SIBO (Small Intestinal Bacterial Overgrowth): Symptoms, Causes, Diagnosis & Natural Support

If you often feel bloated after meals, struggle with excessive gas, or experience unpredictable bowel habits, you’re not alone. These symptoms can have many possible causes, and one of them is Small Intestinal Bacterial Overgrowth (SIBO).

This guide explains what SIBO is, what causes it, how it’s diagnosed, and the evidence-based conventional and natural approaches that may help support recovery and reduce the risk of recurrence.

What Is SIBO?

SIBO stands SIBO stands for Small Intestinal Bacterial Overgrowth. It occurs when bacteria that normally live in the large intestine begin to grow in the small intestine—where they are present in much lower numbers under healthy conditions.

These bacteria ferment carbohydrates before your body has fully digested and absorbed them, producing gases such as hydrogen and methane. This excess gas can interfere with normal digestion and contribute to a wide range of digestive symptoms.

Unlike a general imbalance of the gut microbiome, SIBO specifically affects the small intestine, where most nutrient absorption takes place. As a result, symptoms may extend beyond the digestive system, particularly if the condition persists over time.

Common SIBO Symptoms

Symptoms vary from person to person, but many people notice that they begin or worsen 30 minutes to three hours after eating, particularly after meals containing fermentable carbohydrates (FODMAPs).

Digestive symptoms

• Bloating, especially after meals
• Abdominal pain or cramping
• Excessive gas or belching
• A feeling of fullness after eating only a small amount
• Diarrhoea, constipation, or alternating between the two
• Food intolerances, particularly to high-FODMAP foods
• Nausea in some people

Symptoms outside the gut

Because the small intestine is responsible for absorbing nutrients, long-standing SIBO may contribute to symptoms beyond the digestive tract, including:

• Fatigue or low energy
• Brain fog or difficulty concentrating
• Vitamin B12 deficiency
• Iron deficiency
• Unintentional weight loss in some cases
• General feelings of poor wellbeing

Not everyone experiences all of these symptoms, and many overlap with other digestive conditions such as IBS, coeliac disease, food intolerances, and inflammatory bowel disease. This is one reason why an appropriate assessment is important before beginning treatment.

What Causes SIBO?

SIBO is not simply about having “too many bacteria.” It’s about bacteria growing in the wrong part of the digestive tract. Under normal circumstances, the small intestine contains relatively few bacteria compared with the large intestine. Several natural defence mechanisms—including stomach acid, digestive enzymes, bile, immune function, and the migrating motor complex (MMC)—help keep bacterial numbers under control.

When one or more of these protective mechanisms becomes impaired, bacteria can multiply in the small intestine and contribute to symptoms.

The most common factors associated with SIBO include:

Impaired Gut Motility

One of the most common underlying causes of SIBO is slowed movement of food through the small intestine. Between meals, the migrating motor complex (MMC) acts like the gut’s natural housekeeping system, sweeping food particles and bacteria down into the large intestine.

If this cleansing wave becomes disrupted, bacteria have more opportunity to remain in the small intestine and multiply.

Poor motility may occur in people with IBS, hypothyroidism, diabetes, connective tissue disorders, or after certain viral or bacterial infections.

Food Poisoning and Gastroenteritis

Research has shown that some people develop SIBO after a bout of food poisoning or infectious gastroenteritis. In certain cases, damage to the nerves that regulate the migrating motor complex may contribute to persistent digestive symptoms long after the original infection has resolved.

Low Stomach Acid

Stomach acid is one of the body’s first lines of defence against unwanted microbes entering the digestive tract. Reduced stomach acid—whether related to ageing, long-term use of acid-suppressing medications, or other factors—may allow more bacteria to survive and reach the small intestine.

Proton Pump Inhibitors (PPIs)

Medications used to reduce stomach acid, such as proton pump inhibitors (PPIs), have been associated with an increased risk of SIBO in some studies. However, these medicines are important for many people and should never be stopped without medical advice.

Previous Abdominal Surgery

Scar tissue (adhesions), blind loops, intestinal diverticula, or other structural changes following abdominal surgery can slow the movement of food through the intestine, creating an environment where bacteria may accumulate.

Diabetes and Other Medical Conditions

Conditions that affect nerve function or intestinal movement—including diabetes, scleroderma and Parkinson’s disease—may increase the risk of SIBO by slowing normal digestive motility.

Antibiotic Use

Although antibiotics can be life-saving, repeated or prolonged courses may alter the balance of the gut microbiome. In some people, these changes may contribute to digestive symptoms and increase susceptibility to microbial imbalances.

Chronic Stress

Chronic stress affects more than just how you feel—it can influence digestion, stomach acid production, gut motility and communication between the brain and the digestive tract. While stress alone does not cause SIBO, it may contribute to factors that make bacterial overgrowth more likely in susceptible individuals.

Can Candida and SIBO Occur Together?

Yes. Some people experience both SIBO and Candida overgrowth at the same time, particularly when underlying factors such as repeated antibiotic use, digestive dysfunction, or disruption of the gut microbiome are present.

However, they are distinct conditions. SIBO involves an overgrowth of bacteria in the small intestine, whereas Candida overgrowth refers to an imbalance involving yeast. Although some symptoms overlap, each condition requires appropriate assessment and an individualised treatment approach.

How Is SIBO Diagnosed?

SIBO can be difficult to diagnose because its symptoms often overlap with other digestive conditions, including irritable bowel syndrome (IBS), coeliac disease, food intolerances, inflammatory bowel disease (IBD), and even Candida overgrowth.

While symptoms may raise suspicion, they cannot confirm SIBO on their own. This is why an appropriate assessment is important before beginning treatment.

Breath Testing

The most commonly used test for SIBO is a hydrogen and methane breath test. After drinking a solution containing either glucose or lactulose, breath samples are collected over several hours to measure gases produced by bacteria in the small intestine.

Elevated levels of hydrogen or methane may suggest bacterial overgrowth, although breath testing is not perfect and results should always be interpreted alongside a person’s symptoms and medical history.

Hydrogen, Methane and Hydrogen Sulphide

Different types of bacteria produce different gases, which can influence symptoms.

Gas	More commonly associated with
Hydrogen	Diarrhoea and loose stools
Methane	Constipation and slower gut motility
Hydrogen sulphide	Less common, but may be associated with diarrhoea and distinctive-smelling gas

Researchers continue to study hydrogen sulphide SIBO, and testing for this gas is not yet as widely available as hydrogen and methane breath testing.

Can You Tell From Your Symptoms?

Some symptom patterns may increase suspicion of SIBO, particularly if you:

• develop bloating within one to three hours after eating
• feel worse after eating high-FODMAP foods such as onions, garlic, beans, apples or wheat
• wake with a relatively flat stomach but become increasingly bloated as the day progresses
• notice that antibiotics temporarily improve your symptoms before they return.

However, these symptoms are not unique to SIBO, which is why self-diagnosis can be unreliable.

If you have ongoing digestive symptoms, it’s worth discussing them with your healthcare provider to determine whether breath testing or further investigation may be appropriate.

How Is SIBO Treated?

1. Conventional Treatment

Prescription antibiotics such as rifaximin, and in some cases rifaximin combined with other antibiotics depending on the type of SIBO, are commonly used as first-line medical treatment. The choice of therapy depends on individual circumstances and should be guided by a healthcare professional.

Others choose herbal antimicrobial protocols, either alongside conventional treatment or as part of an individualised plan developed with their healthcare practitioner.

Treating SIBO requires a comprehensive, multi-phase approach. You can’t just kill the bacteria—you also need to restore digestive function, rebalance your microbiome, and keep it from coming back.

Let’s look at the six key steps:

2. Dietary Support

One of the fastest ways to feel better is to adjust your diet. Because SIBO bacteria thrive on fermentable carbohydrates, removing these can significantly reduce bloating and gas.

Popular SIBO Diet Options:

• Low FODMAP diet – limits fermentable sugars that feed bacteria
• Specific Carbohydrate Diet (SCD) – removes complex carbs that are hard to digest
• Elemental diet – a short-term, liquid protocol using pre-digested nutrients

These diets are designed to reduce the amount of fermentable carbohydrate available to intestinal bacteria, which may help relieve symptoms.Transitioning to a gut-healing diet doesn’t have to feel overwhelming. The Yeastrix Reset Meal Plan is a gentle, 7-day roadmap designed to ease your gut into a lower-FODMAP, anti-inflammatory way of eating. It’s perfect for those dealing with SIBO, bloating, or food sensitivities, and it takes the guesswork out of what to eat while your gut is healing.

While dietary changes can significantly improve symptoms, diet alone may not eliminate bacterial overgrowth. Many people find that diet works best alongside other treatment strategies.

3. Herbal Antimicrobial Support

Instead of jumping straight to pharmaceutical antibiotics, many people opt for natural antimicrobial herbs. Some clinical studies have reported that certain herbal antimicrobial protocols achieved breath-test results comparable to rifaximin in selected patients, although larger, high-quality clinical trials are still needed.

Top Natural Antimicrobials for SIBO:

• Oregano oil – broad-spectrum antimicrobial
• Berberine – commonly used in herbal protocols designed to support microbial balance
• Neem and garlic extract – commonly included in herbal protocols designed to support microbial balance.

Rather than relying on a single herb, many practitioners use carefully selected combinations of botanicals that work together to support microbial balance.

4. Support Healthy Digestion

Efficient digestion is one of the body’s natural defences against bacterial overgrowth. When food isn’t broken down and absorbed effectively, more undigested carbohydrates remain available for bacteria to ferment. This fermentation produces gases such as hydrogen and methane, contributing to bloating, abdominal discomfort, and excessive gas.

Digestive enzymes help break down proteins, fats, and carbohydrates into smaller molecules that are easier to absorb. While enzymes do not treat SIBO directly, they may help improve digestion and support digestive comfort in some individuals as part of a comprehensive management plan.

Some people with SIBO may also have reduced stomach acid, impaired bile flow, or pancreatic enzyme insufficiency, all of which can contribute to poor digestion. Identifying and addressing these underlying factors is an important part of restoring normal digestive function.

We recommend Yeastrix Active Enzymes, formulated by Eric Bakker, ND. It contains a comprehensive blend of 13 digestive and systemic enzymes, together with Bacillus coagulans, to support efficient digestion, nutrient absorption, and overall gut health.

Whether used alongside dietary changes, herbal antimicrobials, or conventional treatment, digestive enzymes may help reduce digestive discomfort and support the recovery process.

👉 Explore Yeastrix Active Enzymes

5. Probiotics

The role of probiotics in SIBO remains controversial. Some people experience symptom improvement, while others notice temporary worsening. Research suggests that certain strains may be helpful in selected individuals, but responses vary.

Look for strains like:

• Lactobacillus plantarum
• Bifidobacterium infantis
• Bacillus coagulans
• Lactococcus lactis

The Yeastrix Daily Probiotic contains 17 strains selected to support overall gut microbiome health.

Some practitioners prefer introducing probiotics after antimicrobial treatment, while others include selected strains during treatment. The best approach varies between individuals.

👉 Explore Yeastrix Daily Probiotic

6. Restore Healthy Gut Motility

As discussed earlier, the migrating motor complex (MMC) acts as the intestine’s natural cleaning wave between meals. Supporting healthy motility is one of the most important ways to help reduce the risk of SIBO returning.

To support healthy motility:

• Don’t snack too often (space meals 4–5 hours apart)
• Some practitioners recommend natural prokinetic herbs such as ginger following treatment to support healthy gut motility.
• Manage stress and sleep. Good sleep, regular meal spacing and stress management may help support normal digestive motility.

7. Address the Root Cause

SIBO has a relatively high recurrence rate if the underlying cause isn’t identified and addressed. While reducing bacterial overgrowth is an important first step, long-term improvement often depends on restoring the normal function of your digestive system.

Depending on the individual, this may involve:

• Supporting healthy gut motility and the migrating motor complex (MMC)
• Correcting underlying digestive disorders that affect normal digestion
• Managing medical conditions such as hypothyroidism or diabetes that can slow intestinal motility
• Reviewing medications with your healthcare provider if they may be contributing
• Gradually rebuilding a healthy gut microbiome after treatment
• Maintaining a balanced, nutrient-rich diet that supports long-term digestive health

For many people, preventing recurrence requires looking beyond the bacteria themselves and addressing the factors that allowed the overgrowth to develop in the first place.

Although SIBO can return, many people experience long-term improvement when treatment is combined with strategies that support healthy digestion and address underlying contributing factors.

Can SIBO Come Back?

SIBO has a relatively high recurrence rate, particularly when the underlying cause has not been identified or treated. Recurrence usually happens when motility is impaired, or the gut ecosystem isn’t properly restored.

That’s why we recommend a phased protocol:

1. Reduce symptoms and inflammation
2. Treat overgrowth
3. Rebuild digestion and flora
4. Prevent relapse

Although recurrence is common, many people experience long-term improvement when the underlying causes are identified and managed appropriately.

Quick Treatment Summary

Managing SIBO usually requires more than simply reducing bacterial overgrowth. A comprehensive approach that supports digestion, addresses underlying causes, and helps restore a healthy gut environment offers the best opportunity for long-term improvement. The following summary brings together the key steps discussed in this guide.

Step	Purpose
Diagnose correctly	Confirm SIBO and identify the gas type
Reduce bacterial overgrowth	Antibiotics or herbal antimicrobials
Improve digestion	Diet, enzymes and digestive support
Restore motility	Support the migrating motor complex
Prevent relapse	Address underlying causes

Final Thoughts

Although SIBO can be frustrating, many people experience significant improvement when treatment addresses both the bacterial overgrowth and the underlying factors that allowed it to develop.

Rather than focusing on a single solution, a comprehensive approach—including appropriate diagnosis, dietary changes, digestive support, healthy gut motility, and treatment of contributing conditions—offers the best opportunity for long-term improvement.

If you suspect you may have SIBO, speak with a qualified healthcare professional who can recommend the most appropriate investigations and treatment plan for your individual situation.

Frequently Asked Questions

References

1. Pimentel M, et al. American College of Gastroenterology Clinical Guideline: Small Intestinal Bacterial Overgrowth. Am J Gastroenterol. 2020.
2. Ghoshal UC, Ghoshal U. Small intestinal bacterial overgrowth. J Gastroenterol Hepatol. 2017.
3. Pimentel M, et al. The North American Consensus on Breath Testing. Am J Gastroenterol. 2017.
4. Chedid V, et al. Herbal therapy is equivalent to rifaximin for treatment of SIBO (pilot study). Global Advances in Health and Medicine. 2014.
5. American College of Gastroenterology SIBO Clinical Guideline.

Continue Reading

• What Causes IBS Symptoms?
• Understanding Your Gut Health Healing Timeline: A Complete Beginner’s Guide
• What Is Candida Overgrowth? Symptoms, Causes & Natural Ways to Support Gut Health
• Grapefruit Seed Extract for Candida: Benefits, Research & Gut Health Support
• Can Antibiotics Cause Candida Overgrowth? What You Need to Know

This article is intended for educational and informational purposes only and is not a substitute for professional medical advice, diagnosis, or treatment. Always consult with a qualified healthcare provider before starting any new treatment or supplement, especially if you have a pre-existing medical condition or are taking medication. The recommendations here reflect a naturopathic approach and are not meant to replace conventional care when it is required. Individual results may vary.