Measurement library
What these tests actually measure
Each entry states the physical quantity the assay detects, the compartment it is sampled from, what the number cannot describe, and the reading it is most often given that the measurement does not support. Nothing here interprets a reader’s own result.
Comparison
Validity classes describe how well the measurement has been validated against what it is used to represent — not how useful any individual result is.
| Measurement | Compartment | Validity class | Most common misreading |
|---|---|---|---|
| Hydrogen and methane breath testing | Exhaled breath (end-alveolar air), sampled at intervals after an oral substrate. | Research grade | Treating a positive result as a bacterial count, or a negative result as proof that fermentation is not contributing. |
| Serum zonulin (commercial assay) | Serum or plasma. | Not recommended as a standalone measure | Reading a numeric zonulin value as a quantified 'leaky gut' score, then tracking it as a treatment response marker. |
| Faecal secretory IgA | Stool, from the portion of a single bowel movement that was sampled. | Poorly validated | Reading a low value as a 'depleted' mucosal immune system and a high value as 'immune activation'. |
| Faecal calprotectin | Stool, reflecting neutrophil migration into the intestinal lumen. | Validated against a defined reference standard | Treating a normal value as evidence that nothing is wrong with the gut, or an elevated value as a specific diagnosis. |
| Faecal short-chain fatty acids | Stool, i.e. the residue remaining after colonic absorption. | Exploratory | Reading low faecal butyrate as proof of butyrate deficiency at the epithelium. |
Entries
- Hydrogen and methane breath testing
Exhaled hydrogen and methane concentrations over time after a defined carbohydrate substrate, reflecting fermentation by gas-producing organisms accessible to that substrate.
What it does not measure: It does not count small-intestinal bacteria, identify which organisms are present, locate where fermentation occurred, or establish that fermentation is causing symptoms.
- Serum zonulin (commercial assay)
Whatever protein the specific commercial kit binds. Published validation work reports that widely used kits do not specifically detect pre-haptoglobin-2.
What it does not measure: It does not provide a validated measure of intestinal permeability, and it does not indicate barrier repair or barrier damage over time.
- Faecal secretory IgA
The concentration of secretory IgA in the portion of stool that was sampled and assayed.
What it does not measure: It does not measure mucosal immune competence, immune 'exhaustion', or antigen-specific responses, and it does not support a high/low interpretation of immune activity.
- Faecal calprotectin
Neutrophil-derived calprotectin in stool, tracking neutrophilic intestinal inflammation.
What it does not measure: It does not localise inflammation, distinguish its cause, or exclude non-neutrophilic mucosal problems. It is not a microbiome measure.
- Faecal short-chain fatty acids
Concentrations of acetate, propionate, and butyrate remaining in stool at the time of collection.
What it does not measure: It does not measure production rate, colonocyte uptake, or epithelial oxidative capacity. Low stool butyrate is equally consistent with low production and with efficient absorption.
Page provenance
- Canonical title
- BiomeLogic measurement library — what gut assays physically detect
- Canonical URL
- https://biomelogic.net/measurements
- Author
- Mohammed Attallah — Systems Biology Consultant
- Publisher
- BiomeLogic
- Version
- 1.0
- First published
- n.d.
- Last substantive revision
- n.d.
- Last evidence review
- n.d.
- Evidence classes present
- Assay validation literature; Clinical consensus / methodology; BiomeLogic editorial classification
- Publication-eligible references
- 0 of 5
Scope
An index of the gut-related measurements BiomeLogic reasons about, each stated in terms of the physical quantity detected, the compartment sampled, the validity class of the measure, and the reading it does not support.
What this page does not establish
- Any interpretation of an individual reader's result.
- Reference ranges, cut-offs, or decision thresholds.
- That any listed test should or should not be ordered.
Cite this page
Mohammed Attallah (n.d.). BiomeLogic measurement library — what gut assays physically detect (Version 1.0). BiomeLogic. https://biomelogic.net/measurements