You have eliminated gluten. You have tried probiotics. You eat well, you exercise, and you still bloat within an hour of almost every meal. Your energy is unpredictable. You have developed reactions to foods you used to tolerate. And every gastroenterologist you have seen has told you it is IBS and offered you a low-FODMAP diet.

If this sounds familiar, you may have SIBO, small intestinal bacterial overgrowth,  and the reason it keeps getting missed is that it requires a specific test that most gastroenterologists do not routinely order.

What SIBO actually is

SIBO is a condition in which bacteria that should be confined primarily to the large intestine migrate into and proliferate in the small intestine, where they do not belong. The small intestine is designed to absorb nutrients, not to host large colonies of fermenting bacteria. When bacteria are present in excess, they ferment the carbohydrates you eat before your small intestine can absorb them, producing hydrogen and methane gas that causes rapid, significant bloating.

There are two main types:

Hydrogen-dominant SIBO tends to produce diarrhea, urgency, and loose stools alongside bloating. The bacteria ferment food rapidly, accelerating gut transit.

Methane-dominant SIBO (also called IMO — intestinal methanogen overgrowth) tends to produce constipation, severe bloating, and slow gut transit. Methane gas itself slows intestinal motility, creating a self-perpetuating cycle.

The symptoms that suggest SIBO

• Bloating that begins within 30-90 minutes of eating, especially after carbohydrates, legumes, or raw vegetables
• Inconsistent bowel movements, constipation, diarrhea, or alternating between both
• Food sensitivities that have developed or worsened over time
• Fatigue that worsens after eating
• Nutritional deficiencies despite eating well, particularly B12, iron, and fat-soluble vitamins
• History of food poisoning, antibiotic courses, or abdominal surgery
• Diagnosis of IBS that has not responded fully to standard interventions
• Histamine intolerance

Why it develops

The single most important protective mechanism against SIBO is the migrating motor complex (MMC), the housekeeping wave that sweeps bacteria from the small intestine into the large intestine between meals. The MMC only activates during fasting. When people eat frequently (every 2-3 hours), snack constantly, or have impaired motility from hypothyroidism, stress, or autonomic dysfunction, the MMC does not run adequately and bacteria accumulate.

Other major contributing factors include low stomach acid (which normally kills bacteria before they reach the small intestine), prior antibiotic use, and structural abnormalities from surgery or adhesions.

How SIBO is diagnosed

The gold standard is a lactulose or glucose breath test, which measures hydrogen and methane gas produced by bacterial fermentation. This is a simple at-home test available through functional medicine practitioners and increasingly through gastroenterologists. It requires a specific preparation diet and a 2-3 hour collection period.

A GI-MAP comprehensive stool test can reveal patterns consistent with SIBO, particularly low secretory IgA, elevated inflammatory markers, and dysbiosis patterns, but the breath test is the definitive diagnostic tool.

The treatment approach

SIBO treatment requires addressing both the bacterial overgrowth and the underlying reason motility failed.

Antimicrobial protocols for hydrogen-dominant SIBO typically involve rifaximin (pharmaceutical) or herbal antimicrobials including allicin (Allimax), berberine, and oregano oil (ADP from Biotics Research) for 4-6 weeks.

Methane-dominant SIBO/IMO requires additional agents targeting methanogens, neomycin alongside rifaximin, or Atrantil (a botanical combination of horse chestnut and peppermint), alongside the core antimicrobial protocol.

Biofilm disruption with Interfase Plus 30-60 minutes before antimicrobials improves treatment outcomes by breaking down the protective biofilm that makes bacteria resistant to treatment.

Motility restoration is non-negotiable for preventing recurrence. Ginger 500mg 20-30 minutes before meals, post-meal walking 10-15 minutes after every meal, and prokinetic support (Motility Pro or low-dose naltrexone in some cases) help restore the MMC function that prevents re-accumulation.

Diet during treatment is typically a low-fermentation diet (reduced FODMAPs and fermentable carbohydrates) for the duration of the antimicrobial protocol, followed by a gradual reintroduction to prevent nutrient deficiency.

Why SIBO keeps coming back

Recurrence rates for SIBO are high when the underlying drivers are not addressed. The most common reasons for recurrence: motility was never fully restored, stomach acid remains low, the patient returned to frequent grazing between meals, or an underlying condition like hypothyroidism or autonomic dysfunction continues to impair the MMC.

A comprehensive SIBO protocol addresses all of these factors, not just the bacterial overgrowth itself.

If you have suspected SIBO that has not been properly investigated or treated, I offer complimentary discovery calls to discuss a comprehensive approach. Apply at sarahfunctionalnutritionist.com/apply.

Sarah Khan, MBA, PhD is an Integrative and Functional Nutritionist specializing in gut health, SIBO, autoimmune disease, and complex multi-system cases.