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
16 articles · recurrent SIBO
Mast-cell activation, tryptase & histamine
23 articles · mast cell activation
Long COVID, post-viral gut–immune & POTS
18 articles · Long COVID gut symptoms
Colonocyte bioenergetics, butyrate & oxygen
20 articles · colonocyte bioenergetics
Bile acids, TUDCA & C. difficile ecology
7 articles · bile acid dysfunction
Gut–hormone axis, fertility & estrobolome
8 articles · gut microbiome and fertility
Lab-pattern interpretation
6 articles · lab pattern interpretation
35 articles · showing 12
- SIBO· September 30, 2026· 29 min· Mechanistic inference
10 Things I Have Learned About Long COVID From Client Data and Research
I have not written in depth about Long COVID for a while, although it has continued to appear repeatedly in the complex cases I analyze.
#long-covid#sibo#pots - SIBO· September 23, 2026· 25 min· Mechanistic inference
10 Things I Learned About SIBO That Explain Why It Keeps Coming Back
The more I study SIBO and work through people who have been dealing with it for years, the less I think the most important question is simply what will kill the bacteria.
#sibo#bile-acids#hormones - SIBO· September 14, 2026· 19 min· Mechanistic inference
ME/CFS, Butyrate, and Host Capacity: What a Severe Case Reveals About the Microbiome–Host Relationship
I have been studying the gastrointestinal physiology of ME/CFS for some time, but a severe long-duration case I am currently analyzing has pushed me to think much more carefully about what we actually mean when we say that the microbiome
#sibo#histamine#mast-cells - SIBO· September 7, 2026· 35 min· Mechanistic inference
The Histamine Problem Nobody Explains: Why Some People Suddenly Start Reacting to Everything
The more I research histamine, and the more I work through complex cases involving MCAS, POTS, dysautonomia, SIBO, food reactions, gastrointestinal dysfunction, hormonal changes, medication sensitivities, flushing, itching, headaches
#sibo#mcas#histamine - SIBO· September 5, 2026· 6 min· Mechanistic inference
The Rifaximin Trap: Killing SIBO Without Fixing Why It Keeps Coming Back
The more I research SIBO and work through complex gastrointestinal cases, the more I think we are asking the wrong question.
#sibo#pots#dysautonomia - SIBO· September 3, 2026· 17 min· Mechanistic inference
Mold Toxicity Is More Than Exposure: The Mitochondria–Gut–Immune Cascade Behind Chronic Illness
From my research into mold, mycotoxins, mitochondrial physiology, gut ecology, immune signaling and host genetics, and from the patterns I continue to examine while working through complex gastrointestinal, autonomic, neurological
#microbime#mast-cell-activation#mold - 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
Receive new articles.
New mechanistic essays delivered when published. Compatible with the existing Substack readership at @mohammedattallah.