Normal Small Intestine Ecology
A healthy small bowel stays nearly sterile through steady muscular sweeping.
- <10³: Normal bacterial count (CFU/mL jejunum)
- ~90 min: MMC cycle length (between meals)
- ~6 min: Fasting phase III duration (the sweeping wave)
- <10 ppm: Baseline breath H2 (fasting value)
Low bacterial burden by design
Small bowel bacteria stay far sparser than the colon.
The housekeeper wave
Phase III contractions sweep residue and microbes distally.
A healthy gut resets itself every ninety minutes between meals.
Additional defenses
Gastric acid, bile, and the ileocecal valve add backup control.
Migrating Motor Complex Impairment
Weakened sweeping waves let bacteria linger and start multiplying.
- Up to 80%: MMC phase III loss (in severe dysmotility)
- 4+: Common causes (diabetes, scleroderma, surgery, opioids)
- 2–3×: Transit time increase (slower luminal clearance)
- 10³→10⁵: Early density rise (CFU/mL range)
Why motility fails
Neuropathy, scleroderma, or surgery blunt the sweeping reflex.
Stasis begets growth
Stagnant chyme becomes a stable feeding ground for bacteria.
Fewer sweeping waves let each bacterial generation persist longer.
A self-reinforcing cycle
Bacterial toxins can further blunt motility, worsening stasis.
Bacterial Overgrowth Establishes
Colonic-type bacteria colonize the small bowel far above normal levels.
- >10⁵: SIBO threshold (CFU/mL small bowel)
- ~30–85%: Prevalence in IBS (reported across studies)
- Colonic-type: Dominant species shift (coliforms, anaerobes)
- Days–weeks: Symptom onset (after motility decline)
Crossing the threshold
Density surpassing 10⁵ CFU/mL defines clinical overgrowth.
Species migrate upstream
Colonic bacteria populate segments normally kept near-sterile.
Overgrowth turns the small bowel into a fermentation chamber.
Mucosal irritation
Excess bacteria damage brush-border enzymes and villi.
Fermentation and Nutrient Malabsorption
Bacteria ferment sugars before the wall can absorb them.
- H2 + CH4: Gas produced (fermentation byproducts)
- Elevated: B12 deficiency risk (bacteria consume B12)
- Common: Fat malabsorption (bile acid deconjugation)
- Minutes: Bloating onset (after fermentable meal)
Carbohydrates ferment early
Bacteria intercept sugars before villi can absorb them.
Bile acid deconjugation
Bacterial enzymes disrupt bile acids, impairing fat uptake.
Gas, bloating, and diarrhea trace back to bacterial fermentation.
Nutrient deficiencies accrue
Bacteria compete for vitamin B12 and other nutrients.
Breath Test Confirms SIBO
Rising exhaled hydrogen and methane confirm bacterial overgrowth.
- Glucose/Lactulose: Test substrate (ingested solution)
- ≥20 ppm: Positive H2 rise (within 90–120 min)
- ≥10 ppm: Methane threshold (any timepoint)
- 2–3 h: Test duration (serial breath sampling)
How the test works
Bacteria metabolize the substrate, releasing gases absorbed into blood.
Gases reach the breath
Hydrogen and methane diffuse into blood, then exhaled air.
An early, sharp hydrogen rise is the hallmark of SIBO.
Guiding treatment
Results steer antibiotic choice and dietary management.