What Causes SIBO?

 

SIBO usually develops when the gut’s natural defence mechanisms are disrupted,  most commonly impaired gut motility (the migrating motor complex), structural changes in the digestive tract, or alterations in stomach acid and digestion.

Low stomach acid (known as hypochlorhydria, and in more severe cases achlorhydria) may increase susceptibility to SIBO by weakening the stomach’s protective acid barrier, allowing more bacteria to survive and reach the small intestine. In some people, chronic gastritis — including patterns associated with Helicobacter pylori — can also be linked with reduced acid production.

Certain medications that suppress stomach acid, particularly proton pump inhibitors (PPIs) such as omeprazole and lansoprazole, have been associated with an increased risk of SIBO. These drugs can alter the upper gastrointestinal environment and microbiome, making bacterial overgrowth more likely. PPIs may also cause diarrhoea in some individuals, potentially due to microbiome changes or increased susceptibility to gut infections.

Other common contributors to SIBO include:

• Previous food poisoning or gastroenteritis

• Slow gut motility

• Abdominal surgery or adhesions

• Structural abnormalities of the digestive tract

• Chronic stress

• Co-existing fungal overgrowth (SIFO)

• Long-term medication use (including PPIs and opioids)

• Nutrient deficiencies or malabsorption

Because the causes of SIBO vary from person to person, successful treatment requires identifying and addressing each individual’s underlying drivers — not simply reducing bacterial levels alone.

 

 

Symptoms of SIBO

 

The signs and symptoms of SIBO are non-specific and are similar to other digestive disorders such as irritable bowel syndrome (IBS), lactose intolerance and fructose malabsorption. Common complaints include:

• Abdominal pain and discomfort
• Bloating
• Indigestion
• Diarrhoea
• Constipation
• Unintentional weight loss
• Inability to tolerate high fibre foods including vegetables, broccoli, beans, lentils, onions and garlic
• Belching
• Excessive gas and flatulence
• Anxiety or brain fog
• Malabsorption,  difficulty tolerating fatty foods, Anemia-  (Iron, B12, Ferritin deficiency)
• Leaky gut leading to joint pain, or body pain rashes on skin and severe food intolerances
• Rosacea

Does the NHS test for SIBO?

The answer is Yes and No. SIBO is becoming more mainstream, however the NHS still does not routinely pinpoint SIBO symptoms. If you are offered SIBO testing it will be via a gastroenterologist and there may be long waiting times on the NHS.

The majority of SIBO diagnostics conducted on the NHS tends to use glucose as the sugar solution. This may be problematic and produce false negatives. Glucose is usually absorbed within the upper portion of the small intestine (only the top two feet ) so if hydrogen and/or methane are detected in this test it indicates an overgrowth in upper end of the small intestine, closest to the stomach.

The problem with the glucose breath test is that is unable to identify the growth of bacteria it in the last section or distal end of your small intestine. This means the test may produce a false negative result.

Because of the large amount of symptom overlap of SIBO with other gastrointestinal conditions like IBS, it is important that proper testing is done to ensure a correct diagnosis and treatment. If symptoms point to SIBO, then a breath test is usually requested.

 

Do you have questions or would to see how we can assist you?

SIBO Testing & Treatment in the UK

What Is SIBO?

SIBO develops when excessive bacteria accumulate in the small intestine. Unlike the colon, the small intestine is not designed to host large numbers of microbes. When overgrowth occurs, digestion becomes impaired and inflammation may develop.

Common symptoms include:

• Persistent bloating or abdominal distension

• Excess gas or belching

• Diarrhoea, constipation, or alternating bowel habits

• Abdominal pain or cramping

• Reflux or nausea

• Fatigue and brain fog

• Skin issues

• Nutrient deficiencies

• Increasing food sensitivities

Many people diagnosed with IBS are later found to have underlying SIBO.

Types of SIBO

Not all SIBO is the same. Treatment depends heavily on which gases are elevated on your breath test.

Hydrogen-Dominant SIBO

Often associated with diarrhoea, bloating, and urgency. This type generally responds well to rifaximin or targeted herbal antimicrobials.

Methane-Dominant SIBO (also called IMO – Intestinal Methanogen Overgrowth)

Commonly linked to constipation, slow gut motility, and severe bloating. Methane cases are typically more stubborn and usually require combination treatment (for example rifaximin plus another agent, or structured herbal protocols including allicin).

Hydrogen Sulfide SIBO

Associated with diarrhoea, abdominal pain, and sometimes strong-smelling gas or stools. This type can be harder to detect and often requires a more nuanced treatment approach.

Understanding your SIBO subtype is essential. Guessing frequently leads to relapse.

 

SIBO Breath Testing in the UK

SIBO is diagnosed using a breath test that measures hydrogen, methane, and sometimes hydrogen sulfide gases produced by gut bacteria.

We arrange home breath testing kits across the UK and provide if you book a consultation can offer a full interpretation of results, explaining:

• Which gas pattern you have

• Severity of overgrowth

• Likely root causes

• Most appropriate treatment pathway

Breath testing allows us to move away from guesswork and build a targeted plan.

In some cases, we also recommend blood tests to assess malabsorption and nutrient deficiencies (such as B12, iron, or folate), or stool testing to evaluate candida, fat digestion and overall gut health.

SIBO Treatment Options

There is no single treatment that works for everyone. Successful care depends on addressing both the bacterial overgrowth and the underlying causes that allowed it to develop.

Rifaximin for SIBO

Rifaximin is the most widely studied antibiotic for SIBO. It works locally in the gut and is generally well tolerated.

In hydrogen-dominant SIBO, rifaximin can be effective. However:

 

• It is not routinely available on the NHS for SIBO

• Private prescriptions in the UK typically cost £250–£400 per course

• Relapse rates are high if underlying causes aren’t addressed

For methane-dominant cases, rifaximin alone is usually insufficient and is often combined with another agent or replaced with herbal protocols.

👉 Read more about  “Rifaximin vs Herbal Therapy for SIBO” article.

Herbal Therapy for SIBO

Herbal antimicrobials are increasingly used either instead of, or alongside, antibiotics. This is what we use at our functional medecine clinic.

Commonly used  herbs include:

• Berberine

• Oregano oil

• Allicin (garlic extract)

• Neem

• Combination botanical formulas

Research shows herbal protocols can be as effective as rifaximin for some people, particularly in methane-dominant or rifaximin-resistant cases.

Herbal therapy may also offer additional benefits such as anti-inflammatory support and gentler long-term use when required. We select herbs based on your gas pattern, symptom profile, and tolerance.

Side effects can still occur if doses are too high or supplements are mixed inappropriately, and interactions with medications are possible. For this reason, we strongly recommend professional guidance.

 

Methane SIBO (IMO): Intestinal Methanogen Overgrowth -Why Treatment Is Different

Methane-dominant SIBO is driven by methane-producing organisms that slow gut motility. This often leads to constipation and stubborn bloating.

Treatment typically involves:

• Combination antimicrobial therapy

• Targeted herbs such as allicin

• Prokinetics to restore gut movement

• Nutritional strategies to prevent relapse

Hydrogen Sulfide SIBO

Hydrogen sulfide SIBO often presents with diarrhoea and abdominal discomfort. In these cases we frequently find oregano oil to be helpful, alongside gut-lining support and sulphur-pathway balancing.

 

Why SIBO Often Comes Back (Relapse Prevention)

Up to 30–45% of people relapse within months if underlying causes are not corrected.

Common contributors include:

• Slow gut motility

• Low stomach acid

• Previous food poisoning or gastroenteritis

• Surgical history or adhesions

• Long-term proton pump inhibitor use

• Chronic stress

• Co-existing fungal overgrowth

• Ongoing dysbiosis

Our protocols don’t stop at antimicrobial treatment. We also focus on:

• Motility support (prokinetics)

• Gut lining repair

• Nutritional rehabilitation

• Long-term relapse prevention strategies

This is what allows lasting improvement rather than repeated short-term fixes.

Diet and SIBO

Dietary changes are an important part of managing SIBO, but they are not a cure on their own.

We often modify low-FODMAP principles into a lower-fermentable, lower-sugar approach that many clients tolerate better.

In some cases, an elemental diet may be used for short periods to reduce bacterial fermentation.

Because restrictive diets can negatively affect beneficial gut bacteria over time, we aim to reintroduce foods carefully once treatment is underway and support microbiome recovery.

 

Candida, IBS, and Other Associated Conditions

Candida and SIBO can co-exist (sometimes referred to as SIFO). In these cases antifungal support may also be required.

SIBO is frequently linked with IBS, rosacea, coeliac disease, Crohn’s disease, and malabsorption syndromes.

Addressing SIBO can significantly improve symptoms in many of these conditions.

Our Clinical Approach

We never use blanket protocols.

Every client receives an individualised plan based on:

• Breath test results

• Symptom profile

• Medical history

• Root causes

• Nutritional status

Our approach may include:

• Breath testing and full interpretation

• Personalised antimicrobial protocols (herbal and/or pharmaceutical)

• Dietary guidance

• Gut repair support

• Prokinetics and relapse prevention strategies

No two clients receive the same protocol.

Book a SIBO Consultation

If you suspect SIBO or already have positive test results and want expert guidance, we offer private consultations to help you:

• Arrange and interpret SIBO breath testing

• Choose between rifaximin, herbal therapy, or combination approaches

• Build a personalised treatment plan

• Address underlying causes

• Prevent relapse

We work with clients across the UK and internationally via online appointments.

Book a SIBO Consultation Today

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Are there any other tests that be conducted to test for SIBO?

The gold standard to detect small intestinal bacterial overgrowth is an invasive test whereby an endoscope is used to collect a fluid sample from your small intestine. This fluid is then tested in a laboratory.

 

Can I get Rifaximin from my GP?

Obtaining Rifaximin through your general practitioner (GP) can often be a challenging process. It typically necessitates a referral to a

Gastroenterologist, which may result in considerable waiting times and associated expenses. In addition to the cost of a private

Gastroenterologist consultation, you will be required to cover the expenses associated with antibiotics. Using herbal antibiotics may be a much faster route and offer an economical alternative.

Antibiotics may have side effects such as gastrointestinal upset, allergic reactions, and disruptions to the natural gut microbiome. Herbal treatments, when used appropriately, are often associated with fewer and milder side effects.

Unfortunately side-effects can also occur with herbal antibiotics if the dosage is too high or if they are mixed inappropriately. Moreoever there can be interactions with medications. We have also found that the quality of supplements found on the high street is variable so would recommend booking in a consultation with our SIBO specialists.

Less damage to the Gut Microbiome

Unlike antibiotics, certain herbs like berberine and oregano oil are less likely to harm your gut’s healthy bacteria. This means they have a milder impact on your overall gut health.

Long-Term Management of SIBO

Herbal treatments may be more suitable for individuals who require long-term management of SIBO, as antibiotics are typically used for shorter durations due to concerns about antibiotic resistance and the gut microbiome.

Combination Therapy

In some cases, a combination of herbal and antibiotic treatments may be considered for SIBO, as this can capitalize on the benefits of both approaches.

The choice between herbal an antibiotic treatments may also depend on an individual’s overall health including any pre-existing conditions or allergies.

 

The good news is that research indicates that the efficacy of herbal antibiotics is equivalent to Rifaximin for the treatment of Small Intestinal Bacterial Overgrowth. Clinically this is what we have witnessed.

Herbal antibiotics are readily available and can be bought over the counter from professional supplement shops. Below is a list of the most effective SIBO supplements that we frequently use in our clinic.

Herbal Antibiotics

Oregano Oil: Oregano oil contains compounds like carvacrol and thymol, which have antimicrobial properties that can help reduce bacterial overgrowth.

Berberine: Berberine, found in herbs like goldenseal and Oregon grape, has been shown to inhibit the growth of pathogenic bacteria in the gut.

Neem: Neem, a tree native to India, has antibacterial properties and may help control SIBO.

Peppermint Oil: Peppermint oil can relax the muscles of the small intestine and alleviate symptoms like bloating and abdominal pain.

Allicin: Allicin and Allimed are often used for Methane dominant SIBO and may help with reducing archaea. This supplement is based from Garlic; however the fermentable element has been removed and even if garlic is a high-fodmap foods, many people can tolerate it.

Atrantil: Atrantil is very effective for wind and bloating. There can be interactions with medications such as blood thinners, anti-depressants.

What supplements are best for Hydrogen Sulfide SIBO?

Typically we find Oregano oil to be of the greatest benefit.

Biofilm Disruptors

Biofilm disruptors such as Lactoferrin and NAC have also been of benefit. Biofilms are groups of microorganisms such as bacteria and fungus, that are protected by a layer slime. This makes antimicrobia and antibiotic therapy very difficult. However using a biofilm disruptor can help infiltrate these organisms and then clear out the leftover matrix, minerals, and bacterial DNA of the organisms.

Candida and SIBO can co-exist- SIFO AND SIBO

In some cases candida and yeast infections may co-exist, (Small Intestinal Fungal Overgrowth) and it will be important to address both by taking anti-fungals as well. Grapefruit Seed, Caprylic acid have often helped enormously. a very common comorbidity for SIBO sufferers, affecting around half of SIBO cases (5).

How long will it take to treat SIBO?

The duration of treatment will vary greatly from each individual. On average 4-8 weeks is needed. Some patients respond after just 3-4 weeks, other may need 3 rounds of anti-microbials. Sometimes you will find that your SIBO symptoms disappear and then slowly return after three months. We also recommend taking some prokinetics, possibly some hydrochloric acid if needed or bitters.

Is there a cure for SIBO?

In many cases, SIBO can be successfully treated by directly addressing the bacterial overgrowth. The most common first-line antibiotic prescribed is Rifaximin. The problem with antibiotics is that they are not always initially effective with one study finding that in people with SIBO-related IBS, two-thirds had to be retreated with Rifaximin, with some needing re-treatment up to 5 times. This raises the very serious concern of developing bacterial antibiotic resistance.

We have successfully used herbal treatments such as oil of oregano, lemon balm, and red thyme oil, we have found these to be an effective alternative treatment for SIBO. A 2014 study found that herbal treatments were just as effective as the antibiotic Rifaximin in treating SIBO. And from the same study, herbal treatments were just as effective as triple antibiotic therapy in people that did not respond to rifaximin.

What types of Dietary modifications do you recommend?

One of the key components of managing SIBO naturally is adjusting your diet. The goal is to reduce foods that encourage bacterial overgrowth while promoting a balanced gut microbiome.

Some of the diets that we may use include the Low FODMAP Diet: Fermentable oligosaccharides,disaccharides, monosaccharides, and polyols. (FODMAPs) are types of carbohydrates that can exacerbate SIBO symptoms. A low FODMAP diet restricts these compounds and may help alleviate symptoms. This is quite a complex diet and we will simplify it to make it much easier for you to follow and ensure it is taiored for SIBO patients.

Elemental Diet: An elemental diet involves consuming pre-digested nutrients in liquid form, which may give the gut a break from bacterial fermentation and promote healing.

What types of bacteria are present in small intestinal bacterial overgrowth?

According to Dr Pimentel, there are a specific strains of bacteria including Klesbiella Escherichia coli and Enterococcus that may be detected in patients with small intestinal bacterial overgrowth. These are likely linked to IBS-D and Hydrogen dominant SIBO. Unfortunately Klebsiella species, may produce toxins that damage the mucosa. This may lead to malabsorption.

Certain types of bacteria can cause malabsorption in SIBO

Research indicates that fat malabsorption or bile acid diarrhea may be linked to a predominance of bacteria that metabolize bile salts to unconjugated or insoluble compounds.

Certain types of bacteria can cause bloating without diarrhea in SIBO

It appears that some patients who experience bloating without diarrhea have an abundance of microorganisms that metabolize carbohydrates to short-chain fatty acids and gas.

Is there a link Between SIBO and IBS?

Is there a link between Irritable Bowel Syndrome and SIBO?

The causes of irritable bowel syndrome are still unknown. However without a doubt, symptoms of SIBO and IBS are very similar. earlier, SIBO is frequently found in 30-85% of patients fulfilling criteria of irritable bowel syndrome (30%-85%)[9-11,14,15,]. Dr Pimental believes that SIBO is the primary cause of irritable bowel syndrome.

What is the link between and intestinal methanogen overgrowth and SIBO with constipation?

However if you suffer with IBS-C, Irritable bowel syndrome with constipation, this may be due to an organism named Methanobrevibacter smithii. This is classified as an archaeon and actually overgrows outside of the small intestine and is referred to as intestinal methanogen overgrowth.

Is there a link with Coeliac disease and SIBO?

A wide range of 9% to 55% (10) of patients have been diagnosed with SIBO as a complication of coeliac disease. If you are not responding to a gluten-free diet you may wish to test for SIBO.

 

Is there a link with Rosacea and SIBO?

Yes—research shows SIBO is more common in people with rosacea, and in a randomised trial, treating SIBO (with rifaximin) led to major improvements or near-clearance of the skin for many patients. It isn’t the case for everyone, but if you have rosacea plus bloating or IBS-type symptoms, testing for SIBO is sensible because addressing it can reduce flushing and bumps.

 

Is there a link with Chrons disease and SIBO?

SIBO is found in about 25% of patients with Crohn’s disease (11,12) . In fact the symptoms of SIBO are very similar to Crohn’s disease ( increased bowel movements and lower body weight).

Is there a link between malabsorption and SIBO?

We often also recommend that a vitamin and mineral blood test is conducted to detect any nutrient deficiencies such as B12, folate and iron deficiencies. In some cases we also recommend a stool evaluation to test for fat malabsorption.

Prokinetics

These can also very important as well when treating SIBO. The term prokinetic means simply to promote movement and, in the context of the gastrointestinal tract. These are not be confused with laxatives. A prokinetic is useful to stimulate the MMC complex- motor migrating complex and is best taken at bed before fasting and help clear bacteria out of the small intestine.

Some examples include:

• Ginger root and ginger formulas (1000 mg )
• Motility activator-This is less likely to cause side-effects with patients who have acid reflux.
• Pure encapsulations-MotilPro
• Bio-Mi Kinetic

The Importance of Diet and SIBO

Dietary changes are also an important part of managing SIBO. Because bacteria feed on carbohydrates, then a diet that aims to reduce these can help. A low FODMAP diet is sometimes recommended to treat SIBO and which also has proven effective in treating IBS. FODMAPs are short-chain carbohydrates such as lactose, fructose, fructans (long chains of fructose molecules) and sugar alcohols that are commonly present in dairy products, grains, legumes and certain fruits and vegetables. The reduction in fermentable carbohydrates in the diet helps to starve excess bacteria of their important food source.

Following the low FODMAP diet for extended periods of time may lead to a reduction of healthy gut bacteria know as Bifidobacteria. Therefore it is important after treatment SIBO and following a low-fodmap diet to take probiotics to replenish the concentration of healthy gut bacteria (7). The low FODMAP may also results in calcium deficiency.

The elemental diet is another option for people with SIBO. The diet supplies nutrients in an easy-to-digest form. The easier and quicker digestion and absorption of nutrients mean there is less available for bacteria to feed off. In a 2-week study of people with SIBO-related IBS trialling an elemental diet, 80 percent returned a normal lactulose breath test after 1 month.

With SIBO, different dietary changes work for different people. That is where working with an experienced nutritionist to assist in tailoring changes to your diet to manage symptoms of SIBO can be of help.

The SIBO breath test (Small Intestinal Bacterial Overgrowth) is also an excellent test that is now available and is also of tremendous benefit to IBS sufferers.

Do you have questions or would to see how we can assist you?

Book a consultation with us at our IBS clinic on Harley Street London or virtually

 

Other Services:

• Food Intolerance Testing UK
• Functional Medicine Consultations
• Candida and Gut Health Programmes
• Gut Microbiome tests

 

 

References

1. Clin Gastroenterol Hepatol. – Breath testing for small intestinal bacterial overgrowth: maximizing test accuracy.

2. Wur J Gastroenterol Hepatol. – Breath tests in the diagnosis of small intestinal bacterial overgrowth in patients with irritable bowel syndrome in comparison with quantitative upper gut aspirate culture.

3. Gut Liver. – Small Intestinal Bacterial Overgrowth and Irritable Bowel Syndrome: A Bridge between Functional Organic Dichotomy.

4. Dig Dis Sci. – Comparison of scintigraphy and lactulose breath hydrogen test for assessment of orocecal transit: lactulose accelerates small bowel transit.

US National Library of Medicine – Small Intestinal Bacterial Overgrowth: A Comprehensive Review.

US National Library of Medicine – How to Interpret Hydrogen Breath Tests.

Springer Link – Effects of Rifaximin Treatment and Retreatment in Nonconstipated IBS Subjects.

US National Library of Medicine – Herbal Therapy Is Equivalent to Rifaximin for the Treatment of Small Intestinal Bacterial Overgrowth.

US National Library of Medicine – Efficacy of the low FODMAP diet for treating irritable bowel syndrome: the evidence to date.

Springer Link – 14-Day Elemental Diet Is Highly Effective in Normalizing the Lactulose Breath Test

7. US National Library of Medicine – Staudacher HM, Whelan K: Altered gastrointestinal microbiota in irritable bowel syndrome and its modification by diet: probiotics, prebiotics and the low FODMAP diet.

8. US National Library of Medicine – Lazzini S, Polinelli W, Riva A, Morazzoni P, Bombardelli E: The effect of ginger (Zingiber officinalis) and artichoke (Cynara cardunculus) extract supplementation on gastric motility: a pilot randomized study in healthy volunteers.

9. Pimentel, Am J Gastroenterology 2000, 2003)(Pimentel, 2006)

10. Small intestinal bacterial overgrowth syndrome– World Journal of Gastroenterology Jan Bures, Jiri Cyrany, […], and Marcela Kopacova

11. Castiglione F, Rispo A, Di Girolamo E, Cozzolino A, Man- guso F, Grassia R, Mazzacca G. Antibiotic treatment of small WJG| www.wjgnet.com

12. Lin HC. Small intestinal bacterial overgrowth: a framework for understanding irritable bowel syndrome. JAMA 2004; 292: 852-858 – Lupascu A, Gabrielli M, Lauritano EC, Scarpellini E, San- toliquido A, Cammarota G, Flore R, Tondi P, Pola P, Gas- barrini G, Gasbarrini A. Hydrogen glucose breath test to detect small intestinal bacterial overgrowth: a prevalence case-control study in irritable bowel syndrome. Aliment Pharmacol Ther 2005; 22: 1157-1160

13. pimentel M, Chow EJ, Lin HC. Eradication of small inte- stinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol 2000; 95: 3503-3506

14. Ford AC, Spiegel BM, Talley NJ, Moayyedi P. Small intestinal bacterial overgrowth in irritable bowel syndrome: systematic review and meta-analysis. Clin Gastroenterol Hepatol 2009; 7: 1279-1286

15. Mann NS, Limoges-Gonzales M. The prevalence of small intestinal bacterial overgrowth in irritable bowel syndrome. Hepatogastroenterology 2009; 56: 718-721

16. Gastroenterology – William L Hasler, M.D: Lactulose breath testing, bacterial overgrowth, and IBS: just a lot of hot air?

17. Curr Opin Gastroenterol. 2014 May; 30(3): 332–338.  – Bile Acids and the Gut Microbiome – Jason M. Ridlon,1,2 Dae Joong Kang,1 Phillip B. Hylemon,1,2 and Jasmohan S. Bajaj2,3,*