Small Intestinal Bacterial Overgrowth


SMall Intestinal Fungal Overgrowth

"60-80% of all Irritable Bowel Syndrome (IBS) is actually SIBO."

But what is IBS?

IBS aka Irritable Bowel Syndrome

About IBS:

  • IBS is a gastrointestinal syndrome characterized by chronic abdominal pain and altered bowel habits in the absence of any organic cause. 

  • Affects about 10-15% of the population in North America

  • IBS is a diagnosis or exclusion which is why it roughly accounts for $30 billion in health care dollars each year.

  • IBS is a syndrome and not a disease.


What is SIBO?

Small intestine bacterial overgrowth is a condition where bacteria which are normally found lower in the large intestine have overgrown in the small intestine instead.

What is SIFO?

Small intestinal fungal overgrowth is a condition where candida or yeast have taken over the intestines, often as a result of inadequate good bacteria. This state may be a result of poor dietary choices leading to poor good bacteria and immune compromise. 

What is wrong with having these "bad" bugs in our gut?

They damage the microvilli 

Cause malabsorption of nutrients

create leaky gut 

create inflammation 

create symptoms 

Causes of SIBO and or SIFO:​

  1. Pre-disposing conditions: 

    • Chronic pancreatitis (SIBO in up to 40%)

    • Immunodeficiency (IgA deficiency, AIDS)

    • Autoimmune conditions (damage the nerves in the gut, reducing motility, causing bacterial overgrowth).

    • Low stomach acid (SIBO increased w/ long term PPI use)

    • Liver cirrhosis

    • Scleroderma

    • Diabetes Melitus

    • Motility Disorders/ Slow bowels

    • Stress reduces the migrating motor complex, reducing motility.

    • Joint hypermobiliy syndromes (Ehlers Danlos, Marfans)

    • Medication use such as: Opioids, Chronic antibiotic use, Acid blocking medications, Long term corticosteroid use, Anti-diarrheals.

    • Food poisoning (from bacterial pathogens such as Campylobacter jejuni, Shigella, E.coli, and Salmonella)

    • Anatomical/Structural abnormalities (obstructions, diverticula, fistulae, removal of galbladder (cholecystectomy), gastric bypass, removal of ileocecal valve or Ileocecal valve dysfunction, intrabdominal adhesions, blind loops).

    • Elderly 17, 18 (present in up to 90% of 70-94 yo)

  2. Conditions associated with SIBO

  • Diabetes (gastroparesis)

  • Parkinson's Disease (54% have SIBO15)

  • Osteoporosis

  • Anemia

  • Celiac disease

  • Irritable Bowel Disease: (Crohn’s disease and Ulcerative Colitis)

  • Chronic Liver disease

  • Fibromyalgia

  • Rosacea

  • Cystic fibrosis

​Signs and symptoms of SIBO and or SIFO:

  1. Any disease state arising from nutrient deficiencies.

    • Neuropathy from B-12 deficiency,

    • Anemia from B-12, folate or iron deficiency

  2. Gas, flatulence, bloating, belching, indigestions, heartburn, central abdominal pain, loose and frequent bowel movements. Less commonly, constipation.

    • Symptoms are worse with: garlic, dairy, apples, raw veggies, onion, mushrooms.​


  • Anti Vinculin and Anti CDT B Antibody Test (IBS Blood Test)

    • The IBS Blood test measures antibodies against the bacterial toxin Cytolethal Distending Toxin B (CdtB) and the small intestine nerve protein Vincu lin.  If the test is positive, it means that there is a motility issue originating in the nervous system of the intestines and rules out inflammatory bowel disease with 98% probability. Whether test is negative or positive, a breath test is warranted. The breath test diagnoses SIBO from all causes, whereas the IBS blood test only detects SIBO from food poisoning etiology, and doing the breath test in this instance helps us determine best treatment strategy.

  • SIBO Breath test for Hydrogen and Methane Gas

    • Breath testing measures the hydrogen (H) & methane (M) gas produced by bacteria in the SI that has diffused into the blood, then lungs, for expiration.  H & M are gases produced by bacteria, not by humans.  The gas is graphed over 2 or 3 hours & compared to baseline.  Patients drink a sugar solution of glucose or lactulose after a 1 or 2 day preparatory diet.  The prep diet removes much of the food that would feed the bacteria, allowing for a clear reaction to the sugar drink. 

    • Two types of tests may be used: Lactulose or Glucose. A 3 hour Lactulose is a superior test.

    • In the first 3 feet of small bowel, with glucose you can definitely tell if there is bacterial overgrowth. With lactulose which doesn’t get absorbed, it may get to the colon too fast.  Use correct dose of lactulose 10g

  • H pylori breath test 

    • A great adjunct to rule out H pylori related causes​.

How Can We Improve SIBO/ SIFO​?

  1. Kill off the bad bacteria in the intestines

  2. Improve motility

  3. Repopulate the microbiome 

  4. Improve integrity of the membrane of the intestines

  5. Ensure that deficiencies are accounted for (enzymes and nutrients)

Antibiotic versus Herbal Protocols

  • Antibiotics and herbal protocols were both equally effective but both have about a 50% efficacy. Their relapse rates are also equal. However, antimicrobial therapy can cost around $1000 and I have only seen this amount be covered by some US health insurance coverages. This is why we start with the herbal protocol in conjunction with the low FODMAP Diet.

Why the Low FODMAP Diet is not enough as a stand alone treatment:

The diet is a great way to starve the bacteria that are producing the unwanted gase(s). It can even relieve discomfort, but as soon as you start to challenge the diet and eat soluble fibers, you will experience symptoms all over again. The antimicrobials help keep the bad bacteria at bay while you train and select the good bacteria to stay and crowd out the bad bacteria by reintroducing fiber slowly. 

It is also not a sustainable diet and can only be done for a short period of time as it is restrictive and can result in weight loss, and most patients with SIBO are having trouble gaining weight.

SIBO Breath Test

How to do the Test & Reading the Test

How to do the SIBO Breath Test:

Preparation phase:

  • 2-4 weeks before test:

  • Wait 4 weeks from your last dose of antibiotics, colonoscopy or barium enema.

  • Wait at least 2-4 weeks from your last dose of antifungals, Pepto-Bismol TM or herbal/ natural antimicrobials

  • 7 days before the test:

  • Avoid the use of laxatives, stool softeners, and or stool bulking agents as well as antacids containing aluminum or magnesium hydroxide. (Magnesium citrate etc is fine)

  • 24 hours before the test:

  • The purpose of the prep diet is to get a clear reaction to the test solution by reducing fermentable foods the day before. In some cases, two days of prep diet may be needed to reduce baseline gases to negative.

  • Foods you can eat before you start your 12 hour fast:

    • Baked or broiled chicken, fish, turkey (salt and pepper only), white bread (only), plain steamed white rice, eggs, clear chicken or beef broth (not bone broth or bouillon) with no vegetable pieces, water, plain coffee, tea, no sugar/ artificial sweeteners or cream, oil, salt, and pepper.

    • Vegetarians may have tofu with salt and pepper.

    • Do not take probiotics.

  • 12 hours before the test

  • Don’t eat or drink anything other than water for 12 hours prior and during the test.

  • Do not take non essential medications or supplements during the test.

  • Do not chew gum, eat candy or use mouthwash until the test is complete.

  • 1 hour before the test:

  • No smoking (includes second hand smoking), for at least 1 hour before or at any time during breath test.

  • No sleeping or vigorous exercise for at least 1 hour before or at any time during the breath test.

  • Doing the test

  • Do not use toothpaste.

  • Brush teeth and tongue without toothpaste. Rinse with water.

  • Write your full name, DOB, Gender, DOC, and tube number 1-6/8.

  • Take your first tube collection. Record collection time.

  • 1 breath before lactulose; exhale normally until tube fills with condensation. Tip, exhale slightly before you start to fully exhale and bring the apparatus to your mouth.

  • Stir lactulose solution into 8 oz water and drink entire amount within 5 minutes. Do not drink water for the following one hour.

  • Do another breath test in 20 minutes and every 20 minutes after that, until 6-8 tubes are used.

The classic positive for SIBO has been considered to be a double peak, with the first peak representing the SIBO and the second peak representing the normal large intestine bacteria. This is an infrequent presentation in our experience. More frequently we see one peak that rises highest in the third hour, representing distal SIBO and then the normal large intestinal (LI) bacteria.

Reading your SIBO Breath Test:

Hydrogen (H), Methane (M), Hydrogen Sulfide (HS)


What we are looking for:

If H <20 ppm= neg, H >40 ppm= definite pos for Hydrogen

If M <3 ppm=neg, M >12 ppm= definite pos for Methane

H and M should increase quiet rapidly after drinking the drink in the first 100-120 minutes.

A flatline test: possibly HS positive bacteria.