A Functional Medicine Approach To SIBO

Dr. Shawn Greenan, DACM, CFMP®
A Functional Medicine Approach To SIBO

Small intestinal bacterial overgrowth (SIBO) is a debilitating condition that affects millions of people worldwide.

SIBO is commonly overlooked in the allopathic medical world but can affect up to 80% of patients with IBS.  

Over time SIBO can lead to chronic inflammation & immune conditions and could be putting you at risk for other ailments, including poor absorption of food and nutrients.  

What Causes SIBO

In order to maintain healthy gut bacteria, you must have proper stomach acid and normal bowel motility. Anything that affects these two components of digestion can allow harmful bacteria to overgrow.

Most gut bacteria live in the large intestine, the end of your digestive tract. But, in the case of SIBO, there is an overgrowth of bacteria in the small intestine

Gut bacteria are vital to our health, but they cause problems if they aren’t where they are supposed to be. Unlike your large intestine, your small intestine normally has relatively few bacteria due to the rapid flow of contents and the presence of bile. But if the small intestine’s function has slowed, it causes an ideal breeding ground for the overgrowth of bacteria.

Common Causes of SIBO

  • Low stomach acid
  • Acid reducing Medications (PPIs, Tums, Pepcid, Prilosec, immunosuppressants)
  • Gastroparesis
  • Celiac Disease
  • Chronic Constipation
  • Slow digestion/motility
  • Surgery (scar tissue: C section, endometriosis, hysterectomy, tummy tuck)
  • Hypothyroid (low thyroid hormone)
  • Stress (high cortisol)
  • A diet high in sugar, processed carbs, and alcohol
  • Infection (h. Pylori, e. Coli, klebsiella)
  • Food poisoning (most likely with IBS-D/SIBO-D)
  • Structural (ileocecal valve disorder, bariatric)

SIBO Signs and Symptoms

  • Bloating worse at the end of the day
  • Constant Burping
  • Patient feels better on Low FODMAP diet
  • Patients’ symptoms get better after antibiotic treatment
  • Feel worse after taking probiotics
  • An uncomfortable feeling of fullness or gas immediately after eating
  • Loose stools

Complications of SIBO

Small intestinal bacterial overgrowth (SIBO) can cause systemic problems, including:

  • Poor absorption of fats, carbohydrates, and proteins. Your small intestine is responsible for helping break down foods, and the overgrowth of bacteria can hinder this process, causing malabsorption, loose stools, gas, and bloat.
  • Vitamin deficiency. You need a healthy small intestine lining to absorb nutrients.
  • Weakened bones (osteoporosis). Over time nutrient depletion, including calcium depletion, can lead to bone diseases, such as osteoporosis.
  • Kidney stones. Poor calcium absorption can eventually result in kidney stones.

Functional Medicine Testing for SIBO

A SIBO breath test is the most common test for diagnosing SIBO. This is a non-invasive at-home test that evaluates bacterial overgrowth of the small intestine.

Patients begin by breathing into a tube after fasting overnight to get a base read. They then drink a specialized mixture to see if the bacteria in the small intestine releases hydrogen, methane, or a combo of both. After drinking, patients are asked to do a breath sample over a 3-hour time frame at 20 minutes, 40 minutes, 60 minutes, 90 minutes, 120 minutes, 150 minutes, and 180 minutes.

SIBO Test Results

Your patient will be positive for SIBO if the breath test shows one of the following:

  • Their hydrogen levels increase 20ppm during the 3 hours from the original starting point.
  • Their Methane levels increase 12 ppm during the 3 hours from the original starting point.
  • Combined (hydrogen + methane) increase 15 ppm during the 3 hours from the original starting point

Sample Report of Positive Hydrogen Dominant SIBO Report

As you can see patient went from baseline of approximately 10 ppm to 60 ppm at the 90 min sample and continued to increase. This is over the increase of 20 ppm during the 3 hour test. Patient is therefore hydrogen dominant SIBO.

Functional Medicine Treatment of SIBO

Clinical management of SIBO involves nutritional therapy, antimicrobial therapy, motility supplements, and preventative measures to prevent reoccurrence.

For nutritional therapy, most practitioners will recommend a Low FODMAP or Elemental Diet to decrease the overgrowth of bacteria.


The low FODMAP diet is a very restrictive temporary eating plan. FODMAP stands for Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols, which are short-chain carbohydrates that ferment in the small intestine and can feed the overgrown bacteria. Following a low FODMAP diet has been shown to decrease abnormally high levels of intestinal bacteria.

Low FODMAP is a three-step elimination diet:

  • First, eliminate high FODMAP foods.
  • Slowly reintroduce FODMAPs after 4 to 6 weeks to see which foods cause pain, gas, or bloat.
  • Once you identify the foods that cause symptoms, you can avoid or limit them while going back to enjoying the others.

Elemental Diet

Another option functional medicine practitioners like to use to kill off overgrown bacteria quickly is the elemental diet. The elemental diet has a very high success rate and only takes two weeks.

The elemental diet is much stricter than low fodmap and requires patients to drink the elemental nutrient drink in place of all meals for 2-3 weeks. This diet works by starving bacteria. Herbal antimicrobial treatment is not needed if patients are prescribed the elemental diet.

Herbal Antimicrobials

Functional Medicine Practitioners will commonly use herbal antimicrobials (antibiotics) alongside a low FODMAP diet for 4-6 weeks. Patients should be warned that they will have bacteria and possible candida die off (if present) and may feel worse before feeling better up to 3-4 weeks during treatment.

Treating SIBO with herbal antimicrobials depends on if the patient is Methane or Hydrogen dominant. The most common herbs used are allicin and berberine.

  • Methane Dominant SIBO: Allicin
  • Hydrogen Dominant SIBO: Berberine
  • Methane & Hydrogen Dominant SIBO: Allicin + Berberine


It’s vital to assess what caused the SIBO in the first place to prevent future relapse.

Patients will need to be on a prokinetic (supplement to help motility) for at least 90 days after treatment. Remember, slow motility allows bacteria to stay in the small intestine for too long.

I also recommend prescribing digestive enzymes as well as testing for hypochloridria (low stomach acid). If patient has low stomach acid, increasing acid levels is essential.


SIBO is commonly overlooked in the medical world but can affect up to 80% of patients with IBS. An easy at-home test can give your patients a definitive diagnosis, and the proper treatment protocols can provide your patients better overall health and outlook on life.

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Dr. Shawn Greenan, DACM, CFMP®
Acupuncture Physician Certified Functional Medicine Practitioner®
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