Why SIBO Keeps Coming Back: Causes and Solutions

If you’ve battled SIBO (Small Intestinal Bacterial Overgrowth), you may have noticed that even after treatment, symptoms can return. Understanding the why behind SIBO recurrence is key to long-term relief!

Common Triggers of SIBO

Food Poisoning – Certain bacteria like Campylobacter, Salmonella, and E. coli can damage the gut lining and lead to bacterial overgrowth. These pathogens can release CDTB toxins, which may trigger autoimmune reactions and impair gut motility.

Maldigestion – When your body can’t properly digest and absorb nutrients, bacteria may thrive in the small intestine.

Low Stomach Acid – Adequate stomach acid is essential to kill off harmful bacteria. Low levels can be caused by zinc deficiency, dehydration, B6 deficiency, or medications.

Low Bile Production – Gallbladder removal or insufficient bile can prevent proper digestion of fats, creating an environment where bacteria can overgrow.

Motility Issues – The migrating motor complex (MMC) acts like a broom, sweeping the small intestine when you’re fasting. Impaired motility, often due to low serotonin, dysbiosis, or autoimmune nerve damage, increases the risk of SIBO.

Low Immunity / Secretory IgA – helps control bacterial populations in the gut. Low IgA levels can make you more prone to overgrowth.

Structural Issues – Surgical adhesions, endometriosis, or scar tissue can create pockets in the intestines where bacteria accumulate.

Dietary Factors – Very restrictive or plant-based diets lacking certain amino acids can reduce bile production and nutrient availability needed to regulate gut bacteria.

Autoimmunity and SIBO

Recurring SIBO may be linked to autoimmune processes. Bacterial toxins like CDTB can trigger molecular mimicry, where your immune system creates antibodies that mistakenly attack your own proteins, such as vinculin, a key component in the gut’s pacemaker cells (interstitial cells of Cajal). These cells regulate the MMC, so damage can slow gut motility, leading to recurrent SIBO or IBS-like symptoms.

Testing for anti-CDTB and anti-vinculin antibodies (e.g., through IBS Smart testing) can help identify if autoimmune activity is contributing to recurring SIBO.

Supporting Your Gut: Functional Nutrition and Lifestyle Strategies

Start with building before killing – Work on gut healing, motility, and immune support before aggressive antimicrobial treatments. This can take several weeks but is critical for lasting results.

Support stomach acid – Adequate hydration, zinc, sodium, and B6 can help optimize acid production.

Support bile flow – Ensure enough protein and amino acids in your diet, and consider working with a practitioner if you’ve had a gallbladder removal.

Balance minerals – Potassium, magnesium, and other minerals are critical for gut and enzyme function.

Motility support – Intermittent fasting (3–4 hours between meals), supplementation with 5-HTP, tryptophan, or melatonin, and gentle movement can improve MMC activity.

Immune support – Work on supporting secretory IgA and overall immune resilience to prevent bacterial overgrowth.

Address structural concerns – Scar tissue, adhesions, and post-surgical changes may require hands-on therapies or physical intervention to restore optimal gut function.

Takeaway

Recurring SIBO isn’t just about killing bacteria; it’s about addressing underlying causes like motility issues, low stomach acid, nutrient deficiencies, immune imbalances, structural problems, and autoimmune triggers. By supporting the gut, hormones, and immune system through functional nutrition and lifestyle interventions, you can reduce the likelihood of SIBO coming back and improve overall gut health.