The limits are published alongside the reasoning.
- Evidence tiers
Every article carries an explicit evidence tier, so established biology is never presented as if it were clinical proof.
Read the claim ledger - What this does not prove
Mechanistic pieces are required to state their own limits and the competing explanations that would fit the same data.
See the counterarguments - Published corrections
Where the reasoning has been revised, the revision is recorded rather than quietly edited away.
Review the standards
Pick the sentence that sounds like your situation.
- Why does my SIBO keep coming back?
- Are SIBO breath tests actually reliable?
- Why don't antihistamines settle my symptoms?
- Can I have mast cell activation with normal tryptase?
- Why won't my Long COVID symptoms resolve?
- Why did COVID trigger this in me and not others?
- Why are my labs normal when I feel terrible?
- Why doesn't my stool test match my symptoms?
- Why does every protocol stop working after two weeks?
- Why did butyrate or probiotics make me worse?
- What do bile acids have to do with my gut symptoms?
- Can gut health affect my hormones and egg quality?
Educational mechanistic writing. It does not diagnose, and it does not replace the clinician treating you.
Seven mechanistic threads run through this library.
Recurrent SIBO & breath-test interpretation
14 articles · recurrent SIBO
Mast-cell activation, tryptase & histamine
19 articles · mast cell activation
Long COVID, post-viral gut–immune & POTS
13 articles · Long COVID gut symptoms
Colonocyte bioenergetics, butyrate & oxygen
19 articles · colonocyte bioenergetics
Bile acids, TUDCA & C. difficile ecology
5 articles · bile acid dysfunction
Gut–hormone axis, fertility & estrobolome
3 articles · gut microbiome and fertility
Lab-pattern interpretation
6 articles · lab pattern interpretation
29 articles · showing 12
- MCAS & Mast Cells· August 27, 2026· 18 min· Mechanistic inference
The Antihistamine–Stomach Acid Connection: Why Low Acid Is Often a Signaling Problem, Not Just a Digestion Problem
Long-term acid suppression and H2 antihistamines act on the same histamine signal that parietal cells use to secrete acid. A mechanistic look at why persistent reflux, early fullness, poor protein tolerance, iron and B12 abnormalities and recurrent dysbiosis can follow — and why low stomach acid is often a signalling problem rather than a digestion problem.
#histamine#h2-receptor#stomach-acid - Case Reasoning· August 26, 2026· 18 min· Clinical pattern observation
Long COVID, MCAS, Mold, Heavy Metals, SIBO and Mitochondrial Collapse: A Case That Shows What Happens When We Treat the Target but Forget the Host
A complex case combining Long COVID, ME/CFS physiology, hyperadrenergic POTS, MCAS-type hyperreactivity, recurrent SIBO and methanogen overgrowth, mycotoxin findings, elevated toxic metals and profound mitochondrial respiratory-chain impairment — read as a single host-capacity failure rather than a list of separate targets.
#long-covid#me-cfs#hyperadrenergic-pots - SIBO· August 24, 2026· 16 min· Mechanistic inference
Why SIBO Keeps Coming Back: MMP-9, EMT, and the Collapse of Host Capacity
Chronic intestinal inflammation can change the identity and metabolism of the epithelial cell itself. A mechanistic reading of MMP-9, E-cadherin, beta-catenin and epithelial-to-mesenchymal transition, and why that shift can keep reselecting the microbial pattern behind recurrent SIBO.
#sibo#sibo-recurrence#mmp-9 - Frameworks· August 14, 2026· 17 min· HCM interpretation
The TUDCA Trap: When a “Protective” Bile Acid Feeds the Gut Problem It Was Supposed to Fix
Why a bile acid widely described as protective can behave differently inside a dysbiotic intestine, depending on microbial transformation and where it is absorbed. A reasoning framework for supplement decisions, not a recommendation.
#tudca#bile-acids#supplements - Host Capacity Model· August 12, 2026· 20 min· Mechanistic inference
Mold, Mycotoxins, SIBO, and Chronic Illness: How Enteric Nervous System Dysfunction and Loss of Host Capacity Create a Self-Reinforcing Biological Loop
How mycotoxin exposure, enteric nervous system dysfunction and loss of host capacity can form a self-reinforcing loop behind recurrent SIBO, methanogen overgrowth and severe constipation.
#mold#mycotoxins#sibo - Case Reasoning· August 3, 2026· 12 min· Clinical pattern observation
The Microbial Metabolites That May Be Rewiring the Brain: The Hidden Link Between SIBO, IBS, MCAS, Autism, ADHD, Glutamate, and Catecholamine Dysfunction
HPHPA, hydrogen sulfide, D-lactate and ammonia are microbial metabolites that may pressure catecholamine regulation through dopamine β-hydroxylase, COMT and mitochondrial ATP. A case-anchored look at the hidden link between SIBO, IBS, MCAS, POTS, ADHD-like symptoms and autism-spectrum features — a metabolite-driven mechanism rather than a purely compositional dysbiosis.
#hphpa#clostridia#dopamine-beta-hydroxylase - SIBO· August 2, 2026· 13 min· Mechanistic inference
Beyond Bacteria: Is Bile Acid Ecology One of the Missing Pieces in Chronic SIBO?
Over the last several years, I have spent countless hours studying chronic gut dysfunction while working with individuals suffering from small intestinal bacterial overgrowth (SIBO), hydrogen sulfide overgrowth, mast cell activation syndrome (MCAS)-related gastrointestinal sym…
#bile-acids#sibo#bile-acid-malabsorption - Frameworks· July 30, 2026· 11 min· HCM interpretation
SIBO, MCAS, POTS and Food Intolerance May Be One Self-Sustaining System
For years, SIBO, MCAS, POTS, dysautonomia, food intolerance, chronic fatigue, neurological symptoms, and mitochondrial dysfunction have been treated as separate diagnoses.
#sibo#mcas#pots - Host Capacity Model· June 11, 2026· 28 min· Mechanistic inference
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.
#host-capacity-model#colonocyte#butyrate - SIBO· June 1, 2026· 22 min· Mechanistic inference
What May Be Driving 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.
#gerd#acid-reflux#ppi - Frameworks· June 1, 2026· 22 min· HCM interpretation
What May Be Driving Fibromyalgia? The Mitochondrial, Mast Cell, and Small Fiber Neuropathy Mechanisms Standard Treatment Misses
Fibromyalgia has four upstream drivers: mitochondrial dysfunction, mast cell activation, small fiber neuropathy, and gut-brain axis dysfunction. Lyrica and Cymbalta act on central amplification, not on the peripheral lesions producing the input — which is why response is so often partial.
#fibromyalgia#chronic-pain#mitochondrial-dysfunction - Frameworks· May 31, 2026· 22 min· HCM interpretation
What May Be Driving Chronic Migraine? A Mechanistic Reading of Treatment-Resistant Migraine
Chronic migraine has four upstream drivers: mitochondrial bioenergetic failure, dural mast cell activation, gut-brain axis dysfunction, and hormonal-vasomotor instability. Most treatment-resistant cases (including CGRP antibody non-responders) need the dominant driver addressed at its upstream point.
#chronic-migraine#migraine#cgrp
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