Small Intestinal Bacterial Overgrowth (SIBO) has become an increasingly recognized digestive health concern affecting millions of Americans. According to Dr. Josh Axe, a well-known functional medicine practitioner and certified doctor of natural medicine, SIBO can be effectively treated using natural approaches that address both symptoms and root causes. This comprehensive guide explores Dr. Axe’s protocol for treating SIBO naturally, combining dietary modifications, herbal antimicrobials, essential supplements, and lifestyle changes to restore gut health and eliminate bacterial overgrowth.
Understanding SIBO: The Root of Many Digestive Issues
Small Intestinal Bacterial Overgrowth occurs when bacteria that normally reside in the large intestine migrate and proliferate in the small intestine. This bacterial imbalance can disrupt digestive processes, nutrient absorption, and overall gut health.
Dr. Axe explains that SIBO is often misdiagnosed as IBS (Irritable Bowel Syndrome) due to the similarity of symptoms, yet it requires a specific approach to treatment. Unlike the large intestine, the small intestine should have relatively few bacteria. When excessive bacteria colonize this area, they can ferment carbohydrates and produce gas, leading to uncomfortable symptoms.
Common Symptoms of SIBO
According to Dr. Axe, SIBO symptoms can include:
- Abdominal bloating and distension
- Excessive gas and flatulence
- Abdominal pain and cramping
- Diarrhea or constipation (or alternating between both)
- Nutritional deficiencies
- Food sensitivities
- Fatigue
- Brain fog
- Skin issues
Dr. Axe notes that many of these symptoms overlap with other digestive disorders, making proper diagnosis essential before beginning treatment.
Dr. Axe’s Two-Phase Dietary Approach to SIBO
Dr. Axe recommends a two-phase dietary approach to treating SIBO naturally, which helps to starve harmful bacteria while promoting healing of the gut lining.
Phase 1: FODMAP Elimination Diet (2 Weeks)
The first step in Dr. Axe’s SIBO treatment protocol involves eliminating FODMAP foods for two weeks. FODMAPs (Fermentable Oligosaccharides, Disaccharides, Monosaccharides, and Polyols) are types of carbohydrates that aren’t fully absorbed in the digestive tract and can ferment, feeding the bacteria that contribute to SIBO.
As Dr. Axe explains on his website, “To get started ridding your small intestine of bacteria overgrowth, start with a FODMAP elimination diet for two weeks” [1]. This approach helps to reduce bacterial fermentation and gives the gut a chance to begin healing.
Foods to Avoid During FODMAP Elimination:
| FODMAP Category | Foods to Avoid |
|---|---|
| Fructose | High-fructose fruits, fruit juices, honey, high-fructose corn syrup, maple syrup, processed sugars |
| Lactose | Conventional dairy and processed products with dairy |
| Fructans | Wheat, garlic, onion, asparagus, leeks, artichokes, broccoli, cabbage |
| Galactans | Legumes, cabbage, Brussels sprouts, soy |
| Polyols | Artificial sweeteners like sorbitol, xylitol, erythritol (found in sugar-free products) |
Foods to Enjoy During Phase 1:
Dr. Axe recommends focusing on easily digestible, nutrient-dense foods during this phase, including:
- Pineapple (contains digestive enzymes)
- Bananas (help with digestion and energy)
- Carrots and cucumbers
- Leafy greens
- Squash
- Quinoa
- Sprouted nut butters
Dr. Axe emphasizes the importance of dietary diversity even during this restrictive phase: “Don’t get in a rut eating only certain foods during this first phase; be as diverse as possible” [1].
Phase 2: The GAPS Diet Protocol
After the initial two-week FODMAP elimination, Dr. Axe recommends transitioning to the GAPS (Gut and Psychology Syndrome) diet. According to Dr. Axe, “By eliminating FODMAPS from your diet for two weeks, and then transitioning to the GAPS diet and protocol, you can start the healing process and be well on your way to killing the bacteria causing your SIBO symptoms” [1].
The GAPS diet, developed by Dr. Natasha Campbell-McBride, focuses on healing the gut lining, rebalancing gut bacteria, and preventing toxins from entering the bloodstream. This approach helps to further address the root causes of SIBO while promoting overall digestive health.
Dr. Axe recommends incorporating organic coconut oil during this phase, explaining: “According to the Mayo Clinic, medium-chain triglycerides are easier to digest for people with blind loop syndrome” [1]. The medium-chain fatty acids in coconut oil are particularly beneficial for those with digestive issues.
Key Supplements in Dr. Axe’s SIBO Protocol
In addition to dietary changes, Dr. Axe emphasizes the importance of targeted supplementation to address bacterial overgrowth, heal the gut lining, and replenish nutrients that may be deficient due to SIBO.
1. Probiotics: The Foundation of Gut Health
Dr. Axe places particular emphasis on probiotics for SIBO treatment. He references a study in which probiotics showed an 82% improvement rate compared to only 52% for those treated with antibiotics [1]. This research supports the use of specific probiotic strains to combat SIBO effectively.
Dr. Axe recommends probiotics containing beneficial strains such as:
- Lactobacillus casei
- Lactobacillus plantarum
- Streptococcus faecalis
- Bifidobacterium brevis
For those with more advanced SIBO, soil-based organisms (SBOs) may be more beneficial. These include probiotic formulations specifically designed to survive stomach acid and reach the intestines intact. Dr. Axe’s website mentions several soil-based probiotic options that can be particularly effective for SIBO [2].
2. Herbal Antimicrobials
Dr. Axe supports the use of herbal antimicrobials as a natural alternative to conventional antibiotics for SIBO treatment. Research has shown that certain herbal formulations can be as effective as pharmaceutical antibiotics like rifaximin for reducing bacterial overgrowth.
Key herbal antimicrobials recommended in Dr. Axe’s protocol include:
Oregano Oil
Dr. Axe highlights oregano oil as a powerful natural antimicrobial: “A 2014 study published in Global Advances in Health & Medicine found evidence that use of herbal antimicrobials is just as effective as the antibiotic usually given for the treatment of SIBO” [3].
Oregano oil contains compounds like carvacrol and thymol, which exhibit strong antibacterial properties against many of the microbes involved in SIBO.
Berberine Extract
Found in plants like goldenseal and Oregon grape, berberine has potent antimicrobial properties that can help reduce bacterial overgrowth in the small intestine.
Garlic (Allicin)
Garlic contains allicin, which has powerful antimicrobial effects particularly effective against methane-producing bacteria often present in SIBO. Dr. Axe often recommends supplements containing stabilized allicin for maximum effectiveness.
Other Beneficial Herbs
Dr. Axe also mentions several other herbs that can be beneficial for treating SIBO:
- Wormwood oil
- Lemon balm oil
- Indian barberry root extract
3. Essential Oils
Dr. Axe frequently discusses the benefits of essential oils for digestive health, including SIBO treatment. According to his website, “In addition to dietary changes and supplements, the use of essential oils has been shown to be helpful for people with SIBO symptoms” [1].
Key essential oils in Dr. Axe’s SIBO protocol include:
- Oregano oil
- Tarragon oil
- Frankincense oil
- Clove oil
When using essential oils for SIBO, Dr. Axe emphasizes the importance of using only high-quality, food-grade oils. He suggests adding a drop or two to water before meals to help reduce bloating and gas.
4. Digestive Enzymes
To support proper digestion and reduce the burden on the digestive system, Dr. Axe recommends incorporating digestive enzymes. These help break down food more efficiently, reducing the chance that undigested particles will feed bacterial overgrowth.
5. Nutrient Supplementation
SIBO often leads to nutritional deficiencies due to malabsorption issues. Dr. Axe recommends supplementing with key nutrients that are commonly deficient in SIBO patients:
| Nutrient | Function | Food Sources |
|---|---|---|
| Vitamin B12 | Supports energy production and nervous system function | Grass-fed beef, wild-caught salmon |
| Iron | Essential for oxygen transport and energy | Spinach, grass-fed beef, lentils |
| Vitamin D | Immune function and inflammation regulation | Sunlight, fatty fish, egg yolks |
| Magnesium | Muscle function and enzyme reactions | Dark leafy greens, nuts, seeds |
| Zinc | Immune support and tissue repair | Pumpkin seeds, grass-fed beef |
| Fat-soluble vitamins (A, E, K) | Various essential functions | Leafy greens, colorful vegetables, healthy oils |
The Elemental Diet: An Advanced Approach for Stubborn SIBO
For those with severe or resistant SIBO, Dr. Axe discusses the benefits of the elemental diet as a more aggressive approach. The elemental diet uses pre-digested nutrients in liquid form to provide essential nutrition while giving the digestive system a rest.
According to Dr. Axe, “Elemental diets are an alternative to medications and herbal treatments like rifaximin or herbal antimicrobials (such as oregano oil) that are used to treat digestive problems, including SIBO” [4].
This approach typically involves consuming specially formulated elemental products that contain:
- Amino acids (protein in pre-digested form)
- Simple carbohydrates
- Essential fats
- Vitamins and minerals
The elemental diet can be followed exclusively (consuming only elemental formulas) or as a semi-elemental approach (supplementing with some whole foods). Dr. Axe notes that this decision should be based on symptom severity and made in consultation with a healthcare provider.
While effective, Dr. Axe considers the elemental diet an advanced strategy: “Even though it can be very beneficial, overall the elemental diet is considered by many to be an ‘aggressive approach’ to restoring digestive health” [4].
Lifestyle Modifications to Support SIBO Healing
Beyond dietary changes and supplementation, Dr. Axe emphasizes several lifestyle factors that can support SIBO treatment and prevent recurrence.
1. Meal Timing and Size
Dr. Axe recommends consuming smaller, more frequent meals to support digestion: “My first recommendation to overcome SIBO is to consume smaller amounts of food during meals. Spread your meals out at 5–6 smaller portions per day rather than 3 larger meals” [1].
This approach helps prevent overloading the digestive system and gives the body adequate time to process food properly.
2. Proper Chewing and Eating Habits
Thorough chewing is essential for proper digestion, as it initiates the breakdown of food and signals the body to prepare digestive enzymes. Dr. Axe emphasizes that “digestion starts in the mouth” and recommends chewing each bite thoroughly [1].
3. Stress Management
Chronic stress can significantly impact digestive function and contribute to SIBO symptoms. Dr. Axe recommends incorporating stress-reduction practices such as:
- Yoga
- Meditation
- Regular exercise
- Acupuncture
- Adequate sleep
4. Hydration
Proper hydration supports all bodily functions, including digestion. Dr. Axe recommends drinking plenty of fresh water throughout the day to maintain hydration and support the body’s natural detoxification processes.
Preventing SIBO Recurrence
SIBO has a high recurrence rate, making prevention strategies an essential part of Dr. Axe’s approach. To prevent SIBO from returning after successful treatment, he recommends:
- Maintaining a diverse diet rich in whole, unprocessed foods
- Regular probiotic supplementation to maintain healthy gut flora
- Supporting healthy gut motility through diet and lifestyle
- Addressing underlying causes such as low stomach acid or structural issues
- Periodic gut health maintenance using herbs and supplements as needed
Dr. Axe’s Comprehensive SIBO Healing Timeline
Based on Dr. Axe’s recommendations, here is a general timeline for treating SIBO naturally:
| Phase | Duration | Key Components |
|---|---|---|
| Initial FODMAP Elimination | 2 weeks | Remove all FODMAP foods; focus on easily digestible options |
| GAPS Diet Transition | 4-8 weeks | Introduce GAPS protocol; incorporate healing foods and supplements |
| Herbal Antimicrobial Treatment | 4-6 weeks | Use oregano oil, berberine, garlic, and other antimicrobials |
| Gut Repair Phase | 4-8 weeks | Focus on gut-healing supplements like L-glutamine, probiotics |
| Maintenance | Ongoing | Diverse whole foods diet, periodic supplementation as needed |
This timeline may vary based on individual needs and the severity of SIBO symptoms. Dr. Axe emphasizes the importance of personalized treatment and working with a qualified healthcare practitioner.
Frequently Asked Questions About Natural SIBO Treatment
Can SIBO be completely cured with natural methods?
According to Dr. Axe, SIBO can be effectively addressed with natural methods, but he prefers not to use the term “cure.” Instead, he focuses on managing symptoms and creating an environment in the gut where beneficial bacteria thrive and harmful bacteria are kept in check. Natural approaches can be very effective, especially when combined with lifestyle changes that address the root causes of bacterial overgrowth [1].
How long does it typically take to treat SIBO naturally?
The timeline for treating SIBO naturally varies depending on the severity of the condition and individual factors. Dr. Axe’s protocol typically involves an initial 2-week FODMAP elimination period followed by transition to the GAPS diet for several weeks or months. Most people begin to see improvement within the first month, but complete resolution may take 3-6 months of consistent treatment, especially for cases of chronic SIBO [1][4].
Is it necessary to follow all aspects of Dr. Axe’s protocol, or can I pick and choose?
Dr. Axe recommends a comprehensive approach to treating SIBO that addresses both the bacterial overgrowth and the underlying causes. While some people may experience improvements with partial implementation, the best results typically come from following the complete protocol. If the full protocol feels overwhelming, Dr. Axe suggests starting with dietary changes and gradually incorporating supplements and lifestyle modifications [1].
Are probiotics always beneficial for SIBO, or can they make it worse?
Dr. Axe acknowledges that not all probiotics are beneficial for everyone with SIBO. While his research indicates that certain strains can be highly effective, he recommends starting with soil-based organisms or specific SIBO-friendly probiotic strains. The timing of probiotic introduction is also important—some people may need to reduce bacterial overgrowth with antimicrobials before introducing probiotics [1][2].
How can I prevent SIBO from recurring after treatment?
SIBO has a high recurrence rate, so prevention strategies are essential. Dr. Axe recommends maintaining a diverse diet rich in whole foods, continuing with periodic probiotic supplementation, addressing any underlying causes (such as low stomach acid or motility issues), and implementing lifestyle changes that support gut health. Regular check-ins with a healthcare provider can help monitor and maintain progress [1].
Conclusion
Dr. Axe’s natural approach to treating SIBO focuses on addressing both symptoms and root causes through a comprehensive protocol that includes dietary modifications, herbal antimicrobials, targeted supplementation, and lifestyle changes. By following this holistic approach, many individuals can effectively manage SIBO and restore gut health without relying solely on conventional antibiotics.
While natural treatment may take longer than pharmaceutical approaches, Dr. Axe emphasizes that addressing the underlying imbalances is essential for long-term relief and prevention of recurrence. With patience, consistency, and proper guidance, SIBO can be successfully managed using the natural methods outlined in this comprehensive guide.
As with any health condition, it’s important to work with a qualified healthcare practitioner who can provide personalized guidance and monitor your progress throughout the SIBO treatment journey.
References:
[1] Dr. Axe. “SIBO Symptoms: Do You Know If You Have SIBO?” https://draxe.com/health/sibo-symptoms/
[2] Dr. Westin Childs. “8 Step SIBO Protocol: Diet Guide, Treatment, Supplements & More” https://www.restartmed.com/sibo/
[3] Dr. Axe. “Oregano Oil Benefits and How to Use” https://draxe.com/essential-oils/oregano-oil-benefits/
[4] Dr. Axe. “Elemental Diet Benefits, Uses & Recipes + How to Follow It” https://draxe.com/nutrition/elemental-diet/
[5] Dr. Axe. “Leaky Gut Diet Plan: What to Foods to Eat, Avoid for Gut Health” https://draxe.com/health/leaky-gut-diet-treatment/
