Gut–immune axis
The gut–immune axis is the continuous interaction between the intestinal microbiota, the mucosal immune system, and the epithelial barrier. The gut houses a large fraction of the body’s immune cells. It must tolerate food and commensal bacteria while responding to pathogens and injury.
Consumer microbiome marketing often compresses this into “70% of your immune system” plus a dysbiosis score. The biology is real; the single-number immunity readout is not.
Hub: Reading your microbiome report.
Layers of gut immunity (and which pages cover them)
| Layer | What it does | How it appears on this site |
|---|---|---|
| Physical barrier | Mucus, tight junctions limit flux | Intestinal barrier |
| Innate inflammation | Neutrophils, calprotectin in stool during active mucosal injury | Gut inflammation markers, Calprotectin |
| Adaptive mucosal immunity | IgA coating luminal antigens; tolerance vs response | Secretory IgA |
| Microbial metabolite signalling | SCFAs via receptors on immune cells | SCFAs |
| Systemic low-grade inflammation hypotheses | LPS translocation in metabolic research | Metabolic health & endotoxemia |
| Taxonomic composition | Who is present, association, not immunity assay | Dysbiosis, Alpha diversity |
Critical rule: these layers do not substitute for one another. Multi-marker synthesis exists because reports stack them anyway.
Clinical vs functional vs report-only inflammation
| Context | Primary tools | Site routing |
|---|---|---|
| IBD flare / bloody diarrhoea | Calprotectin, endoscopy, histology | IBD vs functional gut, Red flags |
| IBS without alarm features | Symptom criteria; selective calprotectin | IBS subtypes, Lacy 2021 |
| Wellness sequencing only | Vendor inflammation score | Sequencing-derived inflammation score, not calprotectin |
A high vendor inflammation index with normal calprotectin often reflects algorithm design (low butyrate producers, Proteobacteria weights), see Gut inflammation markers.
Microbiome patterns discussed in immune research (not diagnostic alone)
| Report / research theme | Immune-relevant interpretation | Page |
|---|---|---|
| Low Faecalibacterium prausnitzii | IBD cohort associations; anti-inflammatory supernatant research (Sokol 2008) | Species page |
| Proteobacteria bloom | LPS-containing cell walls; ecological not serum LPS | Klebsiella & Proteobacteria, Metabolic endotoxemia |
| Post-antibiotic community | Immune reconstitution and infection risk context | Post-antibiotic recovery |
| Shared sickness taxa in meta-analysis | Transit/diarrhoea overlap, not specific autoimmunity | Duvallet 2017, Luminal environment |
Gut–immune vs gut–brain overlap
Immune mediators (cytokines, mast cell products) participate in gut–brain signalling, but that does not make a stool taxon list a brain or mood test. For neural and behavioural routes, see Gut–brain axis.
Histamine and mast cell frameworks overlap immune and symptom narratives: Histamine, MCAS, and food chemicals.
Coeliac, IBD, and when microbiome is downstream
- Coeliac disease, serology and biopsy; not ruled out by “normal” sequencing, Gluten-related disorders
- IBD, immune-mediated; microbiome shifts are secondary to clinical inflammation workup, IBD vs functional gut
- Food allergy vs intolerance, IgE-mediated allergy is not diagnosed from 16S
What not to conclude
| Report line | Do not conclude |
|---|---|
| Low sIgA | Need immune-boost supplements; immunodeficiency without clinical workup |
| High opportunists | Autoimmune flare imminent |
| Low butyrate producers | Must have mucosal inflammation |
| Normal diversity | No IBD ever, clinical alarms still apply |
| Zonulin flagged | Validated permeability diagnosis, Zonulin, Massier 2021 |
Related pages
- Intestinal barrier · Gut inflammation markers
- Secretory IgA · Calprotectin · Zonulin
- SCFAs · Dysbiosis
- Gut–brain axis · Metabolic health & endotoxemia
- Medications and the microbiome, immunosuppressants, antibiotics, PPIs