SIBO: Small Intestinal Bacterial Overgrowth, Causes, and Nutritional Treatment

SIBO (small intestinal bacterial overgrowth) is a significantly underdiagnosed condition estimated to underlie the majority of IBS diagnoses. It occurs when bacteria that normally reside in the large intestine colonise the small intestine in excessive numbers, fermenting foods before they can be absorbed and producing gases that cause characteristic digestive symptoms.

What Is SIBO?

The small intestine normally contains relatively few bacteria compared to the large intestine. When bacteria overgrow in the small intestine, they ferment carbohydrates that should be absorbed further upstream, producing hydrogen, methane, or hydrogen sulphide gases. This fermentation causes the characteristic bloating, pain, and altered bowel habits of SIBO [1].

SIBO is estimated to be present in 60 to 70 percent of people with IBS [2].

Types of SIBO

• Hydrogen-dominant SIBO: fermentative bacteria producing hydrogen gas. Associated with diarrhoea-predominant IBS.

• Methane-dominant SIBO (IMO, intestinal methanogen overgrowth): archaea producing methane. Associated with constipation.

• Hydrogen sulphide SIBO: associated with "rotten egg" gas, diarrhoea, and pain.

Symptoms of SIBO

• Bloating that worsens through the day and after eating

• Abdominal pain or cramping

• Altered bowel habits (diarrhoea, constipation, or alternating)

• Excessive gas, belching, or flatulence

• Nausea

• Nutrient deficiencies despite adequate dietary intake (B12, fat-soluble vitamins, iron)

• Brain fog (bacterial metabolites affect the gut-brain axis)

• Histamine intolerance (SIBO bacteria include histamine-producing species)

Root Causes of SIBO

SIBO recurs when the root cause is not addressed. Common contributors include:

• Impaired migrating motor complex (MMC): the "housekeeping wave" of gut motility that clears bacteria between meals. Damaged by stress, infections, and certain medications.

• Low stomach acid (hypochlorhydria): acid acts as a first-line bacterial defence. PPIs and H. pylori impair this.

• Structural issues (adhesions, diverticula, slow motility)

• Chronic stress (cortisol suppresses gut motility)

• Hypothyroidism (low thyroid slows gut motility)

Treatment Approach

Testing First

SIBO is diagnosed via lactulose or glucose breath testing (hydrogen and methane). Testing confirms the type of SIBO and guides treatment selection. See functional testing for the broader clinical context.

Eradication Phase

Antimicrobial treatment options include rifaximin (pharmaceutical, most evidence-based), herbal antimicrobials (oregano oil, berberine, neem, allicin from garlic), or elemental diet. The choice depends on SIBO type, severity, and clinical presentation.

Restore Motility and Prevent Relapse

Addressing root causes: prokinetics (ginger, 5-HTP, low-dose naltrexone) support the MMC. Spacing meals 4 to 5 hours apart and avoiding grazing allows the MMC to clear bacteria between meals. Addressing intestinal permeability and restoring the large intestinal microbiome completes the protocol.

Dealing with IBS-type symptoms that won't resolve?

Book a Clinical Case Assessment with Kirstie to discuss whether SIBO testing and treatment is appropriate for you.

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References

• Quigley EM. Small intestinal bacterial overgrowth: what it is and what it is not. Current Opinion in Gastroenterology. 2014;30(2):141-146. PubMed

• Pimentel M, et al. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. American Journal of Gastroenterology. 2000;95(12):3503-3506. PubMed