SIBO Treatment

In this article you will learn what SIBO is, the signs and symptoms, underlying causes as well as the best SIBO treatment.

What Is SIBO?

SIBO stands for Small Intestinal Bacterial Overgrowth, a condition where an abnormally high number of bacteria—typically found in the colon—populate the small intestine. These bacteria ferment carbohydrates prematurely, leading to gas production, inflammation, and malabsorption.

Common SIBO Symptoms:

• Bloating (especially after meals).

• Abdominal pain or discomfort.

• Diarrhoea, constipation, or alternating patterns.

• Fatigue and brain fog.

• Food intolerances (e.g., to FODMAPs, histamines).

• Nutrient deficiencies (B12, iron, fat-soluble vitamins).

Left untreated, SIBO can contribute to chronic digestive conditions like IBS, acne rosacea, fibromyalgia, and even autoimmune diseases.

What Causes SIBO?

SIBO is rarely random. It’s typically the result of digestive system dysfunctions that allow bacteria to stagnate or migrate into the small intestine (source).

🔍 Primary Root Causes of SIBO:

1. Low Stomach Acid (Hypochlorhydria)

   • Insufficient acid fails to sterilise food or control bacterial growth.

   • Often caused by chronic stress, aging, or long-term PPI use.

2. Low Pancreatic Enzyme Output

   • Without enzymes, proteins and carbs ferment in the gut, feeding bacteria.

3. Bile Deficiency or Stagnation

   • Bile helps emulsify fats and exerts antimicrobial effects. Sluggish bile can impair digestion and bacterial control.

4. Poor Gastrointestinal Motility

   • If food and waste move too slowly, bacteria accumulate in the small intestine.

   • Common in hypothyroidism, diabetes, or post-infection (food poisoning).

5. Medications

   • Proton pump inhibitors (PPIs), opiates, antispasmodics, antibiotics disrupt digestive secretions or gut flora.

6. Ileocecal Valve Dysfunction

   • This “gateway” between small and large intestine can malfunction, allowing colonic bacteria to migrate upward.

7. Structural Abnormalities

   • Adhesions from surgery, diverticula, or anatomical anomalies can trap bacteria in the small intestine.

How to Test for SIBO

The gold standard for diagnosing SIBO (clinically) is the breath test, which measures hydrogen and methane gas production after ingesting a sugar substrate.

Types of SIBO Tests:

1. Lactulose Breath Test

   • Common and non-invasive.

   • Best for detecting overgrowth in the distal small intestine.

   • May produce false positives if transit is fast.

2. Glucose Breath Test

   • More specific for proximal small intestine overgrowth.

   • Lower risk of false positives but may miss distal SIBO.

Both tests measure hydrogen and methane levels over a 2–3 hour period. A rise in gases indicates fermentation by bacteria, or archae in the context of methane, and thus SIBO/IMO.

The Three Types of SIBO

1. Hydrogen-Dominant SIBO

• Bacteria ferment carbohydrates and produce hydrogen gas.

• Associated with diarrhoea predominant IBS.

• More responsive to antimicrobials and dietary changes.

2. Methane-Dominant SIBO (IMO – Intestinal Methanogen Overgrowth)

• Caused by archaea (not bacteria), especially Methanobrevibacter smithii.

• Produces methane, which slows motility.

• Linked to constipation, and bloating.

3. Hydrogen Sulfide SIBO

• Produces hydrogen sulfide gas (smells like rotten eggs).

• Can cause diarrhoea, fatigue, neurological issues.

• Not always detected by standard breath tests.

• May require specialised testing (e.g., Trio-Smart Test).

You can read our article on hydrogen sulfide here.

SIBO Treatment: A Holistic, Multi-Phase Protocol

SIBO treatment isn’t a one-size-fits-all approach. The most successful outcomes come from addressing the root causes, managing symptoms, and supporting long-term gut restoration. Here are some key considerations, the order in which they are done may vary, based on the context.

Starve and Kill the Overgrowth

Antimicrobial Herbs (Alternatives to Antibiotics)

• Berberine – Antibacterial, anti-inflammatory.

• Neem – Targets multiple strains of bacteria.

• Oregano oil – Powerful broad-spectrum antimicrobial.

• Allicin (from garlic) – Especially effective for methane-dominant SIBO.

Functional Tip: Many practitioners recommend using 2 herbs at a time, or using herbal blends. Also it is often recommended to use them cyclically (2–4 weeks on, 1 week off) and rotate protocols to minimise resistance.

Antibiotics (When Needed)

• Rifaximin – FDA-approved for hydrogen SIBO.

• Rifaximin + Neomycin – Often required for methane overgrowth.

Repair Digestion and Strengthen Gut Function

We’ve already seen how underlying issues in the digestive process itself, can cause SIBO. So supporting the acidity of the stomach, digestive enzyme production, and bile flow can be an essential part of the healing process.

🔥 Support Stomach Acid

Betaine HCl with meals helps sterilise the stomach and break down proteins. However it is not always needed (but in my experience almost always is!). Watch this short video to learn how to figure out if this needs to be part of your protocol:

🍽️ Digestive Enzymes

Broad-spectrum enzymes enhance breakdown of fats, proteins, and carbohydrates. They can be especially helpful in cases of pancreatic insufficiency. If you have completed our Ultimate Gut Health test, the biomarker Pancreatic Elastase will let you know whether digestive enzymes may be required or not.

🧈 Bile Flow Support

Bitters (such as gentian, dandelion root) and Phosphatidylcholine can both help support the billiary system (the liver and gall bladder). Healthy bile is essential for the digestion of dietary fats, but it also has antimicrobial properties and so it essential in maintaining a healthy microbiome in the small intestine too.

Rebuild and Rebalance

🦠 Probiotics for SIBO

While controversial in active SIBO, many strains help:

• Lactobacillus plantarum – Supports gut lining integrity. Read our article Best Probiotics For Gut Health to learn which strain might be most helpful for you.

• Saccharomyces boulardii – Yeast-based, non-bacterial; helps control pathogens.

• Spore-based probiotics (e.g., Bacillus subtilis) – Survive the small intestine, support immune modulation.

🌱 Prebiotics (With Caution)

Prebiotics are the ‘food’ for the good bacteria, but may worsen gas if used too early. So start low (re: dose) and go slow. We recommend and have had great success with partially hydrolysed guar gum (PHGG) which has been shown to improve the efficacy of antibiotics when treating SIBO.

Dietary Strategies

🥦 Low-FODMAP Diet

• Temporarily removes fermentable carbohydrates that feed SIBO bacteria.

• Improves symptoms, but not a long-term fix.

• Reintroduce strategically with guidance.

🧪 Elemental Diet (Severe Cases)

• Liquid formula containing amino acids, glucose, and fats.

• Starves bacteria by eliminating fiber and complex carbs.

• Used for 2–3 weeks under supervision.

🥗 Long-Term Gut-Healing Diet

• Emphasise:

  • Cooked, easy-to-digest vegetables.

  • Wild fish, pasture-raised meat.

  • Bone broth, collagen.

  • Fermented foods (once tolerated).

Lifestyle & Nervous System Support

🧘‍♀️ Stress Reduction

• Chronic stress inhibits motility and digestion.

• Incorporate:

  • Deep breathing.

  • Meditation.

  • Yoga or vagal tone exercises.

🚶‍♂️ Movement & Sleep

• Light movement (like walking) post-meals improves motility.

• Aim for 7–8 hours of quality sleep to support immune repair.

💊 Prokinetics (If Needed)

• Natural options: ginger, 5-HTP, Iberogast.

• Pharmaceutical: low-dose erythromycin, prucalopride.

• Prevent relapse by keeping the gut moving between meals.

Preventing Relapse: The Maintenance Phase

SIBO is notorious for recurrence. Up to 45% relapse within one year. Prevention strategies include:

✅ Addressing the original cause (motility, acid, etc.).
✅ Prokinetic use after meals.
✅ Cycling antimicrobial herbs periodically as and when needed.
✅ Avoiding overuse of antibiotics and PPIs.
✅ Staying active and managing stress.

Final Thoughts: SIBO Treatment Requires a Systems Approach

SIBO isn’t just about eliminating bacteria—it’s about restoring your gut ecosystem, repairing digestion, and preventing recurrence. Whether your symptoms are mild or debilitating, a multi-phase, root-cause-focused approach can help you finally move from symptom management to long-term healing.

If you’re struggling with persistent bloating, IBS, food reactions, or fatigue—don’t ignore your gut. Treating SIBO might be the missing link in your wellness journey.