Your Gut Health Can Improve

No matter who — or where — you are in life,
you can strengthen your gut microbiome.

Lining the inside of your intestines is a biofilm full of countless trillions of bacteria, yeast cells, and colonies.  These microbes influence and control much of the digestive and immune systems.

It’s All About: Dysbiosis vs Symbiosis

A healthy gut is a partnership between microbes and the body as a whole.

When this relationship goes wrong — when the wrong microbes become dominant and “friendly flora” become weak — gut health stops serving the needs of the body. This is called dysbiosis and, while correctable, it creates a heavy burden on the body.

The goal is to move away from the trap of dysbiosis and progress toward symbiosis — where the gut microbes fully support the body’s health.

The solution is often not as simple as throwing supplements at the problem. That may help in less-intense situations, but gut health — and the microbes that affect it — is an intricate fabric, affected by nearly every aspect of our body and environment.

Therefore, overcoming poor gut health requires a long-term approach that includes supplements, sleep cycles, therapeutic light, movement, and environmental factors.

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Understand Gut Health

Microbes — bacteria & yeast — live in colonies, or biofilms.

These biofilms are essentially a slime, or sludge that provides protection from potential threats.

Biofilm forms when bacteria adhere to surfaces in moist environments by excreting a slimy, glue-like substance.

The Biofilm Lifecycle

A biofilm can contain one species, but usually is a mixture of many — often hundreds — of microbial species.

Biofilm facts:

  • Single microbes attach to surfaces within minutes
  • A slimy, glue-like gel forms around the microbe, protecting it
  • Biofilms can grow on any surface
  • Three requirements for a biofilm: a surface, moisture, and nutrients


Symbiosis happens when gut microbes work together with the body.

Healthy, Balanced Flora

Symbiosis is when gut microbes are beneficial, working in concert with the body to 1) maintain immunity from pathogens, 2) digest food and supply nutrients, and 3) break down toxins in the gut.  

Symbiosis defined: When greater than 80% of microbes are “good.”


In symbiosis, people are able to:

  • Eat large meals
  • Stop eating when they are full
  • Go longer without snacking
  • Have powerful hunger urges
  • Eat fairly intuitively
  • Have daily bowel movements


Dysbiosis is when the gut microbes begin to work against the body.

Unhealthy, Imbalanced Flora

Dysbiosis is when too many unhealthy microbes live in the gut.  These bad “flora” release toxins (instead of helpful nutrients) when they digest our food and they don’t help our immunity.  They can even release hormones that adversely affect our brains.

Dysbiosis defined: When less than 80% of microbes are “good.”

  • High inflammation
  • Weight gain
  • Poor sleep
  • Autoimmune symptoms
  • Skin conditions
  • Intolerance to gut supplements
  • Feeling best when not eating, eating less, or avoiding certain foods
  • Insatiable hunger: constant snacking
  • Only tolerating small meals, shrinking appetite


Four Functions

Nutrients / Detoxification / Immunity / Brain Chemicals

Function #1

Nutrient Absorption

The intestines absorb nutrients from food.  

Then, the microbes in the gut create extra nutrients as byproducts of fermentation (which is how they digest food).  

Nutrients created by healthy gut flora include copious amounts of B-Vitamins, Vitamin K, butyric acid, acetic acid, and propionic acid. All of these nutrients are essential for bodily health and resilience.

Function #2


The liver dumps its bile (with toxins) into the intestines.  

These toxins need to stay trapped in the intestines — not leak back into the bloodstream.  With proper bowel movements and stool formation, these toxins will never stay too long and leave the body quickly.

Fiber is critical for absorbing and trapping liver toxins, so they can be excreted in the next bowel movement.

Healthy microbes also break down toxins in the gut, protecting the body further from toxicity.

Function #3


Inside the intestines is outside the body.

When food is in the intestine, it has not entered the bloodstream yet.

On average, humans swallow over a trillion microbes per day (bacteria, fungus, or virus), the gut’s job is to keep it out of your bloodstream, and keep it from getting too comfortable.

How does the gut remain hostile to microbes — and prevent them from growing too much? Enzymes, acids, and a healthy mucosal barrier. The mucosal barrier is quite literally — in scientific terminology — a slime.

Good Microbes Improve Hostility

Good bacteria release their own enzymes and acids, too. This helps fend off invading species in addition to the body’s defenses.

The Gut Lining Is Semi-Permeable

The gut lets good things into the bloodstream (food) and stops the bad things from entering (microbes).

Therefore, your gut lining is “semi-permeable.”

Microbes swimming in the bloodstream is, generally, a very, very bad thing. It’s an infection, and will cause lots of inflammation.

This is why about 70% of the body’s immune cells are located in the gut — designed to keep microbes out of the bloodstream, and inside the gut.

Good Microbes Improve Immunity

“Good” microbes that reside in the gut help keep potential invaders at bay by boosting the host’s immunity. They also help keep the gut lining intact and tight, and not leaky.

When the gut is healthy, it is a formidable immune system against foreign microbes and pathogens. When it’s sick, it is a weak defense.

Function #4

Brain Chemistry

Research is showing that gut flora create chemicals and neurotransmitters that affect the brain:  serotonin, butyrate, GABA, glutamate, and more.

The Gut-Brain Connection

Good and bad microbes directly produce or consume GABA and glutamate, affecting this delicate balance in the body’s neurotransmitters.

Good flora tend to create beneficial brain chemicals and stimulate the vagus nerve to communicate with the brain.  

Bad flora tend to release chemicals that interfere with the communication between the gut and brain, increasing the likelihood of anxiety-like behavior.

In Symbiosis:  

The four gut functions are working well.

In Dysbiosis:  

The four gut functions working poorly.


Causes of Dysbiosis


→  External and internally sourced.

Poor Diet

→ Artificial ingredients, junk foods, over-processed foods.


→ Especially when accompanied by excessive exercise or stress.


→ Especially when accompanied by lack of exercise, poor diet, or constipation.

Restrictive Diets

→ Low carb, low fat, low calorie, vegan, fruitarian, etc.

Exposure to Toxicity

→ Chemicals, mold, sick buildings.


→ Injury, abuse, emotional abuse, neglect, etc.


→ Daily movement is essential for regularity and bile flow.


→ Excessive radiation from wireless pulses, fields from electronics.


→ Located anywhere in the body, can migrate to the gut.


→ Antibiotics can wipe out all good flora.


How A Healthy Gut Works

A healthy gut handles nutrients, toxins, & water properly.

  • Nutrients are absorbed throughout the gut.
  • Toxins from the liver are absorbed and trapped in healthy stool, which forms throughout the colon. The stool is excreted daily in well-formed bowel movements, taking toxins with it.
  • Water is trapped in the gut and reabsorbed (with minerals) in the lower colon, contributing to bodily hydration and fluid balance.

A healthy stool means that healthy microbes are releasing beneficial nutrients:

  • B-vitamins, Vitamin K, butyric acid, propionic acid.
  • Hormones and neurotransmitters are also released by good microbes, improving bodily resilience.

Dietary fiber is necessary because it traps toxins inside the healthy stool — for excretion at the next bowel movement.

  • Without dietary fiber and daily bowel movements, toxins don’t leave the body and are likely to be reabsorbed into the bloodstream (causing inflammation and overwhelming detox organs).

The lower colon reabsorbs water and minerals from stool, keeping the body hydrated.

  • This function is critical for fluid balance & hydration.

Symbiosis Summary

  • Nutrients are well-absorbed into body.
  • Toxins stay trapped in stool → then exit body.
  • Immunity stays high.
  • Brain Chemicals are balanced, healthy.

Low Toxicity, High Immunity = Low Inflammation

Adequate nutrient absorption = Good metabolism, strong immunity, solid detoxification.

The “Goldilocks Speed” Keeps Flora Healthy

A good motto for the gut: “not too fast, not too slow.”  

One daily, well-formed stool is about right.  

When food digests extremely well (and when coupled with a great circadian rhythm), bowel movements tend to even happen at the same time daily.

A river or stream needs moving water to stay fresh.

Regular, daily bowel movements allow healthy flora to thrive and prevent pathogens from becoming too comfortable.


The Effects Of

A constipated gut handles nutrients, toxins, & water poorly.

  • Nutrients are not adequately absorbed — leading to deficiency.
  • Water and minerals are poorly re-absorbed — leading to bloating and dehydration.
  • Toxins are not regularly excreted — leading to inflammation of the intestines and re-entry into the bloodstream.

Stool is unhealthy and compacted.  

  • Good microbes aren’t present.

Bad microbes release toxins when they are fed.

  • Bad microbes release unhealthy hormones and neurotransmitters.

Toxins don’t leave the gut and are reabsorbed into the bloodstream.

Constipation Summary

  • Nutrients poorly absorbed into bloodstream..
  • Toxins can’t leave → re-enter bloodstream.
  • Immunity is weakened.
  • Brain Chemicals are unhealthy, unbalanced.

High Toxicity = High Inflammation

Low nutrients = Low metabolism, low immunity


The Effects Of

A gut with chronic diarrhea handles nutrients, toxins, & water poorly.

  • Nutrients are not adequately absorbed — leading to deficiency.
  • Water leaves quickly — leading to chronic dehydration.
  • Toxins cannot be excreted — leading to inflammation of intestines and bloodstream.

Stool has no chance to form.  

  • Good microbes can’t thrive.

Food is not properly digested and broken down.

  • Nutrients aren’t absorbed
  • Water and minerals are lost.

A weak microbiome allows for bad microbes to become strong.

  • Bad microbes release endotoxins when fed.
  • Bad microbes release unhealthy hormones and neurotransmitters.

Diarrhea Summary

  • Nutrients – no chance to absorb into body.
  • Toxins – not trapped by healthy stool → will re-enter bloodstream.
  • Immunity is extremely weak.
  • Brain Chemicals are unhealthy, unbalanced.

High Toxicity = High Inflammation

Low nutrients = Low metabolism, low immunity


All Microbes Can Grow Fast

Any microbe — bacteria, yeast, fungus — can rapidly grow and reproduce.

Speed Demons –>

Microbes only need food and water (and a surface) to grow. The gut is perfect for this: we constantly eat and drink.

When food feeds the flora that lines your intestine, the flora can double in numbers in well under an hour. A microbe’s environment greatly determines its rate of growth.

Consider that up to 60% of your stool is this flora, which grows as it eats the food you eat.

60% of the stool is microbial life: bacteria and yeasts.

Visualize how healthy stool is formed:

  1. Good flora eats your food,
  2. Flora grows (doubles) rapidly,
  3. You now have fresh bulk to slide easily through the GI tract.

This new bulk is largely colonies of microbes — especially fermenting fibrous and starchy foods, and releasing nutrients (like Vitamin K1+2, butyric acid, & B-Vitamins) or endotoxins (from bad flora).

The Risk

Unfortunately, bad microbes, when they are present, can double and grow just as fast.

This is often what’s happening when someone feels poorly after eating: Bad microbes grow and metabolize the meal, releasing endotoxins and causing an immune response.


The Immune System

& The Gut

The lining of the intestines is the most important interface with the outside world.

The gut lining must decide what gets into the body and what stays outside.  Only one thing should get into the body: Nutrients.

Around 70% of the immune system is located in the gut — and for good reason.

Incredible Surface Area

Designed to maximize the absorption of nutrients, the gut lining has 150X more surface area than the skin. That’s as much surface area as a tennis court.

This presents a challenge, though. The high surface area creates lots of potential entry points for pathogens — and nearly endless gates to guard.

Each of the body’s surfaces are designed to keep the outer world exclusively on the outside.


The gut lining has as much surface area as a tennis court.

Yet, the gut lining is teeming with microbial life — a thick biofilm of microscopic bugs. Imagine a tennis court covered in microbial biofilm.

In good health (symbiosis), this slime helps digest food and protect against invading pathogens.

In dysbiosis, the slime is actively poisoning the body, causing poor digestion of food, and preventing nutrient absorption. It causes ongoing inflammation.

The digestive tract is a warm, moist place where fermentable foodstuffs constantly enter — and then reside.  

The body’s immune system must be strong to keep the hostile microbes at bay.

The Immune System Resides In The Gut

The immune system is so heavily concentrated in the gut: A premier threat to all animals is that the gut becomes inhabited with bad actors — bad microbes.

Microbiota signaling to the immune system plays an important role in preparing the body for potential pathogen infection.

Infants Borrow Mother’s Immunity

Baby’s are born with virtually zero gut microbiome.

However, nature has a strategy to meet this challenge: A mother’s first milk (colostrum) lets a baby benefit from the mother’s immunity as the infant’s own immunity and microbiome develop.

When gut health and immunity is weak, the human digestive system makes for an excellent breeding ground for pathogens.

Inside the intestines is still “outside” the body.  

The intestines decide what to allow into your bloodstream.

Image result for colon
A clean colon — cleared out by fasting/diuretics before a colonoscopy. A healthy mucosal lining will allow well-formed stool to slide right through.

It takes a strong immune system to keep the gut clear of pathogens.


All Microbes “Fight” Other Species

Microbes tend to go dormant when:

  • …in small numbers
  • …challenged by species with larger colonies

Small Numbers vs Big Numbers

When species numbers grow, the species will become more aggressive– attacking other species for territory in the gut.

When their numbers dwindle, species begin to become dormant, and less hostile to their neighbors and their human host.

Microbes “fight” other microbes by releasing harmful chemicals, enzymes, and sometimes by outright consuming other species.

“Bad” microbes will fight good microbes, to gain dominance and vice versa.  Pathogens release endotoxins when they eat your food.

Good microbes — already present in a healthy gut — will also “fight back” against bad flora, to maintain dominance.

When food enters the digestive tract, healthy microbes release nutrients.


The Symptoms of Dysbiosis

It’s likely that dysbiosis is involved in most disease states, and even in the aging process.

Our microbiota and health develop (and age) hand-in-hand.

All Gut Functions Can Become Compromised

  • Food may not sit well, constipation or diarrhea may take hold, and you may not feel very well in your stomach.  
  • You may feel lots of bloating or cramping.
  • After a while, fatigue may set in, brain fog develops, sleep worsens, and muscles get a little weak.  
  • Chronic inflammation, puffiness, and itchiness could become your constant companions.  
  • You could find yourself unable to remember things you’ve read, unable to retain information one day to the next, or have trouble performing tasks physically. 
  • You may just be unable to “control your appetite” and unable to really feel truly satiated.  
  • Your metabolism might seem slow, your hands and feet cold, and/or you could be diagnosed with hypothyroidism.

The Risks of Restrictive Diets

A restrictive diet can relieve symptoms.

However, restrictive diets often cause their own issues over time — as a result of avoiding foods.

Imbalances occur in vitamin and mineral intake. Food avoidance can lead to intolerance of the absent foods. Too much or too little of any food can result in negative changes to the microbiome.

This results in diets bouncing back and forth — perpetually looking for what will give them relief of symptoms or an improvement in energy.

The Long Term

Restrictive diets are rarely a long-term solution.

They are, instead, a band-aid — sometimes giving the body a break from the constant tidal wave of endotoxin, constipation, maldigestion, or other symptoms.

Unfortunately, the root causes that cause digestive and health issues almost certainly continue to exist, and the symptoms can only be avoided by maintaining the diet.

More And More Restriction

Diets frequently become increasingly restrictive over time.

As a first restrictive diet seems to ‘wear off,’ more and more foods are removed to try and achieve the same relief. It can even be difficult to ever reintroduce a food once removed, if only because of the psychological hurdle developed by negative beliefs about previously-avoided foods. The gut flora changes in response to the diet, too. Removing a food can shift the microbiome to a state where certain foods less well digested.

The list of “safe” foods becomes smaller and smaller.

The cure to our digestive problems may not be as simple as removing foods.

After all, restrictive diets can make food intolerances worse. Foods that were once acceptable become less tolerable over time as the gut microbiome changes during restriction.

A Necessary First Step?

There is certainly a place for limited diets.

Dietary restrictions might be a necessary first step to stop feeding the bad flora.

Why? Because it certainly doesn’t make sense to continue eating foods that cause inflammation or an immune response.

However, to avoid the trap of eternal restrictive dieting, gut health must improve so that diverse foods are tolerable and even welcome in the diet.


Bad Microbes

Poison the Body

Any time food is eaten, bad microbes are capable of digesting food and releasing toxic metabolic byproducts.

These toxic byproducts cause inflammation and immune response. In poor gut health, the gut barrier is weak, meaning more toxins enter the bloodstream. Even microbes enter the bloodstream, causing even more inflammation.


In dysbiosis, food gets “eaten” by bad microbes.  

Instead of releasing nutrients (like good flora do), these pathogens release toxins into the gut, which are absorbed into the bloodstream.  

In the bloodstream, endotoxin causes inflammation harms tissues and organs. In dysbiosis, this happens every time food is eaten.  

It’s Detoxified By The Liver

These endotoxins must be removed by the liver.

Over time, the liver becomes overburdened and sluggish, resulting in poor detoxification in the body.  

Ever-rising bodily toxicity causes gut health to worsen further. Good gut flora suffers and bad flora happily take their place in a vicious cycle.  

As gut health worsens, the ability to properly absorb food diminishes, leading to energy deficits and nutrient deficiencies, which may be mild enough to be subclinical — yet strong enough to affect the way someone feels and their long-term health outcomes.

As immunity drops, the body’s viral and pathogenic load often increases, complicating things further and possibly leading to a chronically activated immune system (and more inflammation).

What’s more, the brain chemicals released by bad flora can lead to chronically elevated serotonin, general depressive feelings, and brain fog.

Endotoxins Can Be Debilitating

Healthy habits, foods, and thoughts may not be enough to restore vitality when gut microbes are poisoning the body continuously after every meal.  

  • Toxins can’t leave the system.
  • Nutrients aren’t absorbed from food.
  • Nutrients aren’t created in the gut.
  • Brain chemicals aren’t balanced.
  • The immune system is compromised — leading to chronic low-grade infections in the gut and elsewhere.

The Story Of Dysbiosis

Is one of
high toxicity,
high inflammation,
low nutrient absorption,
& poor brain chemistry.  

It’s been suggested that many of the benefits of fasting (as well as low-carb, carnivore, and vegan dieting) are largely the result of less endotoxin production in the gut. What’s worse, a few days without needed nutrition — or ongoing toxic exposure?


Reduce Endotoxin

…by Restoring Symbiosis

To restore symbiosis in the gut reduces the endotoxin load throughout the body.

Symbiosis, therefore, means less endotoxin — which means less inflammation — throghout the body.

It is not surprising that a small dose of E. coli LPS [endotoxin], injected directly into the bloodstream, can elicit fever and other responses in volunteers.

When the gut microbiome becomes more healthy, less endotoxin enters the bloodstream.

Symbiosis Can Be Restored

When at my worst (for several years), nearly every food used to cause heavy inflammation.  

Things got so bad, to avoid symptoms, I could only eat fresh-pressed vegetable juices.

Now, I eat essentially any food group and feel no rise in inflammation.

And of course, “leaky gut” can play a role here, too — especially when talking about endotoxin.


The ‘Leaky’ Gut

The science surrounding the “leaky gut” is in its infancy.

A leaky gut is a phenomenon where the gut membrane is weakend — causing it to fail to perform its two primary tasks:

  • letting in nutrients into the bloodstream
  • while keeping pathogens out

When the gut lining weakens, it lets everything into the body indiscriminately — particularly undigested food and microbes. This is troublesome because undigested food and microbes cause an ongoing immune and inflammatory response that over time damages tissues and restricts metabolism.

The main theory is that bad microbes cause this:  they set up colonies that burrow into the gut wall and eventually burst through.  

Other theories suggest that the tissues can’t maintain integrity simply due to lack of energy supply as the body weakens.  

The reality could be an “all of the above” situation.

The gut’s permeability is always variable (for instance, permeability increases 80% after exercise). In this syndrome, permeability is chronically increased.  

The leaky gut theory potentially likely autoimmunity and food intolerances, as well.  

A leaky gut can heal over time — mine certainly did — but bad flora and other issues must be addressed.  

Fixing leaky gut is not as simple as “taking lots of L-glutamine for tight junctions” — glutamine can actually cause serious complications by raising levels of glutamate in the body.

The Shocking Importance of

The Circadian Rhythm

Virtually every aspect of gut health is controlled and impacted by the circadian rhythm.

Gut health simply cannot escape the grasp of the circadian rhythm.

The circadian clock in the intestine works in close connection with gut microbiota.

Therefore, your circadian rhythm is a close partner with your gut health:

The GI tract… operates on a ~24-hour circadian schedule that anticipates — and prepares for — changes in the physical environment associated with day and night.

What does this mean?

It means your gut — right now — is operating on a 24-hour schedule.

And if that schedule is off? If it isn’t synchronized with the sun — solar time?

  • Your gut function is not optimized.
  • Your gut is not able to “anticipate and prepare for what happens throughout the day and night”.

The gut’s functions throughout the day and night:

  • Food is digested
  • Nutrients are absorbed
  • Hormones are produced and balanced
  • Pathogens are fended off during digestion
  • Pathogens are fended off during sleep
  • Motility is induced

Your gut microbiome’s activities — and its microbial makeup — change throughout the day.

“It is intriguing to speculate that:

1) Time of day influences human susceptibility to enteric pathogens,

2) Circadian disruption lowers human resistance to enteric pathogens,

3) Jet lag — not just differences in sanitation and hygiene — is a risk factor for traveler’s diarrhea.”

‘N Sync

When the circadian clocks in the brain and gut are aligned — and both are aligned with solar time — incredible things can happen for gut health and the entire body.

How do we achieve this harmony — between the brain, the gut and the sun?

Here’s how: The body’s circadian clocks are deeply controlled by your light environment, meal times, and movement throughout the day.

We need to send correct signals to our circadian clock — day and night.

Proper circadian signalling begins with:

  • early bright light plus late darkness
  • early movement plus late rest
  • early feedings plus late fasting

Discover heaps of methods to establish your circadian rhythm in the Sleep section.

Start here


Who’s in Charge?

Between the gut and the circadian rhythm — which one leads?

Is the gut primarly controlled by the circadian rhythm? Or… is circadian health controlled by the gut?

The answer? Both.

It’s — decidedly — a two-way partnership between your circadian rhythm and your gut health.

So should we tackle the circadian rhythm alone — in hopes it will improves sleep?

Absolutely not. Tackle both — together.

It is clearly — and scientifically proven — that the gut microbiome and the circadian rhythm exist in a “bi-directional relationship”:

Moreover, the abundance, composition, and function of gut microbiota are dramatically altered in circadian [disruption], further indicating a bi-directional relationship between circadian rhythms and the gut microbiome.

Dysregulation of circadian function due to shift work, or perturbed microbiota signaling in the gut, might therefore have drastic effects on the level of inflammation within the GI tract.

From this quote, we see that circadian disruption leads to inflammation — “drastically” — in the gut.

We also see that a compromised microbiota can lead to disrupted circadian signalling, as well.

Who’s in charge? There’s a “bi-directional relationship” between the gut and the circadian rhythm.

Each can harm the other.

Each improves the other.

Bring your gut health into balance — improve your circadian rhythm.

This completes Intro to the Gut.
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