What You Need to Know About SIBO: A Root-Cause Guide

Small Intestinal Bacterial Overgrowth (SIBO) is one of the most discussed yet misunderstood digestive health issues today. If you're experiencing chronic bloating, food sensitivities, or irregular bowel movements, SIBO may be at the root of your symptoms.

In this root-cause guide, you'll learn what SIBO really is, what causes it, how it’s diagnosed, and how to support long-term healing from a functional nutrition perspective.

What Is SIBO, Really?

SIBO stands for Small Intestinal Bacterial Overgrowth, a condition where an abnormal number of bacteria grow in the small intestine — a part of the digestive tract that should normally have a relatively low bacterial count.

These bacteria may ferment carbohydrates in the small intestine, creating gas (methane or hydrogen) and causing symptoms like:

• Chronic bloating (especially 1–2 hours after eating)

• Constipation, diarrhea, or both (IBS-like symptoms)

• Gas and burping

• Food intolerances (especially to FODMAPs, fiber, or fermented foods)

• Abdominal pain or discomfort

• Nutrient deficiencies (especially B12, iron, and fat-soluble vitamins)

• Fatigue or brain fog

What Causes SIBO?

SIBO is not just about bad bacteria. It’s about bacteria in the wrong place — often due to structural or functional issues in the gut that allow them to migrate and stay in the small intestine.

SIBO is not a standalone diagnosis. It's a symptom of something deeper that is affecting your gut motility, structural function, immune system, or microbiome balance.

Here are the most common underlying causes:

1. Impaired Motility

The migrating motor complex (MMC) is a wave-like muscle movement that clears bacteria between meals. Stress, infections, or certain medications can impair the MMC, allowing bacteria to stagnate.

2. Post-Infectious SIBO

After food poisoning or a GI infection, nerve damage in the gut can lead to long-term motility problems, setting the stage for SIBO.

3. Low Bile Flow or Enzyme Deficiency

Bile and digestive enzymes play a key role in breaking down food and keeping bacteria in check. If bile flow is sluggish or enzyme production is low (often from liver/gallbladder dysfunction, inflammation, or pancreatic insufficiency), SIBO may develop.

4. Medications That Contribute to SIBO

• PPIs (Proton Pump Inhibitors): Lower stomach acid, weakening your first line of defense.

• Opioids: Slow gut motility.

• Antibiotics: Disrupt gut microbiota balance, sometimes leading to overgrowth.

5. Hypothyroidism

Low thyroid function can significantly slow gut motility. Research shows people with hypothyroidism are more likely to develop SIBO.

6. Structural Issues

Adhesions from C-sections, surgeries, or conditions like diverticulosis can create blockages or pockets where bacteria thrive. If you've had abdominal surgery and now experience gut issues, this may be relevant.

7. Gut Infections & H. pylori

H. pylori can lower stomach acid and impair immunity, creating a friendly environment for bacterial overgrowth. Recent research shows a strong link between H. pylori and SIBO, especially in younger adults.

How is SIBO Diagnosed?

The gold standard is a jejunal aspirate culture (via endoscopy), but it’s invasive and rarely done. Breath tests are more common and measure hydrogen or methane gas levels after ingesting lactulose or glucose.

Types of SIBO breath tests:

• Lactulose Breath Test (LBT)

• Glucose Breath Test (GBT)

Test results can be false positive/negative; therefore, they must be interpreted in context — your symptoms and history matter as much as the numbers.

Why SIBO Keeps Coming Back

The real frustration with SIBO isn’t just the symptoms — it’s the recurrence. Many people feel better after a round of antimicrobials or antibiotics, only to relapse weeks later. Why? Because if you don’t address the root cause (motility, stress, immune dysregulation, structural issues), the environment that allowed SIBO to flourish will remain unchanged.

The Gut-Brain Axis & SIBO

The MMC is regulated by your nervous system. Stress, trauma, and vagus nerve dysfunction can disrupt this process, creating the perfect storm for bacterial overgrowth. A calm, regulated nervous system is key to restoring gut motility. This means that we need to address your nervous system if we want long-term healing and prevent recurrences.

How SIBO Is Treated — A Functional Approach

In conventional medicine, the go-to treatment is antibiotics. While these can be helpful, they often don’t address the underlying cause, and SIBO frequently comes back.

In functional nutrition, we approach SIBO as a multi-layered issue.

A root-cause SIBO protocol includes:

• Identifying underlying causes

• Reducing bacterial overgrowth (with herbs, diet, or medications)

• Supporting detox pathways and clearing endotoxins

• Repairing the gut lining and motility

• Rebuilding microbiome resilience and immune function

Additionally, we look at long-term strategies to prevent recurrence:

Once we understand the root cause, we can create a long-term plan to support the whole system in continued healing and prevent recurrences. Each protocol is personalized for long-term success.

Common Misconceptions About SIBO

• "I need to stay on low-FODMAP forever." → False. Long-term FODMAP restriction may worsen microbiome health. It should be used strategically.

• "It’s all about bacteria — kill them and you’re good." → SIBO is not just a bacterial issue. It’s a systemic issue involving motility, immunity, and stress response.

• "I tested negative, so I don’t have SIBO." → Breath tests are imperfect. Clinical symptoms and deeper investigation are required.

You Don’t Have to Live with Chronic Gut Symptoms

If you’ve tried probiotics, elimination diets, or gut-healing supplements with no lasting relief, there’s a deeper root cause to uncover.

In my clinical practice, I use functional lab testing, trauma-informed care, and personalized nutrition to help people address chronic digestive conditions like SIBO from the inside out.

👉 Book a free connection call to explore your root cause and begin your healing journey

References

• Tursi A et al. Prevalence of SIBO in Hypothyroid Patients, J Clin Gastroenterol.

• Liu Z et al. H. pylori and SIBO: A Meta-Analysis, BMC Microbiology (2023).

• Shah A et al. Small Intestinal Bacterial Overgrowth: A Comprehensive Review, J Neurogastroenterol Motil (2020).