Your gut isn't broken because of bad bacteria.
The bacteria are bad because your gut cells stopped burning fuel.
The Host Capacity Model reframes SIBO, MCAS, long COVID, and chronic dysbiosis as downstream consequences of a single candidate upstream mechanism — colonocyte bioenergetic failure. This is the framework, the research, and the consulting practice built around it.
Three ways in.
Most visitors take the first one. Pick whichever fits where you are right now.
- I want to know if my case fits — before paying for anythingBook a free 15-min call
- I want to understand the framework firstRead the Host Capacity Model
- I want to know whether my pattern fits the modelTake the Host Capacity Score
Looking for the full menu (practitioners, lab review, services compare)? See all paths →
You've probably been here
a while.
Most people who reach BiomeLogic have already worked with multiple practitioners — conventional, functional, integrative — and have run protocols that helped briefly or not at all. If the patterns below feel familiar, you may be looking at a case the standard models can't resolve because they're aimed at the wrong layer.
- 01SIBO that keeps returning after antimicrobial or prokinetic protocols
- 02MCAS that doesn't respond fully to standard mast cell stabilizers
- 03Post-viral or long COVID symptoms that no specialist can map
- 04Food reactions that change day to day
- 05Mitochondrial-style symptoms with normal labs
- 06Histamine, oxalate, salicylate, and FODMAP intolerance overlap
- 07Multiple specialists, no unified explanation
The Host Capacity Model,
briefly.
The conventional model says chronic gut illness begins with the wrong bacteria. Focus on microbes first, then assume the host will recover. In complex cases, this stalls.
The Host Capacity Model inverts the order. It argues that dysbiosis, SIBO, MCAS, and post-viral symptoms are downstream of a candidate host-capacity mechanism: colonocyte bioenergetic failure — iron-sulfur cluster insufficiency, CD38–NAD⁺–SIRT3 cascade collapse, and loss of mitochondrial throughput at the epithelium.
When the host can't burn fuel, the habitat shifts. The microbiome reorganizes around the new chemistry. Endotoxin and abnormal metabolites cross a porous barrier. Mast cells and the immune system respond. The systemic syndrome follows.
Approaches focused only on bacteria may miss the host-capacity layer. BiomeLogic evaluates host capacity as one possible system-level framework for clinician discussion.
Long-form mechanistic essays.
Why Dysbiosis, SIBO, Hydrogen Sulfide Intolerance, MCAS, and Long COVID May All Be Downstream of a Single Event
Dysbiosis, SIBO, hydrogen sulfide intolerance, MCAS, and long COVID may all be downstream of one event: the colonocyte losing control of oxygen, butyrate, and its own mitochondria. The Host Capacity Model in full.
What Actually Causes GERD and Acid Reflux? Why Long-Term PPI Use Often Makes It Worse
GERD is rarely too much acid. It's lower esophageal sphincter dysfunction with pressure from SIBO, gastroparesis, vagal compromise, and bioenergetic failure. Long-term PPI use often perpetuates the underlying disease through rebound hypersecretion and SIBO induction.
What Actually Causes PCOS? A Mechanistic Reading of Polycystic Ovary Syndrome
PCOS is not primarily ovarian. Gut dysbiosis, insulin resistance, estrobolome dysfunction, mitochondrial failure, and the CD38-NAD+-SIRT3 cascade drive the disease. Birth control and metformin contain the readout while the upstream lesions persist.
The consultation.
- Step 01Intake review (Gate 1)
A short triage form to determine fit before full case submission.
- Step 02Live consultation session
60–90 minutes after full case review and lab integration.
- Step 03Written mechanistic analysis
A defensible model of the case, the candidate upstream mechanism, and the leverage points.
- Step 04A model for your care team
Delivered in a form your existing clinicians can review and discuss.
Educational systems-biology consulting. Not diagnosis or treatment. Designed to work alongside your licensed medical team.
Built with boundaries.
BiomeLogic is educational systems-biology consulting. It does not diagnose, treat, prescribe, triage, or replace licensed medical care. Major framework claims are evidence-tiered, reviewed, and connected to the Claim Ledger where appropriate.
- Educational systems-biology consulting · Not diagnosis
- Not diagnosis or treatment
- Works alongside your licensed care team
- Written mechanistic summary
- Fictional sample report available
- No files required for Gate 1
For full provenance, see the Framework Audit, Counterargument Library, and Claim Ledger.