Understanding SIBO: Causes and Solutions

Small Intestinal Bacterial Overgrowth—better known as SIBO—is one of the most overlooked digestive issues today. Millions of people struggle with chronic bloating, gas, abdominal discomfort, and unpredictable digestion without ever realizing the root cause may be happening inside the first few feet of their small intestine.

Unlike the large intestine, which is designed to house trillions of bacteria, the small intestine should contain very few. When too many bacteria move in—or when the wrong species multiply—they begin fermenting food prematurely. That’s when symptoms begin.

Let’s break down what SIBO is, why it happens, and what you can do to naturally restore balance.

What Exactly Is SIBO?

SIBO occurs when bacteria overgrow in the small intestine, a place where food should be absorbed, not fermented. When bacteria show up where they don’t belong, they feed on carbs and fibers early in the digestive process, producing:

• excessive gas

• bloating that gets worse as the day goes on

• abdominal pain

• diarrhea, constipation, or a mix of both

• foul-smelling gas

• nutrient deficiencies (B vitamins, iron, fat-soluble vitamins)

It’s not about “bad” bacteria. It’s about bacteria in the wrong location.

Common Causes of SIBO

Slow Gut Motility

The small intestine relies on rhythmic muscle contractions, known as the migrating motor complex (MMC), to sweep bacteria downward. When motility slows, bacteria settle and multiply.

Reasons for slow motility include stress, hypothyroidism, diabetes, and previous gut infections.

Low Stomach Acid

Stomach acid acts like a gatekeeper—killing excess bacteria before they reach the small intestine. Low acid (common with aging, PPI use, or chronic stress) makes it easier for bacteria to overgrow.

Food Poisoning and Post-Infectious IBS

A single episode of food poisoning can damage the nerve cells that control gut movement. This is one of the most common underlying causes of SIBO.

Adhesions and Structural Issues

Scar tissue from surgeries, endometriosis, or chronic inflammation can physically slow the movement of food and bacteria.

High Sugar or High-Fermentable Diets

Frequent intake of simple carbs or fermentable fibers feeds bacterial overgrowth and worsens symptoms.

Chronic Stress

Stress slows digestion and suppresses stomach acid, creating a perfect environment for unwanted bacteria to thrive.

Natural Ways to Address SIBO

Successful SIBO treatment has three main goals: reduce overgrowth, improve motility, and restore a healthy microbiome.

Here are natural approaches that complement medical care.

Dietary Adjustments

Reducing fermentable foods can give your gut a chance to calm down. Many people temporarily follow:

• a low-FODMAP approach

• a specific carbohydrate diet (SCD)

• an elemental diet for severe cases

This doesn’t fix SIBO alone, but it helps reduce symptoms while deeper healing happens.

Prokinetics

These support the MMC and keep food moving. Natural options include ginger, iberogast, 5-HTP (for some individuals), and certain herbal blends. Better motility means fewer bacteria settling in the small intestine.

Herbal Antimicrobials

Herbs such as oregano oil, berberine, allicin (from garlic), and neem have been shown to reduce overgrowth effectively. Many practitioners use these as a natural alternative to antibiotics like rifaximin.

Support Stomach Acid

For those with low acid, supporting digestion with betaine HCl (when appropriate), digestive bitters, or apple cider vinegar can help reduce bacterial survival in the upper GI tract.

Heal the Gut Lining

SIBO often coincides with inflammation and leaky gut. Soothing ingredients like slippery elm, marshmallow root, L-glutamine, and DGL licorice can help support mucosal repair and calm irritation.

Restore Microbiome Balance

Once overgrowth is reduced, carefully reintroducing probiotics and prebiotics helps rebuild a healthier gut ecosystem. Timing matters—introducing them too early can worsen symptoms.

Lifestyle and Stress Support

Deep breathing, light movement after meals, proper hydration, and sleep directly affect the gut-brain axis. Calming the nervous system helps restore normal digestive motility.

When to Seek Professional Support

SIBO can look like many other conditions—IBS, food intolerances, celiac disease, pancreatic insufficiency, or gallbladder dysfunction. If symptoms are persistent, testing (such as a lactulose or glucose breath test) can provide clarity.

A functional practitioner, gastroenterologist, or integrative provider can tailor a treatment plan that includes medications, herbal protocols, or dietary therapies.

The Bottom Line

SIBO isn’t just about “too much bacteria”—it’s about bacteria in the wrong place, disrupting digestion, nutrient absorption, and gut comfort. The good news is that with the right strategy—targeting overgrowth, repairing the gut lining, and restoring motility—SIBO is highly manageable.

Understanding the root causes is the first step toward taking back control of your digestion and feeling like yourself again.