Microbiome Interpretation Structured microbiome reference
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SIBO, IMO, and breath testing

Small intestinal bacterial overgrowth (SIBO) and intestinal methanogen overgrowth (IMO) are defined by excessive fermentation in the small bowel, detected primarily by breath tests, not by stool microbiome sequencing.

SIBO, IMO, and breath testing

SIBO (small intestinal bacterial overgrowth) describes excess bacterial fermentation in the small intestine. IMO (intestinal methanogen overgrowth) highlights methane-producing archaea (often Methanobrevibacter smithii) linked to constipation-predominant symptoms in research.

Stool microbiome tests sample the colon. They cannot rule in or out small-intestinal overgrowth reliably.

Breath testing basics

ProbeTypical use
LactuloseHydrogen (and methane) rise suggests small-intestinal fermentation (protocol-sensitive)
GlucoseShorter segment; false negatives possible with distal SIBO
MethaneAssociated with constipation slowed transit in many studies

Limitations: diet prep, prokinetics, PPI use, and non-standard cut-offs affect results. Controversy remains over prevalence and overtreatment in IBS.

Stool microbiome overlap

Stool signalMeaning
Methanobrevibacter detectedSee /species/methanobrevibacter-smithii, not equivalent to breath IMO
High “hydrogen producers” labelsVendor-specific; not breath testing
General dysbiosisNon-specific

Symptom overlap

  • Chronic bloating, distinguish upper vs lower abdominal distension
  • Constipation, methane/IMO literature
  • Brain fog, rare D-lactic acidosis with carbohydrate malabsorption (see Rao et al. in barrier article)

Related: Gut motility, Methane and colonic gas.

Context if you're reading a report

Upper abdominal bloating, early satiety, and constipation are often attributed to stool "dysbiosis" when the problem may be location (small intestine) or methane production, which stool kits measure poorly.

Stool panels may list methanogens or "SIBO-associated" taxa, indirect at best. Breath glucose/lactulose hydrogen/methane tests are the clinical standard (with protocol limitations).

That a stool microbiome report diagnoses SIBO; that a positive breath test always requires antibiotics; or that methane on a report equals IMO without clinical correlation.