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
34 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 23, 2026· 20 min· HCM interpretation
The Metal H. pylori Cannot Live Without: Exploiting the Nickel–Acid Survival Trap
Helicobacter pylori survives gastric acid through urease, a nickel-dependent enzyme. That dependency is also a constraint: nickel must be continuously acquired, transported, assembled and defended. A mechanistic reading of the nickel–acid survival trap and what it implies for how the organism is evaluated.
#h-pylori#nickel#urease - Case Reasoning· August 21, 2026· 13 min· Clinical pattern observation
The Gut–Catecholamine Connection in POTS: How HPHPA May Disrupt Norepinephrine, Vascular Tone, and Methylation
A mechanistic reading of why a microbial aromatic metabolite (HPHPA) may sit upstream of catecholamine handling, vascular tone and methylation load in POTS and dysautonomia. Hypothesis-generating, anchored in organic-acid and microbiome patterns seen in complex cases.
#hphpa#pots#dysautonomia - Case Reasoning· August 18, 2026· 24 min· Clinical pattern observation
Long COVID, Candida, and Klebsiella: When the Gut Loses Its Ecological Control
Post-COVID cases repeatedly show loss of ecological control rather than a single pathogen: Candida and Klebsiella expansion as a readout of failed colonization resistance. What that pattern implies for interpretation rather than eradication.
#long-covid#post-viral#candida - 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 - Host Capacity Model· August 5, 2026· 6 min· Mechanistic inference
Why Dysbiosis Keeps Coming Back: The Overlooked Vitamin B2–Butyrate–Oxygen Connection
Riboflavin sits in the electron-transfer chemistry that lets colonocytes burn butyrate and hold the colon hypoxic. A mechanistic account of why dysbiosis recurs when that oxygen-consuming step is limited.
#riboflavin#vitamin-b2#butyrate - 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 - Case Reasoning· July 29, 2026· 32 min· Clinical pattern observation
What a Two-Decade Steroid-Dependent IBD Case Revealed About Redox Collapse, Malabsorption, Microbial Instability, and Host Capacity
A man in his forties with two decades of steroid-dependent inflammatory bowel disease was taking four grams of vitamin C daily — and his ascorbate marker sat near the bottom of the range. That contradiction opened a full mechanistic case analysis of redox collapse, fat malabsorption, microbial instability, and host capacity.
#case-study#ibd#crohns
Receive new articles.
New mechanistic essays delivered when published. Compatible with the existing Substack readership at @mohammedattallah.