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
12 articles
- 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 - 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 - Mitochondria· May 25, 2026· 5 min· Mechanistic inference
Ulcerative Colitis Starts in the Mitochondrion
For forty years the field treated UC as immune dysregulation. The 2024 and 2025 literature finally admits what was upstream all along.
#ulcerative-colitis#ibd#mitochondria - Mitochondria· April 25, 2026· 6 min· Mechanistic inference
The Iron-Sulfur Cluster Crisis: Why Your Mitochondria Can't Recover (And Why Practitioners Don't Talk About It)
Your SIBO keeps coming back. Your IBS flares without warning. Your energy tanked despite "fixing" your microbiome. Most practitioners will blame the bacteria, the metabolites
#mitochondri#dysbiosis#colonocyte - Case Reasoning· April 20, 2026· 4 min· HCM interpretation
What I've Learned About Long COVID: A Gut-First Framework
I've spent the last few months diving deep into the long COVID literature, and something keeps jumping out at me: we've been looking at this disease from the wrong angle. Most discussions start with t
#butyrate#colonocyte#barrier - Mitochondria· April 20, 2026· 10 min· HCM interpretation
Why Butyrate Supplementation Makes Chronic Gut Dysfunction Worse: The Data They Don't Show You
ou ve probably heard it.
#mitochondri#butyrate#colonocyte - Host Capacity Model· April 18, 2026· 34 min· HCM interpretation
Why It's Impossible to Treat Chronic Gut Dysfunction at the Bacterial Level
What the data across genetics, mitochondrial testing, immune markers, bile acid chemistry, stool sequencing, and motility assessment actually shows in every chronic gut case I see
#butyrate#bile#colonocyte - SIBO· April 15, 2026· 4 min· Mechanistic inference
Why Some People Never Recover From Gut Disorders: The Overlooked Genetic Architecture Driving Butyrate Failure, Dysbiosis, and Chronic Symptoms
Most people still talk about SIBO, IBS, hydrogen sulfide overgrowth, or post-infectious gut dysfunction as if the microbiome alone is the entire story.
#sibo#mitochondri#butyrate - SIBO· April 14, 2026· 15 min· Mechanistic inference
When the Virus Leaves But the Lock Stays: Post-Viral Epigenetic Silencing in Gut Dysfunction and…
When the Virus Leaves But the Lock Stays: Post-Viral Epigenetic Silencing in Gut Dysfunction and the Pharmacological Case for HDAC Inhibition A mechanistic investigation for clinicians — educational purposes only. Not a clinical framework. Not a prescription endorsement. The Parad
#sibo#dysbiosis#colonocyte - SIBO· April 11, 2026· 10 min· Mechanistic inference
Your SIBO Subtype Doesn't Matter — Until You Fix the Cell That Created It
Hydrogen, methane and hydrogen sulfide describe which organisms expanded, not why the terrain allowed it. Why subtype-directed treatment keeps failing when the upstream epithelial failure is untouched.
#sibo#hydrogen#methane - Mitochondria· April 6, 2026· 11 min· Mechanistic inference
When Your Gut Locks Its Own Front Door — Methylation, Epigenetics, and Why Chronic Gut Dysfunction…
When Your Gut Locks Its Own Front Door — Methylation, Epigenetics, and Why Chronic Gut Dysfunction Resists Recovery **Part 1 of 3: The Epigenetic Lock on Butyrate Transport** — — - In my last post, I explored how SIRT3 — a mitochondrial enzyme most people have never heard of — go
#mitochondri#butyrate#colonocyte - Host Capacity Model· March 27, 2026· 13 min· Mechanistic inference
Why Your Gut Won't Heal: The Real Reason Chronic Gut Problems Keep Coming Back
Diets, antimicrobials and probiotics can move the microbial picture without changing the host environment that produced it. A plain-language mechanistic reading of why the same dysbiosis pattern keeps rebuilding itself after treatment.
#dysbiosis#sibo#gut-healing
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