Clean Gut

Clean Gut: The Breakthrough Plan for Eliminating the Root Cause of Disease and Revolutionizing Your Health by Alejandro Junger


The premise of Clean Gut is to get to the root of the illnesses that burden us, and the gut is the center of our health.

Before chronic disease there is inflammation, and before inflammation there is gut dysfunction. By addressing the health of our gut we can reduce inflammation, reverse disease and sustain lifelong health.

An unhealthy gut is responsible for much more than just major illnesses. Tiredness, aches and pains, allergies, mood swings, lack of libido, bad breath, body odor, eczema, and constipation are all directly related to gut dysfunction.

Alejandro Junger explains the anatomy of the gut, how we're damaging it, and how to correct it. The second half of the book provides specific details on how to start a clean gut diet and provides over 50 pages of healthy gut-friendly recipes.

Medicine and Gardening

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Good gardeners know that the health of a plant is in its roots.

When you look at an unhealthy plant you may see the leaves are turning brown. The brown leaves appear to be the problem but in reality, it's just a symptom, the problem is in the roots.

You can't make a plant healthy again by covering up the symptoms. You can't just paint the leaves green, you need to go to the roots. By changing the water, soil, or nutrients you'll be able to affect the color of the leaves, restoring health to the plant.

Good medicine is like good gardening. Unfortunately, modern medicine has gotten caught up in a fight to keep individual leaves vibrant and green while the plant is dying. We still need to get to the root of disease.

That is the premise of Clean Gut, getting the root of disease. Before chronic disease there is inflammation, and before inflammation there is gut dysfunction.

Your overall health is connected to a singular area of the body, your gut. Clean Gut explains how the root of almost all chronic diseases also starts in your gut.

This applies to people even if you're not currently suffering from a chronic illness. 

Many of the minor ailments you may be suffering from— such as tiredness, aches and pains, allergies, mood swings, lack of libido, bad breath, body odor, eczema, and constipation— may also be directly related to gut dysfunction. In addition, a damaged gut will lead to premature aging.

How the gut functions has both a direct and indirect effect on every single cell in the human body, from the cells in your bone marrow deep inside your bones to the hair and skin on the surface.

Just as the health of a garden starts in the plant's roots, the body’s health begins in the gut, its own internal roots.

The gut is the center of health, illness, and dysfunction. If you want to figure out why your leaves are turning brown, so to speak, look at your gut.

Anatomy of the Gut

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Gut, in this book, refers to more than just the body's intestinal tube. Junger uses the word gut to refer to the living organisms inside the gut, the intestinal flora, and the immune and nervous systems within and around the walls of the intestines.

The gut has four main parts:

  1. the digestive tube,
  2. the gut-associated lymphatic tissue,
  3. the intestinal flora, and
  4. the gut’s nervous system.

The Digestive Tube

Your body only comes in contact with the outside world on three surfaces, your skin, your lungs, and your digestive tube. These encompass the three “borders” where the body draws a line between what is inside and what is outside.

The digestive tube is the largest and busiest of these borders. It completes some of the most important survival functions. The digestive tube aids in:

  • Digestion: breaking down food,
  • Absorption: absorbing nutrients essential for life,
  • Elimination: eliminating waste from your blood circulation, and
  • Housing the intestinal flora.

The body acquires nutrients through digestion and absorption.

Digestion is the process by which we break food into smaller pieces. This occurs both mechanically, through chewing, and chemically, via digestive enzymes. Digestion involves many satellite organs, such as the salivary glands, liver, gallbladder, and pancreas.

Absorption occurs when broken-down food comes into contact with your intestinal wall. 

The intestinal wall keeps undigested food and microorganisms out while letting digested food in. The intestinal wall is also in charge of elimination. Removing from the body any metabolic or toxic waste along with whatever food the body didn’t absorb.

The Gut-Associated Lymphatic Tissue (GALT)

Your GALT is responsible for keeping your gut safe. It uses immunoglobulins, or antibodies, to detect and destroy anything that is not considered a nutrient or part of the self. The GALT has many other tools and weapons with which to handle foreign entities.

Your immune system has B cells, T cells, mast cells, phagocytes, and many others, which all serve specific functions. Monocytes, for instance, attack viruses, while neutrophils attack bacteria. Eosinophils are involved in allergic-type reactions, and killer T cells attack cancerous cells.

While the immune system protects the entire body, 80% of these cells are located in the gut, because that's where there is the largest risk of danger. 

The Intestinal Flora

The ribbed walls of your intestines are a home to many types of microorganisms and bacteria that aren't technically a part of your body; they aren't your cells because they don't contain your DNA. However, our bodies and these cells, over time, have developed a strong symbiotic relationship. We provide these organisms a place to live and thrive and, in exchange, they perform a number of critical functions for us.

The size and impact of this bacteria in our gut can hardly be understated. There are more microorganisms in the gut than there are cells in our entire body, and all of the cells combined can weigh as much as the liver, sometimes even more.

This bacteria, known as the intestinal flora, helps the immune system fight invaders. When there is no current threat, the intestinal flora stimulates the GALT in what is known as immunomodulation.

Our immune system usually attacks bacteria, but it seems to have a truce with the bacteria of the intestinal flora, as long as they don’t try to get into the bloodstream through the intestinal wall.

The intestinal flora also aids in digestion.

Certain nutrients, such as the B vitamins, have to be pre-digested by bacteria before the body can absorb them.

Our intestinal flora is also a key player in detoxification. It rids the body of 40% of the toxins in food.

In this sense, they serve as a satellite liver. Put another way, if the gut didn’t have the intestinal flora, the liver would have to work almost twice as hard.

The Gut's Nervous System

Our digestive tube is formed by various muscle cells and immune cells. Tiny nerve filaments, connected to these cells, direct, regulate, modulate, and coordinate their various functions.

The neurons in your gut orchestrate peristalsis and digestion, and modulate immunity and the hormonal system. Without them, the gut would cease to work.

Surprisingly, there are more neurons in your gut than in your head. Additionally, the "brain in your gut" is way more active in the production of neurotransmitters than the brain in your head. Almost 90% of the neurotransmitter serotonin, the neurotransmitter responsible for the feeling of happiness and well-being, is manufactured in the gut.

Survival Disguised as Disease

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What we call disease is actually just different forms of our natural survival mechanisms. The immune system has many different functions that it performs in various situations.

The white blood cells called neutrophils, for instance, attack bacteria, while monocytes, another type of white blood cell, go after viruses. When allergies flare up, eosinophils and mast cells are put to hard work, while phagocytes eat away at dead cells and foreign objects.

However, the immune system reacts uniformly to any and all inflammation.

Inflammation is the name for a set of basic responses that establishes the inner conditions for the immune-system cells to get to work more effectively. Vasodilation and increased permeability of the blood vessels are two basic responses. These allow the migration of immune-system cells from inside the blood vessels into the area where they are most needed.

Inflammation is healthy and natural. The problems occur when inflammation becomes systemic, meaning affecting your entire body.

Systemic inflammation can linger undetected for years and lead to such chronic diseases as heart disease, cancer, diabetes, or any number of autoimmune diseases.

Chronic diseases are a result of systemic inflammation. But before systemic inflammation is a result of gut dysfunction.

Heart Disease

The number-one killer in the United States is coronary artery disease.

When an arterial wall is injured, your body temporary patches the hole with cholesterol plaque in an attempt to heal and prevent further bleeding. Your cells will divide and eventually repair the artery wall at which point the cholesterol will be washed away.

Systemic inflammation, caused by sustained gut dysfunction, never turns off the plaque building mechanism even after the artery is repaired. The plaque keeps getting built until it eventually blocks all blood flow through the artery. 


Cancer is the name used for a number of different diseases with one thing in common: a group of cells that have started to terrorize the body.

These terrorist cells kill innocent cells around them by multiplying excessively, compressing neighboring tissues and organs, competing for nutrients, and releasing toxins into the circulation.

When internal conditions are bad enough, it is more likely for normal cells to become cancerous. These bad conditions: systemic inflammation, nutrient depletion, acidity, absorption of toxins, and an infiltration by invading organisms are all direct consequences of gut dysfunction. 

Cancer is the result of many factors, including genetics. But even genetic factors are connected to the gut.

Carrying the gene for a certain cancer does not guarantee that the cancer will develop. Genes can be turned on and off by the conditions in which the cell is living. Nutrigenomics is the science that studies how nutrients, a lack of nutrients, or toxic molecules absorbed from our food can activate a gene that was previously dormant. The conditions that turn cancer genes on, however, are mostly the result of gut dysfunction.


Serotonin is one of a number of different neurotransmitters that neurons use to communicate.

Serotonin is responsible for feelings of happiness and well-being, and a lack of it is linked to depression.

It requires specific nutrients for its synthesis, such as 5 HTP, vitamin B6, magnesium, and calcium. When the gut is dysfunctional and absorption is reduced, these invaluable nutrients are amongst the first to become scarce. Without them, neurons are unable to assemble enough serotonin.

During gut dysfunction, your gut has to dedicate energy and resources to coordinate survival mechanisms, diverting its attention from the production of healthy levels of serotonin.


What we call allergies are really just an exaggerated response of the immune system to common and essentially mildly threatening foreign materials or invaders. The body comes into contact with a threatening surface and puts into motion certain mechanisms to try to get rid of the foreign material or invader: a sneeze, itch, cough, or tear to expel whatever it is the immune system is alarmed by.

Your immune system at the border in the lungs was responding to pollen in an exaggerated way. Pollen only caused that reaction when meeting cells from the immune system in the lungs that were hypersensitive. They over-responded.

Autoimmune Diseases

Autoimmune disorders are almost always treated in the same way. After a round of painkillers and nonsteroidal anti-inflammatories, treatment continues with prednisone or some other steroid, which depresses the immune system and makes the attack on the tissues less intense or cease altogether.

This is like secretly adding valium to the U.S. Army’s drinking water. The troops will lose their edge; they’ll be half-asleep. This is both good and bad. When the body’s own troops are sleepy and drowsy because of medication, they simultaneously ease their attack on other threats, which makes people more likely to succumb to infections, develop cancers, plus a whole series of other negative side effects, including weight gain, water retention, and other hormone imbalances.

Back Pain

When the immune and nervous systems in the gut battle dysbiosis and hyperpermeability (leaky gut), blood flow increases to meet the higher oxygen and nutrient demands of an army and communication network at war. As a result, the entire gut becomes engorged. It expands and pushes the tissues and organs around it.

It first pushes in the direction of the abdominal wall, since there is less resistance on most people’s abdominal walls due to a general weakness of muscles there. This causes the abdomen to protrude— the

To compensate for all this increased pressure, the body readjusts its posture. The result is back pain in all of its varying forms, each related to the specific ways in which an individual’s body realigns to cope


A female body requires certain basic conditions to support the growth of a baby.

A sense of alarm in the GALT, triggered by dysbiosis and a leaky gut, is enough to prevent pregnancy. It creates an inner atmosphere that the body interprets as unsafe for pregnancy.

Cortisol is a hormone that helps the body adapt to stress. However, in our bodies, when we overproduce one hormone we have to underproduce others to maintain homeostasis, the natural balance our bodies constantly work to achieve.

When the body is overproducing certain hormones to deal with an unstable gut, the body isn't making enough of the other hormones that are necessary to create a pregnancy-friendly environment. 

The hormones that sustain survival mechanisms inhibit the hormones that create an adequate cellular environment for conception and gestation.

Gluten Sensitivity

Gluten is a protein found in grains, such as wheat, rye, and barley. Its sticky, glue-like property makes gluten especially useful to the food industry, which uses it in products as a binder, filler, shaper, bulking agent, texturizer, and stabilizer.

  • Gluten binds juices into food-like products for sweetening purposes.
  • It prevents shrinkage of foods and moisture loss.
  • It helps dissolve fats by emulsifying them into foods.
  • It is added to beverages to provide “body.”
Gluten is associated with cancers of the mouth and throat, esophagus, small intestines, and lymph nodes. It is also associated with type 1 diabetes as well as thyroid disorders, such as Hashimoto’s, the most commonly diagnosed thyroid dysfunction in America.

In order to digest gluten, the intestinal wall produces an enzyme called transglutaminase. Transglutaminase breaks down gluten into its smaller building blocks, the peptides gliadin, and glutenin.

For reasons unknown to modern science, the surface of the glutenin peptide is coded as safe, but gliadin is coded as dangerous in people with a genetic predisposition.

In some people, the breakdown of the natural transglutaminase enzyme will start tearing apart the intestinal wall. 

In its most severe expression, this is known as celiac disease, which presents as weight loss, diarrhea, bloating, abdominal pain, and an overall failure to thrive.

This severe form of presentation is relatively rare, but for every person diagnosed with celiac disease there are an estimated eight others whose symptoms are atypical and therefore much harder to diagnose. Analysis of data has shown that when people are finally diagnosed, they have been suffering for an average of 10 years.

The Clean Gut Program

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As I stated in my statement about these book summaries, the purpose of these summaries are to give the reader an idea if this is a book they would be interested in purchasing.

I will not be going into detail on the program, as I feel that will cross the line of fair use and into copyright infringement.

Here is a high-level overview.

Program Overview

The first phase of the program, which lasts 21 days, you will eat a very minimal and simple diet containing only whole foods known to be gentle on your gut.

The second phase of the diet reintroduces various food into your diet one at a time over the course of a week. By introducing foods one at a time you will be able to identify specific foods that do not promote your long-term gut health.

During the program you will also create your own dietary blueprint to fit your specific needs and lifestyle.

Guiding Principles for Clean Eating

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We face an overwhelming amount of choices about our health, much more than ever before. 

Not only do we have to navigate a landscape of unhealthy food choices, we also have to sort through loads of conflicting health information. To deal with this information overload, simple principles can help us cut through the noise of conflicting opinion.

Principles can help shape how we make decisions as well as give us a constant foundation to turn to when we're unsure where to go next.

What Not to Eat

Certain foods will cause bad reactions within your body. These are your toxic triggers and they prevent your body from functioning properly.

You have to know what not to eat and make the connection between the food you eat and how it makes you feel.

Clean eating has a lot to do with figuring out things for yourself and seeing what works for you and the best method for finding the foods that are toxic triggers for you is by testing them.

What to Eat

There is an overwhelming amount of opinions on the best diet for humans, but one thing that's almost universally agreed upon is an emphasis on whole, unprocessed foods.

This is where “what to eat” connects with “what not to eat.”

A perfect example is gluten and dairy. They are both whole foods, but they are also highly allergenic foods. This is the importance of testing our your diet for yourself.

The basic template for your long-term health is whole foods minus your toxic triggers.

How to Eat

We’ve forgotten how to eat in a way that nourishes our bodies.

  1. Processed foods send the body mixed signals, causing us to overeat and become chemically addicted to these foods.
  2. Since childhood, most of us have built emotional relationships to processed foods.
When the sweet receptors in the brain are overstimulated by sugar-rich foods, sugar easily overrides the mechanisms for self-control.

Processed food is so difficult to digest that our bodies send a tremendous amount of energy from the nervous system to the digestive system. As a result, we're overcome with a wave of sluggishness.

Supplement Right

There is a lot of confusion about supplements.

We have a simple philosophy at Clean: supplements help plug the nutritional gaps that keep us from reaching our health goals. While eating a clean, whole-foods diet is the most important first step, supplements can help correct nutritional deficiencies that have occurred as a result of poor lifestyle choices and impaired gut health.

Understand the Psychology of Clean Living

One of the challenges to living clean is changing our habits. Habits take time to become ingrained, and during that period when we’re learning how to do something new, there are ample opportunities to get off track.

Sometimes we don’t know how to live healthier because there’s an information gap. We are not sure what to do or how to follow through. But most of the time, we do know what works; we just have trouble making the necessary changes.

Move and Chill

Exercise and rest are two of the most fundamental practices for living clean for life.

They also cost the least and can help us make serious gains in our health, if we give them some attention.

When we exercise, we burn fat and excess weight, create endorphins, which make us feel great and improve our mood, and build strength and endurance.

When we get enough sleep and unplug, we give ourselves time to recharge and reflect.

Both moving and chilling directly help us reduce the amount of stress in our lives and make us better at handling stress when it does occur.

Where to Buy

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Buy the book on AmazonBarnes and NobleBAM, or just Google it. (I receive no kickback or commission for these links or summaries. See my disclosure for more.)


  • How Alejandro Junger became interested in gut dysfunction
  • What he learned from a year working in medicine in India
  • An exact, step-by-step plan for the Clean Gut detox and diet
  • The four pillars of gut repair
  • How the 80/20 rule applies to clean eating
  • A quick reference guide of food to eat and foods to avoid
  • A list of supplements to aid your progress
  • The "Big Three:" processed sugar, caffeine, and alcohol.
  • Over 50 pages of Clean Gut recipes
  • And much, much more!
Erik Cianci