Can SIBO Cause Nutrient Deficiencies?

In more significant or long-standing cases, SIBO can interfere with normal digestion and nutrient absorption.

Possible consequences may include:

• Vitamin B12 deficiency
• Iron deficiency
• Fat malabsorption
• Fat-soluble vitamin deficiencies
• Unintentional weight loss

Severe malabsorption is much less common than symptoms such as bloating, gas and abdominal discomfort.

Some people with fat malabsorption notice pale, greasy, difficult-to-flush or floating stools

Read more about SIBO and fat malabsorption

What Causes SIBO?

SIBO usually develops when one or more of the mechanisms that normally prevent excessive bacterial growth in the small intestine become disrupted.

One of the most important factors is impaired intestinal motility.

Slow Gut Motility and the Migrating Motor Complex

Between meals, your small intestine produces waves of muscular contractions known as the migrating motor complex (MMC).

You can think of the MMC as one of the small intestine’s natural cleaning mechanisms. It helps move leftover food, secretions and bacteria through the small intestine towards the colon.

 

f intestinal motility becomes impaired, bacteria may remain in the small intestine for longer and have a greater opportunity to multiply.

Conditions affecting intestinal motility are therefore recognised risk factors for SIBO.

Previous Food Poisoning or Gastroenteritis

Some people report that their digestive symptoms began following an episode of food poisoning or gastroenteritis.

Certain gastrointestinal infections can be followed by persistent changes in bowel function and intestinal motility. This is also one recognised pathway to post-infectious IBS.

For some individuals, altered motility following an infection may create conditions that favour bacterial overgrowth.

Low Stomach Acid

Stomach acid is another of the body’s natural defences against microorganisms entering the digestive tract.

Reduced stomach acid is known as hypochlorhydria.

When acid production is significantly reduced, more bacteria may survive passage through the stomach and enter the small intestine.

Proton Pump Inhibitors (PPIs)

Proton pump inhibitors such as:

• Omeprazole
• Lansoprazole
• Esomeprazole
• Pantoprazole

are commonly prescribed to reduce stomach acid.

Several systematic reviews and meta-analyses have found an association between PPI use and an increased likelihood of SIBO, although this does not mean that everybody taking a PPI will develop bacterial overgrowth.

PPIs can be important medicines and should not be stopped without discussing this with the healthcare professional who prescribed them.

Abdominal Surgery and Structural Changes

Changes to the anatomy of the digestive tract can sometimes interfere with the normal movement and clearance of intestinal contents.

Risk factors can include:

• Previous abdominal or intestinal surgery
• Surgical adhesions
• Intestinal strictures
• Small intestinal diverticula
• Blind loops
• Certain gastric or bariatric surgery procedures

Adhesions following abdominal surgery may occasionally affect the normal movement of the intestine and contribute to bacterial overgrowth.

Other Conditions Associated With SIBO

SIBO is also reported more frequently in people with certain medical conditions, including:

• Gastroparesis
• Coeliac disease
• Crohn’s disease
• Chronic pancreatitis
• Pancreatic exocrine insufficiency (PEI)
• Certain intestinal motility disorders
• Some forms of immunodeficiency
• Irritable Bowel Syndrome (IBS)

Reduced pancreatic secretions and alterations in bile acids may also reduce some of the mechanisms that normally restrict bacterial growth within the small intestine.

There is therefore rarely one universal cause of SIBO. Identifying the factors that may have contributed to bacterial overgrowth can be an important part of preventing symptoms from recurring.

How Do You Test for SIBO?

The most commonly used non-invasive investigation for SIBO is a hydrogen and methane breath test. You can read about how a SIBO test is conducted.

 

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 antibiotics called neomycine 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 medicine clinic.

Commonly used  herbs include:

• Berberine

• Oregano oil

• Allicin (garlic extract)

• Neem

• Combination botanical formulas

Herbal protocols can be as effective as rifaximin for some people.

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

Consultations are held online or via zoom.

The fee for 1 hour is £170.

 

 

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.