Root Causes of SIBO: Why Treating the Symptoms Isn't Enough
- Dr. Rebecca Sand
- Apr 8
- 5 min read
Updated: Apr 16
Fun Fact: SIBO is almost always an ✨epiphenomenon✨ related to underlying conditions that disrupt the normal protective mechanisms of the small intestine
Small intestinal bacterial overgrowth — SIBO — is one of the most commonly misunderstood conditions in gut health. The name tells you what it is, but not why it happens. And without addressing the why, most people end up back where they started.
In a healthy gut, the small intestine is kept relatively sparse when it comes to bacteria. The vast majority of your 38 trillion or so gut microbes live downstream, in the large intestine. SIBO occurs when bacteria that belong in the colon migrate upward and take up residence in the small intestine — or when organisms already present in the small intestine proliferate far beyond their normal numbers.
The result: bloating, gas, abdominal pain, alternating constipation and diarrhea, nutrient deficiencies, and a general sense that your digestive system is working against you. But these are effects.
The real question — the one that determines whether you recover or relapse — is what broke down in the first place.
Cause 1: Impaired Migrating Motor Complex
The most under-appreciated driver of SIBO is a dysfunction in the migrating motor complex (MMC) — the "small intestine dishwasher" as Dr. Sand likes to say, that sweeps through your gut between meals. Think of it as a good wash through: every 90 minutes or so during a fasted state, a powerful wave of muscular contractions moves from the stomach down through the small intestine, flushing debris, dead cells, and any stray bacteria into the colon where they belong.
When the MMC is compromised, bacteria are no longer swept downstream. They accumulate. They ferment! Common disruptors include frequent snacking, hypothyroidism, diabetes, prior food poisoning, and chronic stress. Post-infectious SIBO — triggered by food poisoning — may account for as many as one in three cases, through an autoimmune mechanism that damages the intestinal nerve cells governing the MMC.
Cause 2: Low Stomach Acid (Hypochlorhydria)
Stomach acid is your first line of antimicrobial defense. At a pH of 1.5–3.5, healthy gastric acid is hostile to most microorganisms. When stomach acid production declines — through aging, chronic stress, H. pylori infection, or long-term use of proton pump inhibitors (PPIs) — that barrier weakens. Microbes that would normally be neutralized in the stomach survive to colonize the small intestine.
PPI use deserves particular attention. These medications are among the most widely prescribed in the world, and multiple studies have found a meaningful association between long-term PPI use and significantly elevated SIBO rates. This doesn't mean PPIs are always inappropriate — but the gut consequences should be part of any informed conversation about their long-term use.
Cause 3: Structural and Anatomical Abnormalities
Sometimes SIBO has a mechanical origin. Adhesions from prior abdominal or pelvic surgery, intestinal strictures from Crohn's disease or radiation therapy, diverticula, short bowel syndrome, endometriosis, and ileocecal valve dysfunction can all create conditions where bacteria accumulate and thrive. When the ileocecal valve — which separates the small and large intestine — becomes lax, colonic bacteria can backflow into the small intestine. In these cases, no amount of dietary intervention or antimicrobial treatment will produce lasting results without addressing the underlying structural problem.
One of the best supports for this is Visceral Manipulation, which both Dr. Sand and Dr. Emrick offer at their in-person practice, Open Wellness. These sessions allow us to use our hands to relieve intestinal restriction and provide immediate relief. We can also support "retraining" the bowels to learn more efficient and regular flow.
Cause 4: Immune Dysfunction and IgA Deficiency
Secretory IgA (sIgA) is an antibody produced throughout the gut lining that prevents bacteria from adhering to intestinal cells. Chronic stress, nutritional deficiencies, and inflammatory conditions can significantly reduce sIgA production. When levels drop, bacteria find it far easier to colonize the small intestine. This is one reason why SIBO and stress are so tightly linked — it's not just about motility. The immune dimension matters enormously.
Dr. Sand is a big fan of comprehensive microbiome assessments. These can often help us elucidate SIBO co-infections, like biofilm colonies.
Cause 5: Diet and Fermentable Substrates
A diet high in fermentable carbohydrates — particularly in the context of already-compromised motility — can feed bacterial populations in the small intestine. This is the basis of the low-FODMAP and Specific Carbohydrate Diets often used in SIBO management. But diet is rarely a root cause in isolation. Fermentable carbohydrates don't cause SIBO in a healthy gut — they cause problems when the structural and motility safeguards are already failing. Eliminating all FODMAPs may reduce symptoms, but it doesn't repair a sluggish migrating motor complex.
Cause 6: Systemic Conditions That Alter Gut Function
Several systemic diseases create the conditions under which SIBO can flourish, often by impairing motility, altering immune function, or disrupting the mucosal barrier. These include hypothyroidism, scleroderma, celiac disease, Ehlers-Danlos syndrome (EDS) or other hypermobility conditions, liver cirrhosis and bile acid insufficiency, and POTS/dysautonomia. If any of these underlying conditions are present and untreated, SIBO treatment is unlikely to produce lasting results.
Cause 7: Biofilms & Candida
Biofilms in the small intestine—complex communities of bacteria and fungi such as Candida albicans embedded in a protective extracellular matrix—can quietly drive persistent or recurrent SIBO. Because these microbes embed themselves in a protective matrix, they’re harder for the immune system or antimicrobials to clear, allowing them to stay attached to the gut lining and continue fermenting in the wrong place. Studies published in journals such as Gut Microbes and Clinical Gastroenterology and Hepatology show that organisms living inside biofilms can be far more tolerant to treatment, which helps explain why SIBO often relapses unless the underlying biofilm layer is addressed.
Why SIBO Keeps Coming Back
SIBO has a notoriously high recurrence rate. Studies suggest that within nine months of a successful course of antibiotic or herbal antimicrobial treatment, a significant proportion of patients relapse. This is not because the treatments fail — it's because the treatments address bacterial overgrowth without correcting whatever allowed the bacteria to overgrow in the first place.
Effective, lasting recovery from SIBO requires a layered approach: identifying and addressing motility impairment, supporting stomach acid production, investigating structural abnormalities, managing underlying systemic conditions, reducing the inflammatory and immune burden on the gut, and changing the eating patterns and lifestyle factors that keep the migrating motor complex suppressed. SIBO is often a symptom of a system under strain. The bacteria didn't take over because they're aggressive invaders — they expanded because the gut lost its ability to keep them in check. Restoring that capacity is the actual goal.
Dr. Sand's approach does all of this. As she says to her patients, we're in it for the long-haul! But it's worth it. SIBO does not have to be a life-long condition! Ultimately, Dr. Sand wants you eating normal food and enjoying food again - without the bloat!
Ready to investigate whether SIBO is driving your symptoms? Learn about our SIBO treatment approach.
Interested in learning more about what could be at the root of your digestive issues?
Dr. Sand specializes in identifying conditions complicating the SIBO picture.
Schedule a Meet & Greet with Dr. Sand to get started.
This post is for educational purposes and does not constitute medical advice. Consult with your local healthcare professional before starting or stopping any medication or supplement.
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