that normally live in the large intestine and colonize in the small intestine.  

Dysbiosis is problematic because harmful bacteria can replace the bacteria we need and cause a slew of digestive issues to develop. Treatment should include a protocol to reduce the overgrowth of bacteria, treat the underlying cause, and restore proper bacterial balance. 

In this guide, we’ll explore what SIBO is, what causes it, and how functional medicine providers can effectively diagnose and treat this condition.  

What Causes Excessive Bacteria Growth?

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SIBO occurs when the factors responsible for maintaining bacterial balance in the gut begin to malfunction. Normally, peristalsis and sphincter function are responsible for moving ingested foods and bacteria from the upper digestive tract into the large intestine. If this process fails, the excess food particles create a breeding ground for bacteria, which will then overgrow in the small intestine.  

A consequence of SIBO is nutrient malabsorption. Due to malabsorption, individuals with SIBO often develop micronutrient deficiencies even when eating a balanced, nutritionally dense diet. 

Additionally, SIBO damages the intestinal lining and creates a state of mild to severe intestinal permeability or leaky gut, which can result in food allergies, food sensitivities, and chronic inflammation. 

Symptoms of Chronic Lyme Disease (2)Recognizing SIBO

The symptoms of SIBO are primarily gastrointestinal and include:

  • Abdominal pain
  • Nausea
  • Bloating
  • Indigestion
  • Gas  
  • Diarrhea
  • Constipation
  • Fatigue  
  • Weight loss 

It's essential to identify SIBO early to address bacterial overgrowth and dysbiosis to prevent further damage to the gut and disease development. SIBO is associated with various diseases, including diabetes, lupus, celiac disease, inflammatory bowel disease (IBD), and irritable bowel syndrome (IBS), among others.   

While only a hydrogen breath test can definitively diagnose SIBO, the Vibrant Wellness Gut Zoomer’s commensal bacteria panel measures hundreds of species of microbes, including bacterial species associated with SIBO. 

SIBO Risk Factors  

Several factors may put patients at risk of developing SIBO, including:  

  • Intestinal obstruction or anatomical blockages 
  • Intestinal neuropathy, also known as intestinal pseudo-obstruction 
  • Poor hydrochloric acid or HCL production, also known as hypochlorhydria  
  • Insufficient pancreatic enzyme function, also known as exocrine pancreatic insufficiency (EPI) 
  • Sluggish peristalsis or dysfunction of the migrating motor complex (MMC) 
  • Diverticulitis in the small intestine, also known as small bowel diverticula  
  • Ileocecal sphincter or valve dysfunction 
  • Use of certain medications that cause intestinal dysfunction 

Classifications of SIBO  

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There are different types of SIBO depending on the stage of the condition As SIBO progresses, there is a transition from hydrogen-dominant SIBO to methane-dominant SIBO, also known as Intestinal Methanogen Overgrowth or IMO.

In this article, for simplicity, we’ll refer to these different states of SIBO as hydrogen-dominant, methane-dominant, and mixed SIBO 

Hydrogen-Dominant SIBO   


Hydrogen-dominant SIBO occurs when bacteria in the small intestine produce hydrogen gas. Diarrhea is the major symptom associated with hydrogen-dominant SIBO, and this type of SIBO is the most common. 

Methane-Dominant SIBO  


Methane-dominant SIBO has recently been renamed as Intestinal Methanogen Overgrowth (IMO). Bacteria within the gut produce hydrogen, while archaea produce methane. The archaea responsible for methane-dominant SIBO feed on hydrogen as a source of fuel. So, when referring to methane-dominant SIBO, technically, the B in SIBO, which stands for bacteria, is untrue. Additionally, the methane-producing archaea can be found in any part of the intestinal tract, which would make the SI in SIBO, referring to the small intestine, also untrue. This is why methane-dominant SIBO is now known as Intestinal Methanogen Overgrowth.  

Constipation is the most common symptom associated with Intestinal Methanogen Overgrowth. 

Mixed SIBO


Finally, patients may experience bouts of diarrhea combined with bouts of constipation when suffering from SIBO. These mixed symptoms indicate the overgrowth of both hydrogen-producing bacteria and methane-producing archaea.

Treating SIBO with Antimicrobials

The goal when treating SIBO is to eradicate excessive bacteria within the small intestine or affected area. Thus, antimicrobials are commonly used to treat the condition.  

Antimicrobial treatment varies from person to person due to different tolerance levels based on: 

  • Current state of health  
  • Specific bacterial strains that have overgrown 
  • Challenges that accompany methanogenic archaea’s resistance to antimicrobials 

Antimicrobials can be used to treat all three SIBO types.  

Herbal Antimicrobials and Botanicals 

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Herbal antimicrobials or botanicals can be used to treat SIBO. When using herbal antimicrobials, rotate which ingredients you prescribe to patients to avoid bacteria and archaea resistance.  

Herbal antimicrobials that can be used to treat SIBO include:  

  • Black cumin seed oil 
  • Caprylic acid 
  • Cat’s claw 
  • Cinnamon 
  • Clove 
  • Eucalyptus 
  • Ginger: In addition to its antimicrobial properties, ginger is great for treating SIBO because of its ability to support the Migrating Motor Complex 
  • Nanosilver 
  • Oil of oregano 
  • Oil pulling: Practice oil pulling to reduce overall microbial load on the body, especially in the mouth
  • Olive leaf 
  • Pau d’arco 
  • Peppermint oil 
  • Tannins 
  • Wormwood 

All of the above antimicrobials are also antifungals; hence, these can also be used to treat fungal overgrowths, such as candida, which can present at the same time. Abnormal fungal growth often accompanies the diagnosis of SIBO. Abnormal fungal growth is known as SIFO or Small Intestinal Fungal Overgrowth. 

You can assess the presence of candida (fungal) overgrowth with the Vibrant Wellness Candida + IBS Profile. 

Herbal antimicrobials that can be used with caution: 
  • Allicin-garlic: Garlic is effective against methane producers only. Additionally, patients with liver detoxification permutations cannot tolerate garlic  
  • Berberine: Berberine can lower blood sugar levels. Thus, patients with low blood sugar or associated conditions should avoid berberine or take it with caution 
  • Neem: Neem can dramatically lower blood sugar levels and may have contraceptive properties
Recommended Dosage for Children 

It’s important to note that children’s dosages are lower than adults' and vary by several factors, including weight, size, and tolerances. Kids tend to respond very well to natural treatments. 

Consider using Clark’s or Young’s Rule to calculate children's dosages. 

Suggested Treatment Combinations 

For hydrogen-dominant SIBO, also known as diarrhea-dominant SIBO or SIBO-D, you can recommend one of the following combinations: 

  1. Berberine, neem, and oil of oregano 
  2. Peppermint oil and other botanicals of choice

For methane-dominant SIBO, also known as constipation-dominant SIBO or SIBO-C, you can combine neem, garlic, and oil of oregano as a treatment method.  

For mixed SIBO, you can recommend one of the following combinations: 

  1. Berberine, neem, and garlic
  2. Garlic and oil of oregano 

Pharmaceutical Antimicrobials 

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Pharmaceutical antimicrobials that can be used to treat SIBO include:  

  • Rifaximin (Xifaxan): used alone to treat hydrogen SIBO 
  • Rifaximin (Xifaxan) and Aeomycin or Metronidazole: used in combination to treat methane SIBO 

Biofilm Disrupters and Biotoxin Binders: Add these to your protocol 

Bacteria and fungi form biofilms to ensure their survival, making them resistant to treatment. Therefore, biofilm disruptors should be used 15-30 minutes prior to the antimicrobial treatments. 

Copy of Provider Shoutout - Post Banner (2000 × 1000 px) (3)Biofilm disruptors include:

  • Cinnamon
  • Curcumin
  • Garlic
  • Ginger
  • Mimosa pudica
  • And N-acetyl-cysteine (NAC)

Binders should also be used to bind to the endotoxins that are released by the microbes being killed. Using biotoxin binders will help prevent a healing crisis, also known as a Herxheimer reaction.

Generally, binders are recommended 90 minutes after food, medications, antimicrobial treatments, and other supplements. As this timing can be challenging for patients, many providers will recommend their patients take binders overnight on an empty stomach, when the body repairs and releases toxins accumulated throughout the day. You can also choose to do both, as binders can be taken more than once per day.  

Copy of Provider Shoutout - Post Banner (2000 × 1000 px) (4)Biotoxin binders include:

  • Activated charcoal
  • Bentonite clay
  • Zeolite clay
  • S. boulardii
  • Humic acid
  • Fulvic acid
  • And citric acid

Treating SIBO by Stimulating the Migrating Motor Complex (MMC)  

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The migrating motor complex (MMC) is a system of electrical waves that move through the small intestine during periods of fasting.  

Defects in the MMC are thought to be a chief player in the development of SIBO. The MMC is active only in a fasted state, with the function of sweeping and removing undigested materials in the digestive tract. Defects in the MMC are thought to be a chief player in the development of SIBO. 

Strategies to support the MMC include:  

  • Pharmaceutical prokinetic drugs: to stimulate the migrating motor complex (MMC). Prokinetic means to promote movement. 
  • Low dose Erythromycin 
  • Low dose Naltrexone 
  • Over-the-counter (OTC) prokinetic supplements: to stimulate the migrating motor complex (MMC). Prokinetic means to promote movement.
  • 5HTP 
  • Ginger 
  • Stop anti-acids: acid kills bacteria and helps break down your foods that feed bacteria 
If deficient, supplement with the following at meals because normal digestion at meals is necessary: 
  • To increase stomach acid production: hydrochloric acid (HCL), bitters, and/or apple cider vinegar (ACV)  
  • Digestive enzymes: lipase, amylase, and protease 
  • Ox bile or artichoke 

Natural ways to stimulate the MMC 

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  • Acupuncture 
  • Yoga 
  • Rest 
  • Reduce stress – the “fight or flight” mode temporarily shuts off the MMC 
  • Fasting 
  • Vagal nerve exercises, such as gargling, singing, humming, chanting, yawning, stimulating the gag reflex and diaphragmatic breathing 

To assess alterations in intestinal motility, try the Vibrant Wellness Candida + IBS Profile.  

Diets to Reduce Foods That Feed the Bacteria  

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Recommended SIBO diets include:  

Low FODMAP diet: focuses on reducing or removing difficult-to-digest carbohydrates known as fermentable short-chain carbohydrates. 

Specific Carbohydrate Diet (SCD): eliminates sugars and difficult-to-digest carbohydrates such as grains and grain products. 

Gut and Psychology Syndrome Diet (GAPS): eliminates grains, pasteurized dairy, starchy vegetables, and refined carbohydrates. 

Elemental diet: involves getting total nutrition from a liquid meal replacement and breaking down foods into their most “elemental” form. Proteins, fats, and carbohydrates are broken down into amino acids, triglycerides, and maltodextrins and combined with vitamins, minerals, and electrolytes to create a liquid meal replacement.  

When developing a SIBO diet, bone broth should be avoided unless it is cartilage-free, because the cartilage tissue still attached to the bones contains glycosaminoglycans or GAGS, a substance that feeds bacteria. Collagen proteins or peptides should be avoided for the same reason. The higher up SIBO is along the intestinal tract, the more likely patients will react to GAGs.  

Regardless of SIBO type, treatment ultimately aims to kill and starve the bacteria within the small intestine or other areas to return gut microbiome balance.   

Remember that there is no one-size-fits-all approach—the protocol you prescribe is dependent on the type of SIBO, your patient’s health, lifestyle, and how your patient responds to treatment.  

Give your patients the care they deserve

Suzette Garcia, MSc: MHNE, is a Clinical Educator at Vibrant Wellness. She is a Board Certified Holistic Nutritionist® certified through the Holistic Nutrition Credentialing Board (HNCB) and a Professional Member of the National Association of Nutrition Professionals (NANP). Suzette obtained her Master of Science in Health and Nutrition Education (MHNE) from Hawthorn University and has spent her nutrition career working in the field of functional health and nutrition with a strong focus on food sensitivities, gut health, and hormones. Suzette is fluent in both English and Spanish and offers interpretation of lab test results in both languages.   

In her spare time, you can find Suzette spending most of her time on the waters of South Florida, vacationing to tropical locations, practicing and teaching yoga, working on home improvements, eating good food, and furthering her education in the field of functional health and nutrition. She is a native Floridian. 



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