Understanding and Treating SIBO: A Gut Health Specialist’s Guide

Small Intestinal Bacterial Overgrowth, or SIBO, is a health condition in which bacteria that colonize other parts of the gastrointestinal tract, especially the large intestine, overpopulate the small intestine. Symptoms of SIBO may include bloating, abdominal pain, diarrhea, constipation, and nutrient malabsorption. Other less common symptoms of SIBO include brain fog, mood changes, joint pain, and headaches. SIBO is often a recurrent condition, especially when treated with antibiotics. Many patients with SIBO need multiple courses of antibiotics. Why is that? Treatment of SIBO needs an approach toward the overgrowth itself and, importantly, the underlying factors leading to its development. As a gut health specialist using a root cause-focused approach, it’s so important to discuss the importance of gut motility and holistic strategies that create true healing. The Challenges in Treating SIBO
SIBO can be quite complex and recidivistic. While overgrowth of bacteria seems to be a central problem, issues with gut motility, structural abnormalities, and general health conditions such as hypothyroidism need to be treated to establish long-term results.


Standard treatments like antibiotics often work short-term to diminish the load of bacteria. These medications can often disrupt the balance of the gut microbiome, leading to other imbalances and recurrence of symptoms. It is the dysbiosis itself that may promote the onset of SIBO, and treatment with antibiotics often improves the SIBO in the short term, while their disruption of the microbiome promotes dysbiosis, which may cause recurrent SIBO long-term. A comprehensive treatment strategy should address the root causes and prioritize restoring gut health.

The Role of Antibiotics in SIBO Treatment

Antibiotics, particularly rifaximin (commonly prescribed for SIBO), are often the first-line treatment. Rifaximin is a unique antibiotic because it stays primarily in the gut and has minimal systemic absorption, which reduces some risks of widespread microbiome disruption. However, it can still impact beneficial bacteria and may not address all types of bacterial overgrowth, especially if methane-producing archaea are involved.

Pros of Antibiotics in SIBO Treatment:

  • Rapid reduction of bacterial overgrowth.
  • Targeted action in the gut (rifaximin).
  • Disadvantages of Antibiotics:
  • Microbiome disruption causing dysbiosis
  • High recurrence rates if underlying causes are not addressed.
  • May not be effective for all types of SIBO (e.g., methane-dominant).

In most patients, antibiotics are not a long-term solution given as a single modality of treatment. The incorporation of microbiome restoration and the addressing of motility are important to prevent recurrence.

Anti-Microbial Herbs

There are several antimicrobial herbs which have been used for the treatment of SIBO. There have been studies showing that some of the herbal combinations were just as effective as the antibiotics. Some of these herbs include oregano, berberine, and wormwood. They function by reducing the bacterial load in a similar manner as antibiotics do. In this practice, we tend to favor the herbs over the rifaximin; however, the challenge of the underlying cause still exists with them also. Recurrences are common if the underlying condition is not resolved. Gut motility is the coordinated muscular contractions of the gut that move food and waste through the system. The MMC (migrating motor complex) is an impulse in the gut which helps clear the residual waste. It plays a critical role in sweeping bacteria and debris out of the small intestine between meals. Impaired motility is a key contributor to the development and recurrence of SIBO.

Common causes of impaired motility include:

  • IBS.
  • Vagal nerve dysfunction.
  • Hypothyroidism.
  • Stress and disrupted circadian rhythms.

Supporting Motility in SIBO Treatment

  1. Visceral manipulation is an osteopathic treatment. It is a gentle hands-on approach which helps remove fascial restrictions and mobilize organ motility. At Whole Gut Health this is a standard in SIBO treatment.
  2. Stress Management: Chronic stress disrupts gut motility. The introduction of stress-releasing practices, such as meditation, yoga, or mindfulness, could improve outcomes. We use a targeted mind body – energy-work treatment which helps target a person’s stress, old traumas, and emotional imbalances.
  3. Herbal Prokinetics: These are supplements that stimulate the MMC to improve gut motility. Common options include ginger, artichoke extract, or Iberogast.
  4. Meal Timing: Leaving 4-5 hours between meals, without snacking, gives the MMC optimal time to work.
  5. Vagal Nerve Stimulation: The vagus nerve can be stimulated through practices such as deep breathing, humming, and gargling to support motility.

A Holistic Approach to SIBO Treatment

For effective treatment of SIBO, dietary changes, microbiome support, and motility restoration should all be included.

  1. Dietary Strategies
    Dietary changes can alleviate symptoms and complement treatment. There is no single SIBO diet, but common strategies include the limitation or avoidance of inflammatory foods such as gluten and dairy products, along with high sugar foods. Raw food may often need to be limited in the short term to help reduce fermentation and bloating. It is important to ensure dietary changes are sustainable and nutritionally balanced.
  2. Microbiome Support
    Following SIBO treatment, restoration of gut microbiome balance is important to avoid recurrence and to maintain overall gut health. This includes:
    • Probiotics: Certain strains, like Lactobacillus rhamnosus and Bifidobacterium infantis, may help rebalance the microbiome. It is also beneficial to take soil-based probiotics.
    • Prebiotics: Gradually reintroducing prebiotic fibers such as inulin can support beneficial bacteria growth, but they should be introduced cautiously to avoid symptom flare-ups. As always food is medicine, and a nutritionally complete food is preferred to supplemental therapy.
  3. Addressing Underlying Causes
    Identifying and addressing the root causes of SIBO is crucial to preventing recurrence. Common steps include:
    • Treating hypothyroidism or other hormonal imbalances.
    • Resolving structural issues: adhesions or strictures of the small intestine.
    • Management of stress and sleep for the overall function of the gut.

The Role of Lifestyle in Long-Term SIBO Management

Treatment for SIBO is not about killing the bacteria; it’s about creating an environment where your gut can thrive. Lifestyle factors play a significant role in maintaining gut health and preventing recurrence:

  • Stress Management: Chronic stress can weaken the gut-brain connection, impair motility, and disrupt the microbiome. Implement daily practices such as meditation, journaling, or nature walks.
  • Physical Activity: Regular movement stimulates the digestive system and supports motility.
  • Sleep Hygiene: Prioritize quality sleep to support your body’s natural repair processes.

Integrative Therapies for SIBO
In addition to conventional treatments, integrative therapies can complement SIBO management:

  • Energy medicine may improve motility and reduce stress.
  • Osteopathic manipulative therapies, visceral manipulation, for example, facilitates motility.
  • Herbal Antimicrobials- oregano oil, berberine, and allicin may be alternatives for bacterial overgrowth with less side effect on the microbiome than conventional antibiotics.

Final Thoughts

SIBO requires a personalized and holistic approach to treatment. Though antibiotics, such as rifaximin, may alleviate symptoms, long-term success involves the restoration of gut motility and the nurturing of the microbiome. As a gut health specialist, I encourage patients to view SIBO treatment as an opportunity to improve not just their digestive health but their overall well-being.
If you’re struggling with SIBO or other gut health concerns, I’m here to help guide you through personalized strategies for lasting relief. Together, we can work toward a healthier, happier gut!

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