Bloating, discomfort, fatigue, unpredictable digestion, each of these can be painful, disruptive, and deeply tied to the presence of SIBO. Small Intestinal Bacterial Overgrowth (SIBO), is a condition often overlooked in traditional care and best approached with nuance, empathy, and a focus on long‑term gut resilience.

What Is SIBO and How Does It Affect You?

SIBO refers to an abnormal rise in bacteria in the small intestine, typically beyond 10³ colony‑forming units per milliliter, causing symptoms such as bloating, gas, diarrhea, constipation, vitamin malabsorption, and nutrient deficiencies.

It may also be accompanied or informed by intestinal methanogen overgrowth (IMO), driven by methane-producing archaea like Methanobrevibacter smithii (commdx.com).

What Is the Real Cause of SIBO?

SIBO is not caused by a single factor but rather by disruptions in the natural defenses of the small intestine. The most common contributors include:

• Impaired gut motility, often from conditions like IBS, hypothyroidism, or diabetes
• Structural issues like adhesions, strictures, or altered anatomy from surgery
• Low stomach acid or long-term use of acid-suppressing medications
• Dysfunction of the ileocecal valve (which normally prevents colonic bacteria from entering the small intestine)
• Food poisoning or infections that damage the migrating motor complex (MMC)

These underlying issues allow bacteria from the large intestine, or even the mouth, to colonize the small intestine, where they ferment carbohydrates and disrupt digestion.

Recognizing the Symptoms of SIBO

SIBO symptoms can be wide-ranging and often overlap with other gut conditions, which makes it tricky to diagnose without a detailed clinical evaluation. Common signs include:

• Bloating (especially within 1–2 hours after eating)
• Excessive gas or flatulence
• Abdominal cramping or discomfort
• Diarrhea, constipation, or a mix of both
• Nausea and belching
• Early satiety (feeling overly full quickly)
• Fatigue, especially post-meals
• Brain fog or difficulty concentrating
• Unintentional weight loss
• Nutrient deficiencies (e.g., B12, iron, fat-soluble vitamins)
• Skin issues like acne or rosacea
• Joint pain or systemic inflammation

The symptom profile can also indicate the type of SIBO present. Hydrogen-dominant types often lead to diarrhea, methane-dominant to constipation, and hydrogen sulfide-dominant types may present with foul-smelling gas and a rotten egg odor.

What Does SIBO Stool Look Like?

There is no single "look" to SIBO stool, but certain patterns can be suggestive. Loose, watery stools are more common with hydrogen-dominant SIBO, while methane-dominant SIBO often results in harder, pellet-like stools or chronic constipation.

In some cases, stools may be unusually light, floating, or foul-smelling, indicating fat malabsorption.

Frequent, urgent bowel movements, particularly after meals, may also occur. Stool changes alone are not diagnostic but can help guide clinical suspicion.

Diagnosing SIBO: Sensitivity, Specificity, and Strategy

Standard diagnostic tools include:

• Breath testing using glucose or lactulose substrates, measuring hydrogen and methane within a defined post-load window (e.g., ≥20 ppm hydrogen rise within 90‑120 minutes or methane ≥10 ppm).
• Jejunal aspirate culture, considered a "gold standard," though newer consensus suggests >10³ CFU/mL can be diagnostic in context.

Breath tests are noninvasive and broadly available, though sensitivity and specificity vary; thus, a careful clinical interpretation and sometimes a trial of treatment may guide diagnosis.

How Do You Get Rid of SIBO?

Treating SIBO requires more than just clearing the bacteria; it involves addressing why the overgrowth happened in the first place. The most effective protocols typically include:

• Antibiotics like rifaximin (and neomycin for methane cases)
• Herbal antimicrobials such as oregano oil, berberine, or neem (for those preferring non-pharmaceutical routes)
• Selecting the right probiotics
• Elemental diet to starve bacteria in complex or resistant cases
• Motility agents (prokinetics) to maintain regular small intestine cleansing waves
• Dietary strategies like low-FODMAP or specific carbohydrate diets
• Nutrient support to address deficiencies and rebuild resilience

A stepwise, personalized plan with testing, treatment, and prevention phases is key to lasting results.

Treatment That Feels Like Care

1. Target the Overgrowth

One of the most effective treatments for SIBO is a course of rifaximin, a targeted antibiotic that stays in the gut and minimizes systemic side effects. Backed by research from the National Library of Medicine and Mayo Clinic, it’s especially useful for hydrogen-dominant SIBO. In methane-dominant cases, combining rifaximin with neomycin often yields better results.

Studies show this approach can resolve SIBO symptoms in about 70% of cases. That said, recurrence is common, particularly in older adults or those on long-term acid reducers, so follow-up care and prevention matter just as much as initial treatment.

2. Alternative Strategies When Antibiotics Aren’t Possible

The elemental diet, a nutrient-only formula that starves overgrown bacteria, can normalize breath testing results in up to 85% of patients over 2–3 weeks, but it’s costly and less palatable.

Emerging research is exploring berberine, a plant-based compound, as a potential non-antibiotic therapy, though clinical trials like BRIEF‑SIBO are still underway.

3. Address Nutritional Status & Root Causes

SIBO can deplete key nutrients your body needs, such as B₁₂, iron, and thiamine, and sometimes causes an unusual spike in folate. Replenishing these is essential for energy, immune function, and gut repair. At the same time, we look at what allowed the overgrowth to take hold in the first place.

Things like sluggish gut movement, past surgeries, or certain medications can all play a role. When poor motility is part of the picture, we may use gentle prokinetics to help restore rhythm and support long-term balance.

Supporting Gut Balance

• Clearing SIBO is only one piece of the puzzle. Long-term relief comes when we also support the broader gut ecosystem and nervous system health. At The Gut Health Specialists, we combine clinical expertise with practical lifestyle strategies to help your gut and the rest of you feel stable, nourished, and supported.
• An individualized low-FODMAP or reduced-fermentable diet can ease symptom flares and complement testing protocols. While probiotics aren’t a one-size-fits-all solution, certain strains like Lactobacillus plantarum and casei may be helpful when used alongside other treatments.
• We also place high value on nervous system support. Stress, sleep, hydration, and emotional regulation all impact motility and microbial balance. Practices like breathwork, mindfulness, and daily movement aren’t just “extras”, they’re part of how we rebuild the body’s natural rhythm and resilience. Recurrence is real, but so is long-term resilience.

Plan for recurrence prevention: For those with frequent relapses, repeat treatment cycles, rotating antibiotics, or intermittent courses may be appropriate and always paired with lifestyle support and root‑cause assessment.

Follow symptoms: Retesting after symptom resolution helps confirm remission, but clinical context matters, too.

Collaboration matters: Every individual's gut history, hormone status, life stressors, and dietary needs deserve thoughtful care built around full-body health (not just bacteria counts).

SIBO is a window into gut imbalance, nutrient disruption, and slowed digestion. The best care is rooted in expert diagnosis, evidence-based antibiotic or diet strategies, targeted nutritional support, and lifestyle interventions that foster long-term balance.

To explore how tailored SIBO care could work for you or someone you care about, please visit our gut health resources or book a consultation through our site.

If you're navigating persistent bloating, digestive discomfort, or suspect SIBO may be part of the picture, you're not alone, and you're not meant to figure it out alone either.

At The Gut Health Specialists, we take a root-cause, personalized approach to gut healing that prioritizes your comfort, your data, and your long-term outcomes.

Book a 1:1 consultation to explore tailored testing, treatment options, and care that fits your life. You deserve clarity, not guesswork.