Post Author: Victoria Tyler

How to Treat Small Intestinal Bacterial Overgrowth. A UK Guide to SIBO Natural Treatment and Supplements

If you are searching for how to treat SIBO naturally, you are probably dealing with frustrating symptoms such as bloating, trapped wind, abdominal pain, constipation, diarrhoea, reflux, nausea or food intolerances. You may have already tried changing your diet, taking probiotics, using digestive enzymes or even completing a course of herbal supplements only to find that your symptoms do not go away.

Small Intestinal Bacterial Overgrowth, known as SIBO, happens when bacteria build up in the small intestine where they should not be present in high numbers.

These bacteria can ferment food, produce gas and irritate the gut, which is why symptoms can feel worse after eating, especially after carbohydrates, fibre, fruit, onions, garlic, pulses or gas forming  vegetables.

A natural SIBO treatment plan includes  dietary changes, herbal antimicrobials, targeted supplements based on the specific type of gas that has overgrown,and strategies to improve the Migrating Motor Compkex.

To treat SIBO properly, you need to understand your SIBO type, and why the overgrowth developed in the first place.

For example, someone with methane-dominant SIBO and constipation will  need a different approach from someone with hydrogen SIBO, who experiences diarrhoea and urgency.

In this guide, we’ll explain the main SIBO treatment options available in the UK, including natural treatments, herbal antibiotics, pharmaceutical antibiotics, diet plans, prokinetics, probiotics and relapse prevention. We’ll also look at what the research says about success rates, why SIBO often returns, and how to build a more complete plan for long-term gut health.

What Is SIBO?

SIBO stands for Small Intestinal Bacterial Overgrowth. It happens when there are too many bacteria in the small intestine, or when bacteria normally found in the large intestine start growing higher up in the digestive tract.

The small intestine is where most of your nutrient absorption takes place. It is not meant to contain large amounts of fermenting bacteria. When bacteria build up in this area, they can start fermenting carbohydrates before your body has properly absorbed them. This fermentation produces gases such as hydrogen, methane and hydrogen sulphide, which may contribute to bloating, trapped wind, abdominal pain, diarrhoea, constipation, nausea, reflux and food intolerances.

Recent research suggests that around one third of people with symptoms of Irritable Bowel Syndrome  may test positive for SIBO.

Are There Different Types of SIBO?

Yes. SIBO is often described according to the main type of gas produced during a breath test.

Hydrogen SIBO is often associated with bloating, abdominal discomfort, gas and looser stools or diarrhoea. This happens when bacteria in the small intestine ferment carbohydrates and produce hydrogen gas.

Methane-dominant SIBO, now often called intestinal methanogen overgrowth, or IMO, is more commonly linked with constipation, slow gut motility, trapped wind and feeling very full after meals. Strictly speaking, methane is produced by organisms called archaea rather than bacteria, which is why the term IMO is now used.

Hydrogen sulphide SIBO is less commonly tested for, but it may be associated with symptoms such as diarrhoea, rotten egg-smelling gas, urgency, abdominal discomfort and sensitivity to certain sulphur-containing foods.

Some people also have a mixed pattern, where more than one gas appears to be involved. This is one reason why SIBO treatment should be personalised. Someone with constipation and methane dominance may need a very different plan from someone with hydrogen-dominant SIBO and diarrhoea.

Understanding the type of SIBO can help guide the choice of diet, herbal antimicrobials, probiotics, prokinetics and relapse prevention strategies.

Key Symptoms of Hydrogen SIBO:

• Chronic diarrhoea (hallmark symptom, often loose and urgent)
• Bloating and excessive gas (especially after consuming high-carb or fermentable foods)
• Abdominal cramping or pain (typically relieved after passing gas or stool)
• Unintentional weight loss (due to malabsorption)
• Nutrient deficiencies Difficulty absorbing key vitamins like B12, iron, and fat-soluble vitamins (A, D, E, K)
• Fatigue and brain fog (due to inflammation and poor nutrient absorption)
• Food intolerances (difficulty digesting fibre, dairy, and fermentable carbs)

Common Symptoms of Methane SIBO (IMO)

• Chronic constipation (often unresponsive to fibre)
• Bloating and gas (especially after eating, can be prolonged and uncomfortable)
• Abdominal pain or cramping (due to slowed gut motility)
• Hard, dry stools (often difficult to pass)
• Weight gain or difficulty losing weight (methane slows metabolism and increases calorie absorption)
• Fatigue and brain fog (due to gut-brain axis disruption)
• Food intolerances (especially high-fibre or fermentable carbs like beans and starches)

Managing methane SIBO typically requires targeted antimicrobials, motility support (prokinetics), and dietary adjustments to restore gut balance.

How did I get  SIBO?

SIBO is often under diagnosed because its symptoms mimic other gastrointestinal disorders like IBS.

There are several things that can increase the risk of developing SIBO. These include:

• Long-term use of acid-reducing medication such as proton pump inhibitors, also known as PPIs
• Previous food poisoning or stomach infections
• Ongoing stress
• Slow gut movement, for example gastroparesis
• Chronic constipation
• An underactive thyroid or diabetes
• Autoimmune conditions such as coeliac disease or Crohn’s disease
• Structural problems in the gut, such as narrowing, scar tissue or adhesions
• Previous abdominal surgery

These factors can make it easier for bacteria to build up in the small intestine by reducing stomach acid, slowing digestion, or affecting the normal movement of food through the gut.

Testing: How do you test for SIBO?

Diagnosing SIBO is complex due to symptom overlap with other conditions. The most common diagnostic tool is called a Hydrogen and Methane breath test, which measures hydrogen and methane levels after consuming a sugar solution (lactulose or glucose). Elevated gas levels suggest bacterial overgrowth, but breath tests can produce false positives or negatives; therefore, test results should be interpreted along with clinical symptoms.

Effective Supplements for  for SIBO

There are several ways available for treating SIBO in patients with IBS, including the use of antibiotics, herbal supplements, dietary measures,  probiotics, and prokinetic agents.

SIBO Herbal and SIBO Natural Treatment

If you are looking to treat SIBO naturally you can use herbal antimicrobials. You can buy these without a prescription. They are sometimes referred to as “herbal antibiotics” because certain herbs contain plant compounds that may help reduce bacterial overgrowth in the gut.

One study by Chedid et al. found that herbal therapies were at least as effective as an antibiotic called  rifaximin for the resolution of SIBO on lactulose breath testing.

The choice of herbal antimicrobial depends on the type of gas produced on your SIBO breath test.

The three main patterns are hydrogen, methane and hydrogen sulphide. This matters because someone with hydrogen-dominant SIBO and diarrhoea may need a different approach from someone with methane-dominant SIBO and constipation.

Please note it is very common for herbs to cause side-effects so it is imperative to work under professional guidance.

Some patients experience nausea, reflux, stomach burning, diarrhoea, constipation, headaches, fatigue or “die-off” type symptoms.

Herbs can also interact with medications and may not be suitable during pregnancy, breastfeeding, gastritis, liver conditions, kidney disease or complex medical situations. For this reason, it is best to work with a qualified practitioner rather than trying to combine several strong antimicrobial supplements on your own.

Hydrogen SIBO – how to treat naturally

There are several supplements that may be used for Hydrogen SIBO, these include Oregano, Berberine and Neem.

These herbs can be used as single doses or mixed doses.

• Berberine
• Neem
• Oregano Oil

Oregano Oil

Oregano oil contains plant compounds such as carvacrol and thymol, which have been studied for their antimicrobial effects. In SIBO protocols, oregano oil is often used because it may help target bacterial overgrowth. However, it can be strong and may irritate the stomach lining in sensitive people, particularly those with reflux, gastritis or burning upper digestive symptoms.

Berberine

Berberine is a plant compound found in herbs such as barberry, goldenseal and Oregon grape. It has been studied for antimicrobial, anti-inflammatory and metabolic effects. In SIBO natural treatment, berberine-containing herbs are often used as part of a broader antimicrobial protocol. Berberine is not suitable for everyone and may interact with medication, including diabetes medication, blood thinners and some antibiotics.

Neem

Neem is another herb sometimes used in natural SIBO protocols. It is traditionally used for its antimicrobial and immune-supportive properties. Some practitioners use neem alongside other herbs rather than as a single treatment. As with other herbal antimicrobials, tolerance varies, and it may not be suitable during pregnancy, breastfeeding or in people with certain medical conditions.

Single Herbs vs Combination Formulas

Some people use single herbs, while others use combination formulas that contain several antimicrobial ingredients. Combination formulas may be more comprehensive, but they can also be harder to tolerate, especially for people with sensitive digestion, histamine issues, reflux, gastritis or multiple food and supplement reactions.

For this reason, the best SIBO herbal treatment is usually personalised. The aim is not simply to take the strongest herbs possible, but to choose the right approach for the SIBO type, symptom pattern and underlying cause.

Why Testing Matters Before Choosing SIBO Herbs

Testing can help identify whether hydrogen, methane or another pattern is involved. This is important because methane-dominant SIBO, now often called intestinal methanogen overgrowth or IMO, is more strongly associated with constipation and may require a different treatment approach.

Without testing, it is easy to choose the wrong supplements. For example, someone with constipation and methane dominance may not respond well to a plan designed only for hydrogen SIBO. Likewise, someone with diarrhoea, reflux or a very reactive gut may need a gentler approach before introducing strong antimicrobials.

A natural SIBO treatment plan should therefore consider breath test results, symptoms, bowel habits, diet tolerance, digestive function, motility and relapse risk.

Methane SIBO natural herbal Treatment

For methane-dominant Small Intestinal Bacterial Overgrowth (SIBO), also known as Intestinal Methanogen Overgrowth (IMO), Dr. Allison Siebecker recommend the  following:

1. Allicin

• Note: Use purified allicin rather than whole garlic, as whole garlic is highly fermentable and may aggravate SIBO symptoms.

2. Atrantil:

• Composition: Contains a blend of natural compounds, including Quebracho extract, which targets methane-producing archaea.

3. Berberine:

• Note: Berberine is effective against hydrogen-producing bacteria and is often combined with allicin to address both hydrogen and methane overgrowths.

4. Oregano Oil:

• Note: Oregano oil possesses broad-spectrum antimicrobial properties and is commonly included in SIBO treatment protocols.

Combination Therapy:

For methane-dominant SIBO, combining these herbs can enhance treatment efficacy. A typical regimen might include:

• Allicin  combined with Berberine
• Alternatively, Atrantil combined with Oregano Oil

Supplement Duration:

Herbal antimicrobial protocols are generally administered for 4 weeks, which is approximately double the typical duration of antibiotic treatments.

Our Perspective on Oregano Oil for SIBO

Through clinical experience, we have found oregano oil to be one of the most effective herbal treatments for SIBO due to its broad-spectrum antimicrobial properties. It helps reduce bacterial overgrowth and serves as a natural alternative to pharmaceutical antibiotics.

A study published in European PMC compared herbal therapies—including oregano oil—to rifaximin. The results showed that 46% of patients tested negative for SIBO after herbal treatment, compared to 34% for rifaximin.

For methane-dominant SIBO, a 2020 study in the Journal of Alternative and Complementary Medicine confirmed that oregano oil effectively targets methane-producing bacteria, making it a promising option instead of rifaximin or neomycin.

Key Benefits of Oregano Oil for SIBO:

Contains carvacrol and thymol, which fight SIBO-related bacteria
Studies suggest its effectiveness is comparable to rifaximin
Offers a natural alternative with fewer side effects

If you’re considering herbal treatment for SIBO, oregano oil may be a powerful option to discuss with a healthcare professional. Please note that there are some possible side-effects of Oregano. These include:

 Gastrointestinal upset (nausea, vomiting, diarrhoea) at high doses.
• Mucosal irritation if not diluted properly.
• Allergic reactions (rash or itching).
• Mild blood-thinning effects; caution for those on anticoagulants.

Other considerations to take into account are possible die-off reactions. It’s advisable to start with lower doses and adjust based on tolerance and effectiveness. It is essential to consult with a healthcare provider experienced in SIBO treatment as this is crucial to select the appropriate  dose and monitor for potential side effects. It is essential to ensure that herbal supplements are sourced from reputable manufacturers to guarantee purity and potency.

What is the best diet for SIBO?

The best diet for managing and preventing relapse of Small Intestinal Bacterial Overgrowth (SIBO) is one that helps reduce the fermentation of undigested carbohydrates in the small intestine, controls bacterial growth, and supports gut healing. Several dietary approaches have been shown to be effective for SIBO, and the choice depends on individual tolerance, the severity of symptoms, and the type of SIBO (hydrogen-dominant, methane-dominant, or hydrogen sulfide-dominant). Here are the most commonly recommended diets for managing SIBO:

The preferred prescription antibiotic that is used  to treat  SIBO is called rifaximin, which targets bacterial overgrowth in the small intestine.

Research has shown that rifaximin can have up to 80% success rate in treating SIBO.

However, the recurrence rate is high, with up to 45% of patients experiencing a relapse within a year.

Unfortunately many patients face challenges accessing rifaximin, the antibiotic of choice  through the NHS.

Low-FODMAP Diet and foods to avoid for Hydrogen and Methane SIBO

The Low-FODMAP diet is one of the most researched and effective diets for managing SIBO, particularly for those with IBS-related symptoms.

FODMAPs are a group of short-chain carbohydrates (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) that are poorly absorbed in the small intestine. These include foods like certain fruits (e.g., apples), vegetables (e.g., garlic, onions), legumes, dairy, wheat, and certain sweeteners.

FODMAPs ferment in the gut, feeding the overgrown bacteria, which can cause bloating, gas, and discomfort. By limiting high-FODMAP foods, you reduce the fuel supply to the bacteria in the small intestine, helping to alleviate symptoms.

The Low-FODMAP diet is typically followed in three phases:

• 1. Elimination: Avoid high-FODMAP foods for 4-6 weeks.
  2. Reintroduction: Gradually reintroduce high-FODMAP foods one at a time to identify individual triggers.
  3. Personalization: After identifying food sensitivities, continue with a modified diet that minimizes symptoms.
  4. Long-term use may negatively impact beneficial gut bacteria, so reintroduction of high-FODMAP foods is necessary.

SIBO Probiotics

Whether you should take probiotics for SIBO depends on your type of SIBO, your symptoms, and how your body responds to different strains.

Research on probiotics for SIBO is both lacking and mixed—some studies show they can help, while others suggest they may worsen symptoms.

Probiotic efficacy in SIBO hinges on subtype, strain selection, and timing. During active overgrowth, probiotics risk aggravating symptoms post-treatment, whereas targeted strains may aid recovery.

The best probiotics for SIBO depend on the type—hydrogen-dominant, methane-dominant (IMO), or hydrogen sulfide SIBO—as different strains can either help or worsen symptoms.

Best Probiotics for Hydrogen-Dominant SIBO

Hydrogen SIBO is typically associated with bloating and diarrhoea. The best probiotics for this type include:

• Soil-Based Probiotics (SBOs) – Bacillus subtilis, Bacillus coagulans (e.g., MegaSporeBiotic, Just Thrive). These are resilient and do not contribute to bacterial overgrowth.
• Saccharomyces boulardii – A beneficial yeast that supports gut balance (e.g., Florastor, Seeking Health S. Boulardii).
• Lactobacillus plantarum – Helps reduce hydrogen gas and improve gut barrier function (e.g., Jarrow Ideal Bowel Support).

Best Probiotics for Methane-Dominant SIBO (IMO)

Methane-dominant SIBO, often linked to constipation, is caused by methanogen overgrowth (not bacteria), requiring different probiotics:

• Bifidobacterium infantis, Bifidobacterium lactis – Helps regulate motility and reduce methane gas (e.g., Align, ProBiota Bifido).
• Lactobacillus reuteri, Lactobacillus casei – Supports gut motility and methane reduction (e.g., BioGaia Gastrus).
• Akkermansia muciniphila & Clostridium butyricum – Found in postbiotic formulas, improves gut lining and methane balance (e.g., Pendulum Akkermansia, CoreBiotic).

Best Probiotics for Hydrogen Sulfide SIBO

• Hydrogen sulfide SIBO is associated with sulfur intolerance, gas with a “rotten egg” smell, and gut inflammation. The best options include:

• Bacillus subtilis, Bacillus coagulans (SBOs) – Reduce inflammation and balance gut bacteria (e.g., MegaSporeBiotic).
• Clostridium butyricum – Supports gut lining and reduces hydrogen sulfide production (e.g., MIYAIRI 588, CoreBiotic).
• Lactobacillus plantarum & Saccharomyces boulardii – Help regulate gut balance without worsening sulfur metabolism issues (e.g., Seeking Health S. Boulardii, Jarrow IBS Support).

Probiotics to avoid for SIBO

Some traditional probiotics can worsen SIBO symptoms, especially those with Lactobacillus acidophilus or fermentable prebiotics like inulin, FOS, and GOS, as they can feed bacterial overgrowth.

Prokinetics for SIBO

Prokinetics help stimulate the muscles of the digestive tract, improving peristalsis and preventing food and waste from lingering in the small intestine. By enhancing motility, they reduce the risk of bacterial overgrowth, making them a valuable tool in SIBO management. Slow gut movement can allow bacteria to proliferate in areas where they shouldn’t, so maintaining proper motility is key to preventing relapse.

Research supports the use of prokinetics alongside antibiotics or herbal antimicrobials to both clear bacterial overgrowth and address underlying motility issues. A 2012 study in the Journal of Clinical Gastroenterology found that prokinetics like prucalopride improved gut movement and reduced SIBO symptoms such as bloating and constipation. Some patients also benefit from continuing prokinetic therapy after treatment to help prevent recurrence.

Common prokinetics for SIBO include prucalopride (2 mg daily), domperidone (10–20 mg three times daily), and low-dose erythromycin (50 mg 2–3 times per day). Natural options like ginger (500 mg daily) and Iberogast (20 drops three times daily) may also support gut motility. Since some prokinetics have potential side effects, consulting a healthcare provider is essential to determine the safest and most effective option.

How can you avoid reoccurrence of SIBO?

To prevent the recurrence of SIBO, focusing on improving gut motility is key. Prokinetics, help stimulate motility and ensure food moves efficiently through the digestive system, reducing the risk of bacterial overgrowth.

A diet tailored to support gut health, like a low FODMAP, can limit fermentable carbohydrates that feed bacteria may need to be re-instated if symptoms come back. Additionally, digestive enzymes and hydrochloric acid (HCL) supplements can aid digestion and reduce the chance of undigested food sitting in the small intestine, which can promote bacterial growth.

Stress management plays a vital role in gut health, as chronic stress can impair digestion and motility. Practicing relaxation techniques such as meditation or yoga can help manage stress levels and support digestive function. Avoiding processed foods, which can fuel dysbiosis and inflammation, is also crucial for maintaining a healthy gut. Finally, low-dose antimicrobials like oregano oil can be used to target harmful bacteria, helping to keep bacterial balance in check without causing disruption to the beneficial microbiota.

References:

1. Staudacher, H. M., et al. (2016). “Mechanisms and efficacy of dietary FODMAP restriction in IBS.” World Journal of Gastroenterology.
2. McIntosh, K., et al. (2018). “FODMAP diet and its effects on gut microbiota in IBS and SIBO patients.” Clinical and Translational Gastroenterology.
3. Gibson, P. R., et al. (2017). “The role of diet in the pathophysiology and management of small intestinal bacterial overgrowth (SIBO).” Gastroenterology.
4. Pimentel, M., et al. (2020). “Probiotics in Small Intestinal Bacterial Overgrowth: Clinical Evidence and Treatment Outcomes.” Journal of Clinical Gastroenterology.
5. European PMC Study (2020). “Herbal therapies versus rifaximin in the treatment of SIBO.” European Journal of Gastroenterology & Hepatology.
6. Journal of Alternative and Complementary Medicine (2020). “The effect of oregano oil on methane-producing bacteria in SIBO treatment.”
7. Journal of Clinical Gastroenterology (2012). “Efficacy of prokinetics in improving small intestinal motility and reducing SIBO relapse.”