Small Intestinal Bacterial Overgrowth (SIBO) is one of the most commonly diagnosed gut disorders today. If you’ve been struggling with bloating, gas, constipation, diarrhea, or food intolerances—and you’ve been told you have SIBO—you may feel stuck in a cycle of treatments that don’t seem to work long-term. The frustrating reality is that SIBO is not the root cause—it’s a symptom of deeper gut dysfunction.
If you’re tired of dealing with recurring SIBO, this guide will help you understand why SIBO keeps coming back and how to address it for good.
What is SIBO?
SIBO occurs when bacteria that normally reside in the large intestine overgrow in the small intestine. Since the small intestine is not designed to house large amounts of bacteria, this overgrowth leads to fermentation of food, gas production, bloating, and malabsorption of nutrients. SIBO is often linked to IBS, with research suggesting that up to 80% of IBS cases may be associated with SIBO (1).
Common symptoms of SIBO include:
- Bloating (often worse after meals)
- Excessive gas
- Constipation, diarrhea, or both
- Food intolerances (especially to fermentable carbohydrates)
- Fatigue and brain fog
- Nutrient deficiencies (such as B12 and iron)
How is SIBO Diagnosed?
SIBO is typically diagnosed using a breath test that measures hydrogen and methane gas levels after consuming lactulose or glucose. These gases are produced when bacteria ferment carbohydrates in the small intestine.
Limitations of Testing:
- Breath tests can produce false positives or negatives depending on the test substrate used (2).
- Hydrogen sulfide SIBO (a third type of SIBO) is not always detected on standard breath tests, but the Trio Smart test is the best way to test for all three SIBO gases.
- Some cases of intestinal dysbiosis (imbalance in gut bacteria) may mimic SIBO symptoms, leading to misdiagnosis.
Common SIBO Treatments & Why They Fall Short
Conventional Approach: Antibiotics
Doctors often prescribe antibiotics like:
- Rifaximin (most commonly used for hydrogen-dominant SIBO)
- Neomycin + Rifaximin (for methane-dominant SIBO)
- Flagyl (Metronidazole) (occasionally used for certain cases)
Why Antibiotics Often Fail
- High recurrence rate: Studies show that up to 50% of people relapse within a year after antibiotic treatment (3).
- Doesn’t address root causes: Antibiotics wipe out bacteria, but they don’t fix motility, digestion, or bile flow—issues that cause SIBO in the first place.
- Can deplete beneficial gut bacteria, making future overgrowth even more likely (4).
Herbal Approaches to SIBO
Many people turn to herbal antimicrobials such as:
- Berberine
- Oregano oil
- Neem
- Allicin (garlic extract for methane SIBO)
- Combination herbal products like Candibactin AR/BR and Dysbiocide
Why Herbs Alone Aren’t Enough
- They can also kill beneficial bacteria, increasing the risk of recurrence.
- Herbs don’t restore motility, bile flow, or stomach acid.
- People often self-treat without a clear plan, leading to long cycles of antimicrobial use without resolution.
Why SIBO is Just a Symptom—Not the Root Cause
If antibiotics or herbs alone worked, SIBO wouldn’t relapse so frequently. The real issue isn’t the bacteria—it’s what allowed them to overgrow in the first place.
Think of it this way: If your house floods, you don’t just keep mopping up the water. You find and fix the leak.
Risk Factors for SIBO
Certain conditions increase the likelihood of developing SIBO by impairing digestion, slowing gut motility, or altering microbial balance:
- Head trauma & brain injuries – Can disrupt the gut-brain connection and slow motility.
- Chronic stress – Suppresses digestive function and slows motility.
- Gallbladder removal – Reduces bile flow, which is naturally antimicrobial.
- Slow gut motility – Bacteria sit too long in the small intestine, leading to fermentation and overgrowth.
- Hypothyroidism – A major cause of slow gut motility.
- Post-infectious IBS – Damage from food poisoning or infections can alter gut function.
- Frequent antibiotic use – Disrupts the gut microbiome and can encourage bacterial migration into the small intestine.
- Structural issues – Adhesions from surgery, endometriosis, or trauma can impair motility.
The gutTogether Method for Addressing SIBO
1. Assess – Fully Understand Where the SIBO is Coming From
- Utilize a combination of thorough assessment, pattern analysis, and functional testing.
- None of these alone are adequate, which is why using all three together is so important.
- We cannot just treat a test—knowing why SIBO developed in the first place is crucial.
2. Intervene Using the Trio of Nutrition, Lifestyle, and Supplements
- None of these alone are enough—think of a three-legged stool; if one leg is missing, the entire thing falls over.
- Foundation first:
- Motility: Get bowels moving regularly to prevent bacteria from stagnating. Motility is one of the biggest root causes of SIBO—when food and waste move too slowly through the digestive tract, bacteria have more opportunity to overgrow in the small intestine. The migrating motor complex (MMC), which acts as a ‘housekeeping wave’ to clear bacteria from the small intestine, is often impaired in SIBO cases. Supporting motility through prokinetics, meal spacing, and nervous system regulation is critical for long-term resolution.
- Blood Sugar: Balance blood sugar to support digestive function. Chronically imbalanced blood sugar can contribute to nerve damage, which affects gut motility. When nerves controlling digestion are impaired—often seen in conditions like diabetes or chronic blood sugar swings—the migrating motor complex (MMC) does not function properly, increasing the risk of bacterial overgrowth in the small intestine.
- Nervous System Support: Regulate the nervous system (stress and gut function are deeply connected). Chronic stress and blood sugar imbalances can damage the nerves that control digestion, slowing gut motility and impairing the migrating motor complex (MMC). This disruption can create the perfect environment for bacterial overgrowth. Engaging in daily nervous system regulation practices—such as breathwork, vagus nerve stimulation, and mindfulness techniques—can help restore proper gut function and prevent SIBO recurrence.
- Build Resilience in the body: Address foundational lifestyle factors like sleep and stress management before undertaking an aggressive “kill” protocol. If the body is not ready—if digestion, motility, and nervous system function are compromised—it can be extremely difficult to push out infections. The immune system, detox pathways, and gut lining must be supported first, or the body may struggle to eliminate bacteria effectively, leading to persistent symptoms and recurrence. This is why building resilience and restoring foundational health is essential before targeting overgrowths.
- Support digestion at the root:
- Stomach acid production: Stomach acid is essential for killing off pathogens before they reach the small intestine. It also helps break down proteins and signals the release of digestive enzymes. Low stomach acid can allow bacteria to survive and overgrow, contributing to SIBO.
- Digestive enzymes: These enzymes are crucial for breaking down carbohydrates, proteins, and fats properly. Without them, undigested food particles can ferment in the small intestine, feeding bacterial overgrowth and worsening symptoms.
- Bile flow support: Bile, produced by the liver and stored in the gallbladder, has natural antimicrobial properties that help prevent bacterial overgrowth. Poor bile flow, often due to gallbladder removal or sluggish liver function, can contribute to SIBO recurrence.
3. Prevention – Stop the SIBO Recurrence Cycle
- Once you understand your personal root causes, you can prevent SIBO from coming back.
- You don’t have to become another statistic—50% relapse within a year because they only treated the bacteria, not the cause.
- Sustainable relief comes from knowing exactly what to do:
- Nutrition: Eating in a way that supports digestion and gut motility, which does not include an elimination diet but instead incorporates a wide variety of plant foods to nourish a diverse microbiome.
- Lifestyle: Maintaining sustainable daily habits that keep your gut functioning well long-term, ensuring that changes are practical and achievable for lasting gut health.
- Supplements (if needed): Using targeted support based on your individual needs. Supplements can play a crucial role in maintaining gut motility, supporting bacterial diversity, and preventing SIBO recurrence.
- Examples include (this is where working with a practitioner on your individual root causes and needs can help you create a personalized plan):
- Motility Support: Prokinetics such as ginger, 5-HTP, triphala, etc. help stimulate the migrating motor complex (MMC) to keep bacteria moving in the right direction.
- Bile Flow Support: Ox bile, dandelion root, and artichoke extract promote bile production and flow, which is antimicrobial and prevents bacterial overgrowth in the small intestine.
- Microbiome Diversity: Prebiotics (like partially hydrolyzed guar gum and resistant starch) and polyphenol-rich supplements help feed beneficial bacteria and encourage a diverse microbiome, making it harder for SIBO to return. Prebiotics can be consumed through food and/or supplementation.
- Digestive Support: HCl, digestive enzymes, and bitters improve digestion and reduce fermentation in the small intestine, limiting bacterial overgrowth opportunities.
- Nervous System Regulation: Magnesium, L-theanine, and adaptogens like ashwagandha help manage stress and support the gut-brain axis, which is key for maintaining healthy motility and digestion.
- Examples include (this is where working with a practitioner on your individual root causes and needs can help you create a personalized plan):
If we can maintain motility, proper bile flow, and microbial diversity, we can prevent SIBO from returning and support a healthier gut long-term.
Life After SIBO: What to Expect
Successfully addressing SIBO means not only eliminating the overgrowth but also restoring balance to your digestion, metabolism, and overall gut health. Here’s what life can look like after SIBO when you’ve addressed the root causes:
- Improved Digestion – Less bloating, gas, and discomfort after meals. Your body can properly break down and absorb nutrients.
- More Food Freedom – With a diverse and well-balanced gut microbiome, you may find that you tolerate a wider variety of foods, including fiber-rich and fermentable plant foods.
- Consistent Energy and Mental Clarity – Without bacterial fermentation causing inflammation and fatigue, you may experience better energy levels and sharper focus.
- Regular, Predictable Bowel Movements – Supporting motility and digestion helps keep your bowels moving efficiently, preventing constipation and diarrhea.
- Sustainable Gut Health – Instead of cycling through restrictive diets or repeated treatments, you now have the knowledge and tools to maintain your gut health long-term.
When SIBO is no longer controlling your life, you can enjoy food, feel comfortable in your body, and trust that your digestive system is working as it should.
Struggling with SIBO That Keeps Coming Back?
The gutTogether program® is designed to get to the root cause of your gut issues so you can stop the cycle of bloating, discomfort, and food restrictions. Apply for 1:1 support today and let’s build a plan tailored to your body.
