SIBO Solutions: Functional Medicine’s Answer to Digestive Health

January 16, 2025

What is Sibo?

Small Intestinal Bacterial Overgrowth (SIBO) is a condition where bacteria that normally reside in the large intestine migrate to the small intestine, where their presence and activity can disrupt digestion and absorption of nutrients. While the small intestine naturally contains some bacteria, an overgrowth can lead to a host of digestive and systemic symptoms, affecting quality of life and overall health.

SIBO is often underdiagnosed and misdiagnosed because its symptoms overlap with other digestive disorders like Irritable Bowel Syndrome (IBS). However, addressing SIBO directly can lead to significant improvements in health and well-being.

Signs and Symptoms of SIBO

SIBO presents with a wide range of symptoms that may vary in severity and frequency. Common symptoms include:

Digestive Distress: Persistent bloating, excessive gas, and discomfort after meals are hallmark signs. Diarrhea, constipation, or alternating patterns are also common.
Abdominal Pain: Cramping or discomfort, particularly after eating.
Food Intolerances: Many individuals develop sensitivity to fermentable carbohydrates (FODMAPs), which can exacerbate symptoms.
Nutritional Deficiencies: Chronic SIBO can impair nutrient absorption, leading to deficiencies in vitamins like B12, A, D, E, and K, as well as minerals like magnesium and iron.
Skin Issues: Conditions such as acne, eczema, or rosacea may be linked to SIBO due to systemic inflammation or immune response.
Cognitive Symptoms: Brain fog, fatigue, and poor concentration are common due to the gut-brain connection and potential endotoxin release from bacteria.

Less common symptoms include:

Unintentional weight loss or gain.
Bad breath (halitosis) due to gas production in the gut.
Symptoms of systemic inflammation, such as joint pain or low-grade fever.

How to Test for SIBO

Accurate diagnosis of SIBO is essential for effective treatment. Common testing methods include:

Breath Testing:

This is the most widely used and non-invasive method. The patient consumes a sugar solution (lactulose or glucose), and their breath is monitored over time for hydrogen and methane gases, which are produced by bacterial fermentation in the small intestine. Elevated gas levels indicate SIBO. Preparation is critical for accurate results, as dietary choices and transit time can affect gas production measurements. False negatives may occur if bacteria are localized in certain areas of the small intestine, underscoring the importance of interpreting results in a clinical context.

Pros: Non-invasive, convenient, and widely available.
Cons: Results can vary based on preparation and interpretation, and it may not differentiate between hydrogen-dominant, methane-dominant, or hydrogen sulfide-producing SIBO.

Small Intestinal Aspirate and Culture:

This invasive test involves collecting a fluid sample from the small intestine during an endoscopy and culturing it to measure bacterial growth.

Pros: Considered the gold standard for diagnosis.
Cons: Expensive, invasive, and not commonly performed outside of specialized centers.

Emerging Testing Methods:

Advances in microbiome analysis may allow for stool testing and more accurate assessments of bacterial overgrowth in the near future. These tests are still experimental but hold promise for broader diagnostic options.

Potential Root Causes of SIBO

Understanding the underlying causes of SIBO is critical for effective treatment and prevention of recurrence. Common root causes include:

1. Impaired Gut Motility:

The small intestine relies on coordinated muscular contractions, known as peristalsis, to move food and bacteria through the digestive tract. Conditions like gastroparesis, diabetes, and hypothyroidism can disrupt this process, leading to stagnation and an environment where bacteria can overgrow.
The migrating motor complex (MMC), a cleansing wave of activity that occurs during fasting, plays a crucial role in preventing bacterial accumulation. Stress, poor diet, or lack of fasting periods can impair the MMC, further increasing the risk of SIBO.
Conditions like gastroparesis, diabetes, hypothyroidism, or stress can slow intestinal motility, allowing bacteria to accumulate.

2. Low Stomach Acid:

Stomach acid plays a crucial role in maintaining gut health by killing bacteria before they reach the small intestine, acting as the first line of defense against microbial overgrowth. Conditions like hypochlorhydria (low stomach acid) or the use of proton pump inhibitors (PPIs) significantly compromise this protective mechanism. When stomach acid levels are insufficient, bacteria that should be eliminated can survive and proliferate, increasing the risk of overgrowth in the small intestine. Low stomach acid can also impair the breakdown of food, leading to incomplete digestion, fermentation in the gut, and symptoms like bloating and gas.

3. Structural Abnormalities:

Physical changes to the anatomy of the gut can create pockets or slow down movement, allowing bacteria to colonize areas where they don’t belong. Post-surgical changes, such as those following gastric bypass or bowel surgeries, can alter the gut’s natural flow.
Diverticula, which are small pouches in the intestinal wall, can trap food particles and bacteria, creating a breeding ground for overgrowth.
Adhesions (scar tissue) from surgeries or infections can restrict the normal movement of the intestines, compounding the risk of SIBO.

4. Immune Dysregulation:

The immune system plays a vital role in keeping bacterial populations in check throughout the digestive tract. Chronic illnesses such as autoimmune diseases (e.g., lupus, rheumatoid arthritis) or conditions like HIV can weaken the immune response, increasing susceptibility to bacterial overgrowth.
Frequent infections, prolonged use of immunosuppressive drugs, or chronic stress can also impair immune function, leaving the gut vulnerable to SIBO.
Gut-associated lymphoid tissue (GALT), a critical component of the gut’s immune defense, can become compromised, reducing its ability to regulate bacterial levels effectively.

5. Dietary Factors:

Diets high in sugar and refined carbohydrates provide an easily fermentable fuel source for bacteria, encouraging overgrowth. Processed foods often lack the fiber needed to maintain a healthy gut microbiome, further exacerbating imbalances.
Frequent snacking or grazing prevents the gut from entering fasting states, which are essential for activating the migrating motor complex (MMC) and clearing bacteria. Late-night eating can also disrupt the natural circadian rhythm of the gut, impairing its cleansing processes.
Diets low in diversity and rich in pro-inflammatory foods (e.g., fried foods, artificial additives) can lead to dysbiosis, setting the stage for SIBO.

A Functional Medicine Approach to SIBO

Functional medicine takes a personalized and root-cause-focused approach to SIBO. Key steps include:

1. Antimicrobial Protocols:

Herbal antimicrobials such as oregano oil, berberine, allicin (garlic extract), and neem are effective alternatives to antibiotics for reducing bacterial overgrowth.
Combination therapy may target both hydrogen- and methane-producing bacteria.
It’s essential to work with a healthcare provider to tailor an antimicrobial regimen, as improper use can lead to imbalances, ineffectiveness, or resistance. Regular monitoring ensures the treatment targets the right bacterial overgrowth without disrupting the gut microbiome further.

2. Dietary Modifications:

A low-FODMAP diet can reduce symptoms by limiting fermentable carbohydrates that feed bacteria. This is often combined with antimicrobial treatments for maximum efficacy.
Transition to a nutrient-dense, anti-inflammatory diet that supports gut healing after the initial treatment phase.

3. Prokinetics:

Natural and pharmaceutical prokinetics play a crucial role in maintaining proper gut motility and reducing the recurrence of SIBO.

Agents like ginger, known for its natural motility-enhancing properties, can help stimulate the migrating motor complex (MMC), which clears bacteria from the small intestine during fasting periods. Ginger is easily incorporated through teas or supplements and is generally well-tolerated.
Motilins, a category of medications that mimic the natural gut hormone motilin, stimulate smooth muscle contractions to promote food and bacteria movement through the small intestine. They are often prescribed for individuals with severe motility issues.
Low-dose naltrexone (LDN), originally used for other conditions, has gained popularity for its ability to modulate the nervous system and enhance motility. It also has anti-inflammatory benefits, which can support gut healing in chronic SIBO cases.
The key is to tailor prokinetic therapy to individual needs, ensuring it complements other treatments like dietary adjustments and antimicrobial protocols, to provide lasting relief and prevent recurrence.

4. Gut Lining Support:

Supplements like L-glutamine, aloe vera, marshmallow root, and zinc carnosine play a critical role in repairing and strengthening the intestinal barrier, reducing inflammation, and promoting healing:

L-Glutamine:
- An essential amino acid that serves as fuel for the cells lining the intestines, promoting their repair and regeneration. It’s particularly effective in healing damage caused by inflammation or bacterial toxins, helping to restore gut integrity.
Aloe Vera:
- Known for its soothing and anti-inflammatory properties, aloe vera can calm irritation in the gut lining. It also provides mucilage, which forms a protective layer over the intestinal walls, aiding in the healing process.
Marshmallow Root:
- A natural herb rich in mucilage, marshmallow root helps coat and protect the gut lining while reducing irritation and inflammation. It also supports the repair of damaged intestinal tissues, making it beneficial in cases of leaky gut or SIBO-related inflammation.
Zinc Carnosine:
- A combination of zinc and carnosine that has been shown to enhance gut barrier function by promoting the repair of intestinal epithelial cells. It also reduces oxidative stress and inflammation, further supporting gut healing.
These supplements work synergistically to reduce inflammation, protect the gut lining from further damage, and rebuild the intestinal barrier. Incorporating them into a comprehensive treatment plan can accelerate recovery and improve gut health.

5. Addressing Low Stomach Acid:

Correcting low stomach acid with betaine HCl with pepsin, which can help restore proper stomach acid levels and improve digestion. Start with a low dose and increase gradually under guidance from a healthcare provider.
ACV may help improve digestion and support healthy stomach acid levels. It can be particularly beneficial for those with low stomach acid, a common contributor to SIBO. ACV’s acidity can restore a more favorable environment in the stomach, aiding in digestion and reducing bacterial overgrowth.
- How to Use: Dilute 1-2 teaspoons of raw, unfiltered ACV in 8 ounces of water and drink it 15-30 minutes before meals. Start slowly and monitor symptoms, as ACV might not be suitable for everyone.
- Cautions: Avoid ACV if you have active gastritis, ulcers, or a sensitive stomach. Always consult with a healthcare provider before introducing ACV into your regimen.
Supporting stomach acid production through dietary and lifestyle practices, such as:
- Eating smaller, balanced meals to avoid overwhelming the digestive system.
- Avoiding excessive water intake during meals to prevent dilution of stomach acid.
- Incorporating fermented foods like sauerkraut, kimchi, and apple cider vinegar into meals.
- Practicing stress management techniques, such as deep breathing or mindful eating, to stimulate gastric juices.

6. Treating Underlying Conditions

Addressing underlying conditions is an essential component of SIBO treatment, as these often contribute to its development and recurrence. Key areas of focus include:

Hypothyroidism: Hypothyroidism slows gut motility, increasing the risk of bacterial overgrowth. Managing thyroid function through appropriate medication and lifestyle interventions can improve motility and reduce SIBO recurrence.
- Action Steps:
  - Regularly monitor thyroid hormone levels (TSH, Free T3, Free T4) and optimize them with your healthcare provider.
  - Support thyroid health with nutrient-dense foods rich in iodine, selenium, and zinc.
  - Address stress and sleep issues, as these can negatively impact thyroid function.

Autoimmune Diseases: Autoimmune conditions can impair immune function and disrupt the gut’s natural defense mechanisms. Identifying and addressing triggers for autoimmune flares, such as infections, food intolerances, or chronic stress, can reduce the burden on the gut.
- Action Steps:
  - Work with a functional medicine provider to manage the specific autoimmune condition (e.g., Hashimoto’s thyroiditis, rheumatoid arthritis).
  - Adopt an anti-inflammatory diet, such as the Autoimmune Protocol (AIP), to reduce systemic inflammation.
  - Use gut-healing protocols to repair intestinal permeability, which is often a factor in autoimmune diseases.

Other Chronic Conditions: Conditions like diabetes, chronic stress, and IBS should be addressed as part of a comprehensive SIBO treatment plan.
- Action Steps:
  - Improve glycemic control in diabetes to support gut health and motility.
  - Incorporate stress-reduction techniques such as meditation or yoga.
  - Address overlapping conditions like IBS with a tailored diet and treatment plan.

7. Post-Treatment Gut Rebalancing:

Gradually reintroduce prebiotics and probiotics to encourage a healthy microbiome without triggering symptoms. Start with low doses of single-strain probiotics, such as Lactobacillus or Bifidobacterium species, and monitor your response. Introduce gentle prebiotics, like partially hydrolyzed guar gum or acacia fiber, to avoid overstimulating bacterial growth. Natural sources like small amounts of fermented foods (e.g., sauerkraut or yogurt) can also help. Keep a food and symptom journal to track progress and adjust as needed.

8. Advanced Supplementation

For patients requiring additional support, supplements like Biocidin, GI Detox+, and Olivirex may enhance the effectiveness of SIBO treatment protocols:

Biocidin: A botanical blend with antimicrobial and biofilm-disrupting properties, targeting resistant bacteria in the gut.
GI Detox+: Binds to endotoxins and harmful compounds, reducing die-off symptoms and supporting detoxification during antimicrobial therapy.
Olivirex: An immune-supportive botanical blend that addresses persistent infections, particularly for those unresponsive to initial treatments.

These supplements should be used under the guidance of a healthcare provider, particularly in complex or resistant cases of SIBO.

5. Conventional Medicine Approach to SIBO

Conventional medicine primarily focuses on managing symptoms and reducing bacterial overgrowth with:

1. Antibiotics:

Rifaximin is commonly prescribed for hydrogen-dominant SIBO due to its ability to target bacteria in the small intestine with minimal systemic absorption, reducing the risk of side effects. For methane-dominant SIBO, Neomycin is often added to address methane-producing archaea, as these organisms respond less effectively to Rifaximin alone. The combination of antibiotics can improve symptom resolution in mixed gas cases.
While antibiotics are effective in reducing bacterial overgrowth, they do not address the root causes of SIBO, such as impaired gut motility or low stomach acid. This limitation often leads to recurrence, particularly if no preventive measures, such as prokinetics, dietary changes, or addressing underlying conditions, are implemented. Additionally, repeated antibiotic use can alter the gut microbiome, potentially causing further dysbiosis or resistance over time.

2. Symptom Management:

Medications for diarrhea, constipation, or bloating may provide temporary relief by addressing symptoms like cramping, irregular bowel movements, or excessive gas. For example, antidiarrheal drugs like loperamide can slow gut motility, while laxatives or fiber supplements can assist with constipation. Simethicone-based products may help reduce bloating by breaking up gas bubbles. However, these medications do not address the underlying causes of SIBO, such as bacterial overgrowth, impaired motility, or low stomach acid.
Relying solely on symptom management can mask deeper issues, delaying proper diagnosis and treatment. While these medications can improve quality of life during acute flares, a comprehensive plan targeting root causes is necessary for lasting relief and gut health restoration.

Additional Tips for Managing SIBO

Chew Your Food Thoroughly: Proper chewing aids digestion and reduces the burden on your gut.
Intermittent Fasting: Allowing 12-16 hours between meals can activate the MMC and prevent bacterial accumulation.
Hydration and Electrolyte Balance: Adequate hydration supports gut motility and overall health.
Avoid Overeating: Large meals can overwhelm digestion and exacerbate symptoms.
Track Symptoms: Keeping a food and symptom journal can help identify triggers and monitor progress.

Conclusion

SIBO is a challenging condition that requires a comprehensive, individualized approach for lasting relief. Functional medicine addresses not only the bacterial overgrowth but also the underlying factors that contribute to its development and recurrence.

If you suspect you have SIBO or are struggling with persistent digestive symptoms, Resolve Medical is here to help. We specialize in personalized care plans to restore gut health and improve overall well-being. Schedule a free discovery call today to start your journey toward a healthier gut