Diagnosing and Treating Small Intestinal Bacterial Overgrowth (SIBO)

SIBO Treatment

Indigestion, heartburn, abdominal pain or discomfort, bloating, gas, cramps, diarrhea, constipation — these are all familiar symptoms of gastrointestinal (GI) dysfunction. Less familiar symptoms are food allergies and sensitivities, fatigue, brain fog, and a variety of autoimmune and inflammatory conditions. What most people don’t realize is that about 70 percent of the body’s immune system resides in the gut. When the gut malfunctions, the immune system can go haywire, attacking the body it’s supposed to protect.

Conventional GI treatments typically involve medications to reduce stomach acid and alleviate cramps, diarrhea, or constipation — all of which ignore the root cause and can make the problem worse. Sometimes, the problem isn’t so much with the body’s GI tract as with what’s living inside it. Specifically, we’re talking about the trillions of microorganisms living in the small intestine.


The small intestine is a narrow tube-like organ that’s approximately 20 feet long. It connects the stomach to the large intestine and is responsible for extracting most nutrients from food. The large intestine is a much wider and shorter tube-like organ that primarily absorbs water from undigested food and carries solid waste out of the body.

Bacteria, fungi, and other microorganisms (both beneficial and potentially harmful) naturally reside in the small and large intestines. Breaking down food and producing nutrients that the body cannot obtain from food alone is the job of beneficial microorganisms.

However, when certain microorganisms multiply too fast, they can cause a condition called small intestinal bacterial overgrowth (SIBO) or small intestinal fungal overgrowth (SIFO) — both of which describe a microbial imbalance in the gut (commonly referred to as dysbiosis).

SIBO Graphic

Left untreated, gut dysbiosis can lead to unplanned weight loss, nutritional deficiencies, and even bone loss. It can also damage the lining of the small intestine, which can cause increased intestinal permeability (often referred to as leaky gut) — a condition in which large protein molecules pass through the small intestine into the bloodstream, triggering immune reactions that can result in allergies or sensitivities, chronic inflammation, and autoimmune diseases.

Common Causes of SIBO and SIFO

Common causes and contributing factors that lead to SIBO or SIFO include the following:

  • A diet low in fiber. Fiber improves motility (the movement of contents through the digestive tract) and acts as fertilizer for beneficial bacteria.
  • Anti-spasm medications, such as those used to treat irritable bowel syndrome (IBS), which also slow the movement of food and waste through the GI tract.
  • Diverticulosis — tiny bulging pouches (diverticula) in the small intestine.
  • Emotional stress impacts serotonin levels in the gut thus altering gut motility.
  • Excessive sugar, alcohol, or simple carbohydrates (sweet or starchy foods), which feed bacteria and fungi.
  • Frequent use of antibiotics, which can alter the balance of bacteria in the small intestine.
  • Gastroparesis — a condition that affects the stomach muscles or nerves, inhibiting proper muscle function. This can result in the inadequate grinding of food and the impaired emptying of the stomach contents into the small intestine.
  • Low stomach acid from long-term use of proton pump inhibitors (PPIs, medications used to reduce stomach acid) or from hypochlorhydria — a condition in which the stomach doesn’t produce enough acid. Stomach acid helps break down food, thus preventing it from putrefying in the gut, and it kills potentially harmful bacteria and fungi.
  • Narcotic medications, weaken the muscle contractions that move food through the digestive system.
  • Surgery that has changed the small intestine’s structure, such as gastric bypass surgery.
  • Traumatic brain injury (TBI), can affect the function of the GI tract. One of many effects is that a TBI may damage the vagus nerve’s ability to regulate the parasympathetic nervous system, which ultimately is associated with the microbiome and the communication highway between our brain and gut. For more on this, please read Using Brain Science to Accelerate Healing and Restoring Health Through the Vagus Nerve.

Diagnosing SIBO and SIFO

At Restoration Healthcare, SIBO is diagnosed through the use of a non-invasive hydrogen, methane, and hydrogen sulfide breath test we use called the Trio-Smart Breath Test, which you can take at home and mail to a lab. During the test, you drink a small amount of test sugar and then blow air into nine separate collection bags at regular intervals. Test results indicate whether you have SIBO; intestinal methanogenic overgrowth (IMO), which is associated with constipation; or excess hydrogen sulfide, which is associated with diarrhea.

SIFO, typically an overgrowth of candida yeast (a type of fungi), is more difficult to diagnose. Tests for SIFO include the Comprehensive Organic Acids Test, the GI-MAP, a comprehensive three-day stool analysis, and the Vibrant Wellness’ Wheat Zoomer test. In addition, certain symptoms seem to be more closely associated with SIFO than SIBO, such as the following:

  • Bloating
  • Belching
  • Constipation
  • Gas
  • Distention
  • Fatigue
  • Migraines

Treating SIBO and SIFO

Treatment for SIBO and SIFO focuses on restoring a healthy gut microbiome — the community of microorganisms living in the gut. Effective treatment involves the following:

  • Dietary changes to reduce or eliminate foods that fuel the overgrowth of harmful bacteria and fungi
  • Supplementation with hydrochloric acid and digestive enzymes to improve digestion
  • Antibiotics, antifungals, or both prescriptions and herbal supplements
  • Probiotics — beneficial bacteria
  • Prebiotics — specialized plant fibers that stimulate the growth of beneficial bacteria in the gut
  • Supplements that support the body’s ability to repair the lining of the small intestine
  • Increasing physical activity, when necessary, to increase motility

One diet in particular is commonly used to combat dysbiosis — the FODMAP diet. FODMAPs are foods containing hard-to-digest carbohydrates and sugar alcohols. (FODMAP stands for Fermentable Oligo-, Di-, Mono-saccharides, And Polyols.) The low FODMAP diet is typically used to treat irritable bowel syndrome (IBS) and other functional gastrointestinal disorders (FGIDs). Its effectiveness in treating these conditions is likely due to the fact that it starves harmful bacteria and fungi — withholding the foods that fuel their growth.

Another diet perhaps even more effective in starving harmful bacteria and fungi is the keto diet, which is high in healthy fats and proteins and extremely low in carbohydrates.

However, both diets can be too restrictive, leading to nutritional deficiencies and causing patients to abandon the diet altogether. Often, the better approach is to identify problem foods, which vary from patient to patient. The most common problem foods and substances for people with SIBO include the following:

  • Dairy
  • Garlic
  • Gluten
  • Onions

Fungi, such as candida yeast, prefer sweets. People with SIFO are advised to avoid the following foods and substances:

  • Sugar and most sugar substitutes
  • Glutenous grains, including wheat
  • High-sugar fruits and fruit juices
  • Processed meats
  • Most dairy products
  • Alcohol

Since every patient is different, we work closely with you to identify your problem foods and make targeted dietary modifications, so your diet is nutrient-rich and easier to stick to.

Following the 5R Framework

Our treatment protocol for SIBO and SIFO follows the 5R Framework:

  • Remove: Eliminate the foods that are fueling the overgrowth.
  • Replace: Supplement with acid and enzymes to enhance digestion.
  • Re-inoculate: Supplement with probiotics and prebiotics to restore a healthy balance of microorganisms in the gut.
  • Repair: Supplement with bone broth, collagen powder, L-glutamine, and so on to repair damage to the gut lining.
  • Rebalance: Make lifestyle changes to reduce stress and enjoy life more fully.

Take Control of Your SIBO or SIFO

If you’re experiencing gastrointestinal distress or have any chronic conditions that aren’t responding to conventional treatments, we urge you to consult with a functional medicine practitioner to test for SIBO or SIFO, to either confirm or rule out these conditions. Until you do, you won’t know whether either condition is the root cause of your symptoms. Tests will also show whether treatments currently being tried are providing only temporary relief, or even worsening your condition.

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Disclaimer: The information in this blog post about Small Intestinal Bacterial Overgrowth (SIBO) is provided for general informational purposes only and may not reflect current medical thinking or practices. No information contained in this post should be construed as medical advice from the medical staff at Restoration Healthcare, Inc., nor is this post intended to be a substitute for medical counsel on any subject matter. No reader of this post should act or refrain from acting on the basis of any information included in, or accessible through, this post without seeking the appropriate medical advice on the particular facts and circumstances at issue from a licensed medical professional in the recipient’s state, country or other appropriate licensing jurisdiction.