What Is SIBO?

What Is SIBO? Understanding Small Intestinal Bacterial Overgrowth

If you’re experiencing chronic bloating, abdominal discomfort, or unexplained digestive issues, you may have heard of SIBO. But what exactly is this condition, and how does it affect your digestive health? This comprehensive guide will help you understand small intestinal bacterial overgrowth, its causes, testing methods, and treatment approaches.

What Is SIBO?

Small intestinal bacterial overgrowth (SIBO) is a condition characterised by an abnormal increase in the number of bacteria in the small intestine—particularly types of bacteria not commonly found in that part of the digestive tract. While bacteria are essential for digestion, they should predominantly reside in the colon (large intestine) rather than the small intestine.

In a healthy digestive system, the small intestine contains relatively few bacteria—typically fewer than 10³ organisms per milliliter. The proximal small intestine normally harbours gram-positive organisms like lactobacilli, enterococci, and facultative anaerobes. However, in SIBO, colonic bacteria such as bacteroides, clostridium, and bifidobacteria migrate to and proliferate in the small intestine, where they don’t belong.

SIBO is formally defined as a bacterial population in the small intestine exceeding 10³–10⁵ colony-forming units (CFU) per milliliter, though the exact diagnostic threshold remains debated. Recent research suggests that a threshold of greater than 10³ CFU/mL correlates well with clinical symptoms and is associated with decreased microbial diversity and gastrointestinal symptoms.

How Common Is SIBO?

The actual prevalence of SIBO varies widely depending on the population studied and diagnostic methods used. Research indicates that irritable bowel syndrome, intestinal motility disorders, and chronic pancreatitis are the most common conditions associated with SIBO, accounting for 80-90% of cases. SIBO is more prevalent in females and increases with age due to factors like reduced stomach acid production and decreased intestinal motility.

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Symptoms of SIBO

The symptoms of SIBO result from excessive bacteria in the small intestine interfering with normal digestion and nutrient absorption. Common symptoms include:

Digestive Symptoms

• Bloating and abdominal distension: Often the most prominent complaint
• Abdominal pain or discomfort
• Diarrhoea: More common with hydrogen-producing bacteria
• Constipation: More frequently associated with methane-producing organisms
• Excessive gas and flatulence
• Nausea

Systemic Symptoms

• Weight loss and malnutrition: Due to malabsorption
• Vitamin and mineral deficiencies: Particularly vitamin B12, iron, thiamine, and fat-soluble vitamins
• Steatorrhea (fatty stools): Caused by fat malabsorption
• Fatigue and weakness

The type of bacteria overgrowing can influence symptoms. Hydrogen-producing bacteria are associated with diarrhoea, while methane-producing microorganisms (now classified as intestinal methanogen overgrowth or IMO) are more closely linked to constipation.

What Causes SIBO? Risk Factors Explained

SIBO develops when the body’s protective mechanisms against bacterial overgrowth fail. Several factors normally prevent bacterial overgrowth in the small intestine, including:

• Gastric acid secretion
• Normal intestinal motility and peristalsis
• The ileocecal valve (which prevents back flow from the colon)
• Pancreatic and biliary secretions
• Secretory IgA (part of the immune system)

Major Risk Factors

1. Impaired Gastrointestinal Motility

Normal motility is perhaps the most important protective factor against SIBO. Conditions that slow intestinal transit allow bacteria to accumulate and proliferate. Motility disorders include:

• Gastroparesis: Delayed stomach emptying
• Chronic intestinal pseudo-obstruction
• Scleroderma: A connective tissue disorder affecting gut motility
• Hypothyroidism: Can slow digestive transit
• Parkinson’s disease: Affects gut motility through autonomic dysfunction
• Diabetes mellitus: Can cause autonomic neuropathy affecting the gut

2. Hypochlorhydria (Low Stomach Acid)

Gastric acid plays a crucial role in killing ingested bacteria and limiting their growth in the upper small intestine. Conditions and medications that reduce stomach acid increase SIBO risk:

• Proton pump inhibitors (PPIs): Long-term use is associated with increased SIBO risk, with studies showing 13.2% SIBO prevalence in PPI users versus 1.8% in those taking PPIs with prokinetics
• Helicobacter pylori infection
• Autoimmune gastritis
• Aging: Natural decline in acid production
• Post-gastrectomy: Surgical removal of part of the stomach

3. Structural Abnormalities

Anatomical changes can create stagnant areas where bacteria accumulate:

• Small bowel diverticulosis: Pouches in the intestinal wall
• Surgical blind loops: Created by certain types of surgery
• Strictures: Narrowing of the intestine from Crohn’s disease or radiation
• Fistulas: Abnormal connections between intestinal segments
• Loss of ileocecal valve: Following surgery
• Adhesions: Scar tissue from previous surgeries

4. Systemic Conditions

Several chronic diseases predispose to SIBO:

• Chronic pancreatitis: SIBO prevalence reaches 38.6% in these patients
• Cirrhosis of the liver: Associated with impaired motility
• Chronic renal failure: Studies show 50% have neuropathic motility disorders
• Celiac disease
• Inflammatory bowel disease (IBD): Including Crohn’s disease
• Immunodeficiency disorders

5. Medications

Beyond PPIs, other medications can increase SIBO risk:

• Opioid pain medications: Slow intestinal transit
• Anticholinergic drugs

6. Age and Gender

The incidence of SIBO increases with age due to hypochlorhydria and intestinal dysmotility. SIBO is also more prevalent in females, though the reasons remain unclear.

How Is SIBO Diagnosed? Testing Methods

Diagnosing SIBO can be challenging, and several testing methods are available, each with advantages and limitations.

Breath Testing (Most Common Method)

Breath testing has become the most widely used diagnostic approach for SIBO because it’s non-invasive, relatively inexpensive, and can be performed at home. The test measures hydrogen and methane gases produced when bacteria ferment carbohydrates.

How Breath Tests Work

Bacteria in the intestine metabolise carbohydrates, producing hydrogen and/or methane gas. These gases are absorbed into the bloodstream, travel to the lungs, and are exhaled in breath. By measuring gas levels after ingesting a test substrate, clinicians can detect bacterial overgrowth.

Types of Breath Tests

Glucose Breath Test

• Uses 75 grams of glucose as the substrate
• More specific but less sensitive than lactulose testing
• Glucose is absorbed in the proximal small intestine, so it only tests that region
• Positive result: Rise in hydrogen ≥20 parts per million (ppm) by 90 minutes
• Methane ≥10 ppm at any point indicates intestinal methanogen overgrowth (IMO)

Lactulose Breath Test

• Uses 10 grams of lactulose as the substrate
• Tests the entire small intestine as lactulose isn’t absorbed
• May be affected by orocecal transit time, leading to potential false positives
• Same diagnostic thresholds as glucose testing

Hydrogen Sulfide Testing

• Emerging diagnostic approach for hydrogen sulfide-producing bacteria – people may suspectf this is they react to sulfurous supplements such as NAC or glutathione, or if they experience eggy smelling flatuelnce.
• Can identify a subtype of SIBO associated with different symptoms

Breath Test Preparation

To ensure accurate results, patients must:

• Fast overnight (8-12 hours)
• Avoid slowly absorbed carbohydrates, fiber, and certain foods 24 hours before
• Brush teeth and rinse with antiseptic mouthwash before testing
• Avoid antibiotics for at least 4 weeks prior
• Discontinue proton pump inhibitors, prokinetics, and other relevant medications as directed by your health care profession

Interpreting Results

• Sensitivity: 20-93% for glucose test, 17-68% for lactulose test
• Specificity: 45-86% for glucose test, 44-86% for lactulose test
• Approximately 15-30% of people have gut flora that produce methane instead of hydrogen, so measuring both gases is essential

Emerging Patterns

Recent research has identified breath test patterns previously thought to be normal that may actually represent SIBO:

• Flat-line pattern: No methane and low fixed hydrogen production
• High baseline hydrogen: Baseline hydrogen >20 ppm

Jejunal Aspirate Culture (Gold Standard)

Small bowel aspirate culture is considered the most accurate diagnostic method. During an upper endoscopy, a sample of fluid is collected from the jejunum and cultured for bacteria.

• Diagnostic threshold: >10³ CFU/mL (newer recommendations) or >10⁵ CFU/mL (traditional threshold)
• Advantages: Direct measurement; can identify specific bacteria
• Disadvantages: Invasive, expensive, time-consuming, and results can be contaminated by oral flora

Additional Testing

Once SIBO is suspected, clinicians may order additional tests to:

• Identify underlying causes through imaging (CT, MRI) or endoscopy
• Assess for nutrient deficiencies (vitamin B12, iron, folate, fat-soluble vitamins)
• Evaluate for malabsorption markers – these are included in our Ultimate Gut Health Test.
• Test for structural abnormalities or motility disorders

Treatment Overview: A High-Level Approach

While comprehensive SIBO treatment deserves detailed discussion (covered in our dedicated treatment blog), here’s a high-level overview of the management approach:

1. Antibiotic Therapy

Antibiotics remain the first-line treatment for SIBO (from a conventional perspective), with the goal of reducing bacterial overgrowth rather than complete eradication.

Rifaximin is the most studied and commonly prescribed antibiotic for SIBO:

• Minimally absorbed, acting locally in the gut
• Dosage: 1650 mg/day (550 mg three times daily) for 2 weeks
• Eradication rates: 70-72% overall
• Response rates: 47.4% for hydrogen-positive SIBO, 80% for combined hydrogen and methane
• Favourable safety profile and doesn’t significantly disrupt the gut microbiome
• May actually improve beneficial bacteria populations

Other antibiotics used include:

• Neomycin: Often combined with rifaximin for methane-predominant SIBO (1000 mg/day)
• Metronidazole: 250-500 mg 2-3 times daily
• Ciprofloxacin: 250-500 mg twice daily
• Tetracycline
• Amoxicillin-clavulanate

2. Herbal Antimicrobials

Research has demonstrated that herbal protocols can be as effective as rifaximin in some cases. Common herbal antimicrobials include:

• Berberine
• Oregano oil
• Garlic extract
• Neem

A 2024 study showed that a botanical protocol resolved 100% of hydrogen sulfide SIBO cases and 66.7% of hydrogen cases.

3. Dietary Modifications

Diet plays a crucial role in managing SIBO symptoms:

• Low FODMAP diet: Reduces fermentable carbohydrates that feed bacteria
• Specific carbohydrate diet (SCD)
• Elemental diet: In severe cases, a liquid diet of pre-digested nutrients

It’s important to emphasise the word manage. Diet is about symptom management rather than actual treatment – you are not going to restrict your way out of SIBO.

4. Treating Underlying Causes

Addressing root causes is essential for preventing recurrence:

• Managing motility disorders with prokinetic agents
• Correcting structural abnormalities through surgery if necessary
• Treating chronic conditions like diabetes or hypothyroidism
• Discontinuing medications that promote SIBO when possible

5. Nutritional Support

Replacing vitamin and mineral deficiencies that result from malabsorption.

6. Probiotics in SIBO Treatment

Certain probiotic strains produce antimicrobial compounds that can help address bacterial overgrowth, though probiotic use in SIBO remains somewhat controversial and requires careful strain selection. Specific Lactobacillus and Bacillus species produce bacteriocins, organic acids, and hydrogen peroxide that demonstrate antagonistic effects against common SIBO-associated bacteria. Some research suggests that soil-based organisms and spore-forming probiotics like Bacillus coagulans may be better tolerated in SIBO than traditional Lactobacillus or Bifidobacterium strains, as they’re less likely to colonize the small intestine. The key is selecting strains with documented antimicrobial activity while avoiding those that might contribute to d-lactate production or histamine formation, which can worsen symptoms in susceptible individuals. Probiotics are generally most beneficial when introduced after initial SIBO treatment to help reestablish a healthy microbial balance and prevent recurrence.

7. Prebiotics in SIBO Treatment

Partially hydrolysed guar gum (PHGG) has emerged as a particularly promising prebiotic in SIBO management, with research demonstrating its ability to enhance antibiotic efficacy. Unlike other prebiotics that may exacerbate SIBO symptoms by feeding bacterial overgrowth in the small intestine, PHGG’s unique properties allow it to be well-tolerated even in SIBO patients. Studies have shown that combining PHGG with rifaximin significantly improves eradication rates compared to antibiotic therapy alone, likely by modulating the gut environment and supporting beneficial bacteria while antibiotics target pathogenic organisms. PHGG’s soluble fiber structure is fermented slowly and primarily in the colon rather than the small intestine, which helps restore healthy gut function without worsening small intestinal bacterial proliferation. This makes it a valuable adjunct therapy, particularly when used strategically during or after antibiotic treatment to support gut recovery and reduce SIBO recurrence.

8. Postbiotics in SIBO Treatment

Butyrate, a short-chain fatty acid postbiotic, shows particular promise in treating intestinal methanogen overgrowth (IMO), where archaea rather than bacteria are the primary culprits. Research indicates that butyrate exhibits antagonistic properties against methane-producing organisms like Methanobrevibacter smithii, potentially through competitive metabolic pathways and alterations in the intestinal environment that favour beneficial bacteria over archaea. Butyrate also strengthens the intestinal barrier, reduces inflammation, and supports colonocyte health—all critical factors in both SIBO and IMO recovery. By providing butyrate directly as a postbiotic supplement, patients can bypass the need for colonic fermentation to produce this beneficial compound, which is particularly valuable when the microbiome is disrupted. This approach may help restore gut homeostasis while simultaneously creating an environment less hospitable to methane-producing organisms, making butyrate supplementation a logical therapeutic consideration for IMO cases.

Treatment Success and Recurrence

Approximately 45% of patients experience recurrent SIBO following antibiotic therapy, with higher rates in elderly patients, those who’ve had appendectomies, and chronic PPI users. Multiple treatment rounds (2-5 courses) are often needed, with retesting used to guide further therapy.

For patients with frequent recurrences (more than 4 episodes per year), antibiotic prophylaxis may be considered—typically 5-10 days every two weeks or monthly, rotating antibiotics over 2-3 months.

The Connection Between SIBO and Other Conditions

SIBO has been linked to numerous conditions, grouped into 12 major categories:

1. Gastrointestinal disorders: IBS, IBD, celiac disease
2. Autoimmune diseases
3. Cardiovascular diseases
4. Metabolic diseases: Including obesity
5. Endocrine disorders: Diabetes, hypothyroidism
6. Nephrological disorders: Chronic kidney disease
7. Dermatological diseases: Rosacea, psoriasis
8. Neurological diseases: Parkinson’s disease
9. Developmental disorders
10. Mental disorders: Depression, anxiety
11. Genetic diseases
12. Gastrointestinal cancers

The relationship between SIBO and irritable bowel syndrome (IBS) has received particular attention, with research suggesting SIBO may be a mechanistic driver of IBS symptoms in many patients. Antibiotic therapy shows a 51.2% response rate in IBS patients with SIBO versus 23.4% in those without SIBO.

Why Does SIBO Matter?

Beyond uncomfortable symptoms, untreated SIBO can lead to:

• Malabsorption and malnutrition: Affecting overall health and quality of life
• Vitamin and mineral deficiencies: Including B12 deficiency leading to anemia
• Increased intestinal permeability: Contributing to systemic inflammation
• Bacterial translocation: In severe cases, especially with cirrhosis
• Reduced quality of life: Due to chronic symptoms and dietary restrictions

Moving Forward: What You Should Know

SIBO is a complex condition with multiple contributing factors. If you suspect you have SIBO, consider:

1. Seeing a gastroenterologist: For proper evaluation and testing
2. Comprehensive assessment: To identify underlying causes
3. Appropriate testing: Usually starting with breath testing
4. Individualised treatment: Based on your specific type of SIBO and underlying conditions
5. Follow-up: To ensure treatment success and address recurrences

Remember that successful SIBO management often requires addressing the root cause, not just treating the bacterial overgrowth itself. With proper diagnosis and comprehensive treatment, most patients can achieve significant symptom relief and improved quality of life.

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