02/02/2026
Hey Everyone!
Metabolism and Fermentation: How the Body Is Built, Regulated, or Broken
Health is not determined by food alone, but by how food is processed, interpreted, and delivered to the body’s metabolic control center — the liver.
Two biological systems determine this:
human metabolism
and
microbial fermentation
They are related, but they are not the same — and confusing them leads to deep misunderstandings about health, healing, and disease.
Metabolism: Where the Body Is Built
Metabolism is the process by which food is digested, absorbed in the small intestine, and delivered through the portal vein to the liver to build and maintain the human body.
Only nutrients that pass through this controlled absorption system become:
• muscle
• bone
• connective tissue
• enzymes
• hormones
• immune cells
• brain tissue
Animal foods — meat, fat, and eggs — are efficiently digested and absorbed here.
They provide the amino acids, fatty acids, cholesterol, and minerals required for structural repair and biological construction.
This is direct metabolism:
food becomes body.
Some components of plant foods are also absorbed in the small intestine:
• glucose from starch
• fatty acids from plant fats
• a portion of plant protein
These primarily contribute energy and metabolic signalling, not deep structural repair.
When this system is intact, the body rebuilds quietly and continuously.
Resilience is possible.
Fermentation: Where the Internal Environment Is Programmed
Fermentation is not human metabolism.
It is microbial metabolism.
Large portions of food — fibre, resistant starch, polyphenols, and incompletely digested proteins — pass through the small intestine and reach the colon. There they are converted by microbes into new chemical compounds.
These compounds are absorbed through the colon wall and enter the same portal vein that feeds the liver.
So fermentation is not “outside” metabolism —
it is an alternative chemical input into the metabolic system.
But unlike small-intestinal absorption, it is unregulated.
Microbes decide what is made.
The liver must deal with the result.
Fermentation therefore does not build tissue —
it programs the metabolic environment in which that building occurs.
The Good
When digestion is intact and the microbiome is balanced, fermentation produces:
• butyrate
• acetate
• regulatory metabolites
These support:
• gut lining integrity
• immune balance
• insulin sensitivity
• metabolic flexibility
In this state, fermentation complements metabolism.
The Bad
When digestion or absorption is impaired:
• carbohydrates raise insulin excessively
• proteins escape digestion
• bile chemistry shifts
• microbes gain more fuel
More material reaches the colon, and microbial control increases.
Metabolism weakens.
Fermentation gains influence.
The Ugly
In a sulfur-dominant or pathogenic microbiome, fermentation produces:
• hydrogen sulfide
• ammonia
• endotoxin
• inflammatory bile acids
These travel directly to the liver through the portal vein, where they:
• block mitochondrial respiration
• increase insulin resistance
• alter bile chemistry
• promote fat storage and inflammation
Food that should nourish now becomes metabolic poison — not because it is wrong, but because it is being processed by the wrong system.
Why Sequence Matters
Building must come before regulation.
Human tissues are built from nutrients absorbed in the small intestine.
If that system is weak, microbial fermentation becomes the dominant metabolic force.
Animal foods provide reliable building material.
They restore the physical structure required for healing.
Only then can fermentation become supportive instead of destructive.
The Central Distinction
Metabolism builds the body.
Fermentation programs the environment in which that building occurs.
Some foods provide structure.
Some foods provide signals.
Both matter — but not at the same time and not in the same way.
Understanding this is metabolic literacy.
It explains why the same food can heal one person and harm another,
and why recovery requires order, not ideology.
Health is not about eating “good” foods.
It is about knowing what builds, what programs, and when each is appropriate.
That is where food stops being confusing —
and starts making sense.l