The Biology of a Healthy Gut Microbiome: Diversity, Balance, and Circadian Control

How Diet, Environment, and Host Physiology Shape Microbial Balance and Health

Kendall Toerner

Published: December 11, 2025

The modern story about the microbiome is backwards.

We are told that health depends on feeding bacteria, growing bacteria, and increasing bacterial numbers. More fiber. More fermentation. More probiotics.

But that model doesn’t fit human biology.

Humans are not meant to carry a large, overfed microbial population. We are meant to host a small but diverse microbiome, kept in check by light, timing, and energy availability.

When bacteria overgrow, problems begin.

The Goal Is Diversity, Not Volume

A healthy microbiome is not one that is crowded.

It is one that is controlled.

In nature, humans:

Ate intermittently
Experienced long fasting windows
Lived under strong sunlight
Had high UV exposure on skin
Ate seasonally, often with long periods of low intake

These conditions favor diverse bacteria in low numbers, not massive populations competing for fuel.

Large bacterial loads increase:

Endotoxin production
Immune activation
Inflammatory signaling
Energy loss

Health depends on containment, not abundance.

Why Humans Should Not Constantly Feed Gut Bacteria

Most bacteria live in the large intestine.

Food that reaches the large intestine feeds bacteria directly. Food that is absorbed earlier does not.

A carnivore-leaning diet is important here because:

Protein and fat are absorbed early
Very little reaches the large intestine
Bacteria are not overfed

This does not eliminate bacteria.

It starves excess growth.

In contrast, constant carbohydrate and fiber intake delivers fuel directly to gut microbes, increasing:

Bacterial population size
Turnover rate
Endotoxin release

A large microbiome is not a sign of health. It is a sign of overfeeding.

Overfeeding Bacteria Creates Endotoxins

When bacteria are overfed, they grow quickly.

Rapid growth leads to rapid death and turnover. When bacteria die, they release endotoxins, especially lipopolysaccharides (LPS).

These endotoxins:

Enter circulation
Stress mitochondria
Increase inflammation
Disrupt dopamine and sleep signaling

Many modern inflammatory conditions trace back to excess bacterial turnover, not infection.

Feeding bacteria constantly increases endotoxin load even if the bacteria themselves are “beneficial.”

Sunlight Is a Primary Regulator of the Microbiome

Sunlight shapes the microbiome directly and indirectly.

Ultraviolet light:

Reduces bacterial load on the skin
Prevents overgrowth
Selects for resilient, diverse species

This is normal. Skin was never meant to be sterile, but it also wasn’t meant to be overgrown.

More importantly, sunlight exposure has been shown to increase microbiome diversity, even without dietary changes.

Human studies have shown that UV exposure alone can alter and diversify the gut microbiome, likely through immune signaling, circadian alignment, and vitamin D–related pathways.

Sunlight does not feed bacteria.

It selects and organizes them.

Why Artificial Light Breaks Microbiome Control

Artificial blue light disrupts this balance.

Blue light at night:

Disrupts circadian signaling
Alters immune timing
Increases gut permeability
Changes bacterial behavior

Bacteria respond to light.

Many gut bacteria emit and respond to light signals. When exposed to artificial light at night, bacterial activity increases at the wrong time.

This leads to:

Increased bacterial metabolism
Increased endotoxin release
Increased stress on the host

The gut was never meant to experience light after dark.

Eating Late at Night Makes This Worse

Food after dark feeds bacteria at the wrong time.

When eating occurs at night:

Bacteria become metabolically active
Light-responsive bacterial processes increase
Endotoxin production rises
Sleep quality declines

This is not just about calories.

It is about timing.

Eating after dark exposes bacteria to fuel during a window when the host expects quiet, repair, and darkness.

That mismatch increases inflammation and disrupts recovery.

Why Sunlight Alone Can Improve the Microbiome

One of the most misunderstood points is this:

You do not need to feed bacteria to increase diversity.

Sunlight does this on its own.

By:

Regulating immune signaling
Improving mitochondrial energy
Reducing bacterial overgrowth
Increasing environmental selection pressure

Sunlight favors diverse, low-biomass ecosystems.

This is how healthy ecosystems work in nature.

The Microbiome as a Reflection of Energy State

Bacteria thrive when the host is inefficient.

When mitochondria are weak:

More fuel reaches the gut
More waste accumulates
Bacteria expand

When mitochondria are strong:

Fuel is absorbed early
Less reaches the large intestine
Bacteria remain sparse and diverse

The microbiome reflects host energy efficiency, not the other way around.

Practical Implications

A healthy microbiome is supported by:

Strong natural sunlight exposure
Minimal artificial light at night
Eating earlier in the day
Avoiding constant snacking
Avoiding overfeeding bacteria
Diets that absorb early, not late

You do not need to chase bacteria.

You need to create the conditions where they stay in balance.

Closing Perspective

Humans are not fermenters.

We are light-driven, energy-efficient organisms that host microbes as a secondary system.

A healthy microbiome is:

Small
Diverse
Quiet
Light-regulated

When bacteria are fed constantly, exposed to artificial light, and active at night, they become a source of inflammation instead of support.

Fix the light, timing, and energy, and the microbiome will follow.

References

Patra V et al. UV radiation exposure influences the human gut microbiome. PMID: 31114069
Belkaid Y, Hand TW. Role of the microbiota in immunity. PMID: 25437532
Cani PD et al. Metabolic endotoxemia and inflammation. PMID: 17643355
Zarrinpar A et al. Diet and circadian rhythm effects on the gut microbiome. PMID: 24440016
Paulose JK et al. Human gut bacteria respond to light and host circadian rhythms. PMID: 28296645