The Toxin Solution

Chapter 4. Clean Up Your Gut

With each passing day, more and more people actively seek ways to detoxify. And that is due to increasing public concern about the mounting toxic load that contributes to symptoms and illness. I applaud this development! But knowing that detox is necessary is not the same as fully understanding how to safely detox. Nor does it mean that any and all detox approaches are equally effective. Or right for you. Yes, a quick detox might vastly improve your nutrition, compared with the stuff you were eating before. Yes, a daily diet of green drinks could work for you—if you are an eighteen- to twenty-five-year-old who’s eaten clean foods since childhood, rarely drinks, and never smokes.

But what if you ate a lot of junk food as a child or during your teens? What if you were a party animal who drank and drugged your way through your teens and twenties?

What if in your thirties and forties you are a hardworking professional or a multitasking mom or dad who cuts corners to save time, gulping down a breakfast of doughnuts and coffee, eating takeout while working at your computer, guzzling sodas or downing protein bars to keep your energy going as you rush through the day and work on into the night?

What if, without knowing it, you were born with an underfunctioning detox capacity?

Or what if you have landed in your late forties or fifties with low energy, weight gain, fatigue, stress, anxiety, and poor sleep?

In all these extremely common scenarios—and notice that I don’t even mention people who have joined the swelling ranks of those with chronic illnesses, chronic pain, or even more serious health conditions—you need a more highly calibrated form of detox. Healthy food and drink, while providing you with a sound nutritional baseline, cannot alone rectify the damage already done to your organs of detoxification over your lifetime.

Instead, it’s essential that the organs of elimination themselves (gut, liver, and kidneys) first be repaired. And to ensure that you initiate detox safely, they must be repaired in the right sequence. Otherwise, you can unleash more toxins than your body can safely handle. Yes, you need to detox, but your body’s detoxification organs need help—a lot of help—to detox effectively. And that’s what the next three chapters will provide.

In chapter 2 of The Toxin Solution, you learned the simplest ways to decrease toxic load from all sources as much as possible, given that toxins are everywhere. Then, by following the Two-Week Jumpstart Diet, you further decreased toxins, while adding healthy nontoxic nutrition to give yourself a good baseline. The goal of this and the next two chapters is to introduce the right sequence of specific protocols to support each of the major detox organs—gut, liver, and kidney, in turn. As each organ is cleaned up via my two-week protocols, you can move on to the next. That way, you are encouraging toxins to leave your body in a way that your body can handle.

It Begins with the Gut

In this chapter, I begin with the gut and digestive tract, which is where detox must always start.

Why? Because unless you first clean up the gut, you keep passing along all of its toxins and toxic byproducts to the next organ downline—the liver. A toxic gut, which constantly leaks poisonous metabolites and other noxious substances, overloads the liver and kidneys. Initiating detox without first repairing your gut is like going through your home emptying all the dirt, waste, and throwaways into one giant garbage bag and then emptying that garbage bag into your refrigerator. Unless you are ready to take that garbage out the back door to the refuse containers, the effort is pointless. While this may seem like an extreme comparison, it’s not far off the mark. If your gut is overflowing with toxins it can’t process, it will pass along all that garbage to other areas of your body, where it will undermine healthy function.

To prevent other detox organs from getting overwhelmed, before stirring up toxin release, you must first lower the toxic load in the gut. Following my program will do that. Otherwise, if you begin to detox before this preparation, the body will protest.

That is why in this chapter you will first ensure that your gut is in good shape. In later chapters, I will help you open up key detox pathways in your liver and kidneys.

Conrad’s Story

Conrad’s wife, Maryanne, practically dragged him into my office. I’ve seen this scenario dozens of times, since women are generally much more attentive to health than men. Conrad was embarrassed to speak about his primary problem. He, ahem, was “not taking care” of his wife in bed. He had lost interest and capacity. Maryanne (also a patient of mine) was not happy. Because Conrad was only forty-five years old, this should not have been a problem for them.

Conrad’s diet was quite good, since Maryanne prepared their meals and had been following my nutritional guidance. (Though I suspect he regularly sneaked in unhealthy fast food.)

In a physical examination, I found nothing except for a tender and slightly enlarged liver. When I asked about Conrad’s work environment, I learned that he was an expert in fiberglass-boat repair (another of my patients who worked on boats). Although he took appropriate exposure precautions, they were clearly inadequate. Fiberglass is composed of plastic reinforced by glass fibers. To repair a boat, Conrad had to first use liquid epoxies and resins on the boat surface, next position glass fiber sheets on the damaged area, and finally coat with glues and resins. As you can imagine, this process releases huge amounts of toxic chemicals. While the body can rid itself of some of these chemicals, the process uses up the stores of detox essentials, such as the master antioxidant, glutathione. With constant exposure to toxins, glutathione levels plummet and the detox process is weakened. The result is that the most harmful chemicals can build up in the body. What’s more, a buildup of fiberglass dust is undesirable because it is carcinogenic.

To address Conrad’s toxic load, I put him on my then-standard detoxification program—and learned a hard lesson. When he came back to see me the following week (this time without his wife), he was not doing well. Counter to my instructions, he had gone out for drinks a few times with his buddies and had sneaked a few smokes. Relapsing into his old habits in the midst of a rapid detox made him feel sick as a dog.

What happened? When in the midst of his detox, with toxic chemicals already being released from his fat stores, Conrad smoked and consumed alcoholic drinks. Instead of releasing toxins, he took in additional toxins. Aged beverages, like his favorite whiskey, contain multiple difficult-to-detoxify aldehydes, esters, and ketones. Detox system overload!

So what did we do? First, Conrad stopped the detox program at once. Next, I used the same methods I offer in chapters 5 and 6 to slow his rate of detox (take more fiber and consume more calories). Then I used the protocol in this chapter to prepare his gut, followed by the protocols in the next two chapters to prepare his liver and kidneys. Only after that preparation was Conrad ready to safely let go of all the toxins accumulated from his occupational exposures. After fully completing the Toxin Solution, he was surprised he felt so much better—in all ways. Maryanne was happy again, too.

As you can see, the mistake I made with Conrad early in my professional career is the same one many people make when they initiate a detox program. To detoxify safely, you must balance the rate of toxin release with your ability to detoxify and excrete the toxins. The gut is a big source of toxins for most people. Following the advice in this and the next two chapters will save you from repeating that mistake.

Improving the function of the gut and downline detox organs is a lot easier once you slow the ongoing, daily barrage of toxins, as you have already started doing on this program. Nevertheless, toxicity will likely increase in your body—until you repair the leaky gut and eliminate all toxic gut bacteria, which is what you will do during week one of the Two-Week Gut Protocol in this chapter. My advice is: don’t put this off to another day. The gut-detoxification protocol, which you will learn more about shortly, dramatically decreases the bad bacteria in your gut and improves gut integrity, so that any toxins produced in the gut are less able to circulate through your body.

Although it’s now more widely recognized that the wrong gut bacteria contribute to increased disease risk, when I started seeing patients in 1973 this was essentially unknown. I was one of only two licensed male midwives in all of North America at the time, and most of my practice was helping women and young families. I noted that many women experienced vaginal and digestive upset after one to two weeks of taking broad-spectrum antibiotics. The problems were especially bad in those who had taken antibiotics for years to treat acne or chronic urinary-tract infections.

Although the health-conscious public now understands how to rebuild healthy gut flora through taking probiotics, at the time little was known about this. At first I recommended yogurt, which didn’t help as much as I expected. Then I asked some of the women to bring me their empty yogurt containers so I could look at the labels, and saw that the commercial brands were using probiotic strains that were easy to manufacture and store in grocery stores—but not natural or clinically effective for humans. I next searched the local grocery and health-food stores for yogurts with the right strains, and recommended those to my patients. Although the results were better, they were still not good enough. Prescribed professional probiotic supplements worked a bit better but still did not resolve the problem.

I realized that just supplying a few strains of healthy bacteria was not enough to eliminate the toxic bacterial overgrowth bred by long-term antibiotic use. I then tried several other strategies for killing off the bad bacteria. To test the results, I used something called the Obermeyer test (also known as the Indican test), which measures intestinal toxicity produced by the wrong bacteria in the gut. I quickly found that almost all these patients had a heavy load of toxin-producing bacteria.

After seeing thousands of patients and testing the results, I gradually learned what worked and what didn’t. By following the protocol in this chapter, people suffering from many different kinds of chronic disease have created the foundation for restoring their health. After all, if you can’t digest your food, how can you get the nutrients you need? And if your gut is dumping toxins into your blood, how can your body possibly work very well?

The Two-Week Gut Protocol

What’s going on in your gut? If you are like most people who come to my clinic, probably a whole lot more than you realize. Your gut is filled with bacteria, good and bad. Sometimes, even good gut bacteria release chemicals your body can’t easily handle. But it’s much worse when you eat unhealthy foods and have a gut overgrown with the wrong bacteria. Fast “foods,” ersatz “foods,” or sodas and sweets not only provide unwanted chemicals; they also promote the growth of the wrong bacteria. When the wrong gut bacteria digest food, these bacteria release toxic chemical by-products (called endotoxins) that add to your preexisting toxic load. Broadly defined, this umbrella term refers to any unwanted molecule coming from gut bacteria or food constituents that disrupts metabolism and winds up producing ill health and disease. (The strictest definition of “endotoxin” is bacterial-cell-wall-derived lipopolysaccharides. I prefer the broader definition above as more clinically relevant.) And aggravating these problems is a damaged, leaky gut.

Research shows that leaky gut is present in most chronic diseases, such as depression, diabetes, irritable bowel syndrome, inflammatory bowel disease, and rheumatoid arthritis. My best estimate is that one-third to one-half the North American population have excessive gut permeability. When the gut is leaky, undesirable food constituents and toxins from bacteria more easily enter your body.

These toxins inflame your gut and undermine gut function; but worse, they overload the liver and cause indiscriminate damage throughout the body. If you don’t clean up the gut first, you will pass that toxic mess along to the liver, making its job of getting rid of toxic chemicals even tougher. That’s why the goal of the program you will be following for the next two weeks is to:

1. Kill the bad bacteria in your gut.

2. Bind the toxic chemicals released as the bad bacteria die.

3. Reseed with good bacteria.

4. Repair your gut.

5. Stop the damage going forward.

As you will learn in this chapter, cleaning up gut toxins produces global health benefits. And throughout the rest of the chapter, I will give you a full picture of exactly how the science supports this assertion. You can get started by following this two-week protocol right away, as you continue reading this chapter. Each day, take all the recommended nutritional supplements and herbs. Read on after the protocol for a fuller explanation of how these recommendations will ready your gut to play its crucial role.

The good news is that there is a lot you can do to clean up the gut. And that is what you will do over the next two weeks through the protocols I offer in this chapter.

Table 4.1. Two-Week Gut Detoxification and Improvement Protocol


DAYS 1-7

DAYS 8-14

Step 1.

KILL the bad bacteria

Fiber supplements, 2 grams three times perday



Goldenseal root powder, 1 teaspoonthreetimes per day (six capsules)



Raw garlic c loves, two cloves per day



Step 1.

Repair the gut

Multibacterial probiotic that includes Lactobacillus and especially Bifidobacterium strains, one capsule three times perday



Fresh cabbage juice, 1 quart per day



Quercetin, 250 mgtwotimes perday



DGL, 250-500 mg three times per day, letting lozenges dissolve in the mouth



The Gut and Toxicity

Many people don’t like to think about what goes on “down there” and assume that our digestive systems can handle anything we eat—until symptoms say otherwise.

When I was a third-year naturopathic medical student, my professor, Robert Carroll, DC, ND, started the first class of the year with the provocative statement “Death begins in the colon!” This statement contradicted what I had learned in my two years of basic science courses. The textbooks I studied in those courses contended that the gut was a long tube, covered with a perfect protective membrane that admitted only nutrients the body needed while effectively keeping out the “wrong” bacteria and their toxic afterproducts. Medical wisdom of that time held that the gut was completely impermeable to anything bad. Today, the wide prevalence of “leaky gut” reveals how naive that notion was. But back then, few understood this.

I was therefore surprised to hear Professor Carroll’s claim that the digestive as well as many other health problems that so many people experienced resulted from gut toxicity. Restoring the gut to health and strengthening digestion improve overall health dramatically, he said. Later, as a medical student, when I went on clinical rounds I saw how common gut problems are in people suffering from a wide range of diseases. Still, I remained skeptical about the connection between the gut, toxicity, and health—until I began practicing on my own.

What Goes On in a Toxic Gut?

As I discussed earlier, the primary sources of external toxins are the foods you eat, the lotions and potions you put on your skin, and the chemicals you use to clean your home and care for your garden. However, another very important source of toxins arises from within your body—specifically, from your gut. Technically, the gut—a long tube coiled up in the abdomen, with the mouth at one end and the anus at the other—is actually “outside” the body. Open at both ends, the gut, unlike the rest of the body, is a nonsterile environment, full of bacteria. In fact, there are ten times as many bacteria in your gut as there are cells in your body. Every single day, those bacteria actively produce a lot of metabolites.

Understanding Metabolites

Metabolites are small molecules that are involved in almost all of the body’s metabolic processes. Nearly every physiological function, including energy production, is part of an ongoing chain of activities. The small molecules called metabolites either contribute to, or result from, these activities. But if they are the wrong metabolites, from bad bacteria, they can also poison these life-dependent metabolic processes. I mention this because I use the term metabolite quite frequently. Understanding this is highly relevant to detox. Why? Because health is all about optimizing the balance of molecules, metabolites, and enzyme functions in the body. For this to happen, the critically needed nutrients have to be absorbed from the gut; detox, on the other hand, entails processing the harmful molecules and metabolites out of your system in a way that ensures that they do the least damage. For example, clostridia are bad bacteria that produce highly toxic metabolites that are easily absorbed into the body when the gut membrane’s integrity is damaged.

Bacteria and the Gut

If you have good bacteria in your system, these will produce welcome molecules like B vitamins. But if you have the wrong bacteria, they will produce noxious endotoxin metabolites, with names like indoles and skatoles, that circulate in your system, disrupting metabolism. Although these terms have little meaning to the average person, what if I tell you that indoles and skatoles are also called cadaverine and putrescine, respectively? Does that begin to give you an idea of why you don’t want them? As these names imply, these are metabolites produced during decay.

In my first year as a primary-care naturopathic doctor, during the occasionally slow days of building my practice, I voraciously read medical journals. To my great surprise, one day I read a startling and controversial study reporting that, even in healthy humans, up to 1 percent of ingested proteins are absorbed intact through the intestinal wall—directly contradicting what I had just learned in the standard medical physiology textbooks. Instead of fully digesting the food, the gut allows a very small amount of food proteins, other molecules, and even bacteria to enter the body without being broken down. Hmm, that didn’t sound like an impermeable gut to me. In fact, the body is constantly intentionally sampling the contents of the gut so it can be on guard against infectious organisms. The gut has to be very smart, welcoming in all the needed nutrients, keeping out all the toxins, while carefully letting through a tiny bit of everything so it can protect against infection.

Absorption of any more than a tiny amount signifies that there are gaps in your gut wall and the body is losing control. Just like holes in a wall, these gaps indiscriminately let stuff in. They undermine gut integrity. Just as a balloon with pinprick holes on its surface can’t contain air, a damaged gut cell wall can’t contain the gut bacteria and toxins and keep them from entering your bloodstream. And once in the bloodstream, undigested food molecules can stimulate allergies and other immune reactions.

But that’s not all. The study also revealed that the absorption rate of intact proteins increases to as much as 10 percent during severe gastrointestinal infection when the gut lining is seriously damaged. That was the first solid research I read on how gut imbalances and gut permeability profoundly impact health. The vital importance of a well-functioning gut is better understood nowadays. Today’s integrative medicine clinicians know that gut issues like maldigestion, malabsorption, leaky gut, and harmful bacteria contribute to, and may even cause, most chronic diseases.

Jane’s Story

At age thirty-two, Jane had been recently diagnosed as having the early stages of rheumatoid arthritis. Although her morning pain and stiffness weren’t too bad and easily relieved by two aspirin, she was quite distraught. Her mother and all her aunts suffered from severe forms of the disease, so badly in some cases that their hands were quite deformed. She was not willing to accept her family physician’s prognosis that she was fated to live with a disease that would relentlessly progress despite multiple drugs.

Fortunately, she came to see me before her disease had progressed very far. I explained to her that I thought her joint inflammation was being caused by the triple whammy of a leaky gut (due to food allergies), toxic gut bacteria, and overreactive inflammatory activity. (Inflammation is a normal, important process in our body that replaces damaged tissues and fights infection. Unfortunately, modern lifestyle and diet result in overactivation of this process.) While all of this was new to her, she was eager to do whatever was necessary. Since many people are allergic to wheat and dairy, I suggested that she eliminate them from her diet.

She followed a diet, like the one on this program, that minimized toxins. It consisted of fish, fruits, vegetables, beans, nuts, and seeds. She also took the supplements I recommend for gut cleanup.

By the end of two weeks, her symptoms had already decreased by 50 percent. After one month of carefully following this diet-and-supplement prescription, she had no further pain in her joints. After three months, all her lab-test levels had returned to normal!

Not all of my rheumatoid arthritis patients respond so well. I still vividly remember with great sadness a fifty-five-year-old woman who had had the disease for over twenty years. Her hands were so deformed she could hardly hold a pen, and she was having chronic stomach problems from all the aspirin and other drugs she was taking. Although I applied exactly the same therapy, all we could accomplish was lowering her drug dosage. Sometimes diseases do progress to cause such serious damage, that they are past the body’s ability to heal.

Although people often can heal even supposedly “incurable” diseases, it’s important to act promptly rather than wait too long. The earlier an underlying problem is corrected, the better the outcome.

The gut is one of the hardest-working systems in the body. It has the very challenging job of digesting food—absorbing the nutrients from the food but not the toxins released by bacteria in our gut—while activating the immune system to kill the harmful bacteria off without damaging the desirable bacteria. Turns out the gut is actually pretty smart, maintaining careful control of what is allowed into the body, and what is kept out and then excreted in the stools.

Understanding the Gut Protocol

As you can see, restoring your gut confers many benefits. It will set the stage for detox, and it will help you recover and prevent many other illnesses. In undertaking this protocol, you can also rely on the good results experienced by hundreds of my patients. No one has ever been hurt by it, while many have been grateful to finally get their health back. The results are quite remarkable. Everyone reports simply feeling healthier. The basic approach is to:

 Kill off the toxic bacteria.

 Bind the toxins released from the bad bacteria as they die.

 Recolonize the intestines with good bacteria.

 Use herbs and nutrients to promote healing of the damaged gut cells.

The first step is getting the right nutritional baseline. Following the Two-Week Jumpstart Diet gives you everything you need. The foods and meal plans are high in flavonoids, carotenoids, and fiber to help you decrease gut permeability. Included are a rainbow of healthy fruits and vegetables that will help you safely release gut toxins, decrease inflammation, and make healthy molecules like butyric acid, which promotes intestinal-cell health.1 I suggest that you continue following the diet I recommended in chapter 3 for these next two weeks, while implementing the Two-Week Gut Protocol. At the end of this chapter, I’ll let you know what to avoid going forward to preserve your newly re-created gut health.

Week 3: Step 1. Kill the Bad Bacteria

For three days before starting this program, take fiber supplements, using 2 grams of fiber three times a day. As I mentioned earlier, the fiber helps ensure the prompt excretion of toxic bacteria via the stools.

Beginning on day 1, and for the next seven days, take 1 teaspoonful (six capsules) of goldenseal root powder (Hydrastis canadensis) three times a day. This great herbal medicine kills the harmful bacteria in your gut while being friendly to the healthy bacteria. You can also eat raw garlic if you want to speed up the process, since this interesting vegetable is also good at killing the bad bacteria. (However, please don’t visit me!) About 5 percent of the population, like me, have difficulty detoxifying the complex sulfur compounds found in raw garlic and, to a lesser extent, in other members of the onion (genus Allium) family. While I have never had a patient report problems with this protocol, if it makes you feel unwell, please make sure to slow down the process by taking less goldenseal and garlic, but definitely do not decrease the fiber. Though initially taking fiber may cause you to experience more intestinal gas, your body will adapt within a few days. Be sure to drink plenty of water with the fiber.

Week 4: Step 2. Repair the Gut

Now that you have eliminated the toxic bacteria, you will recolonize the gut with optimal bacteria. Three times per day, outside of mealtimes, take a good-quality multi-bacterial-strain probiotic (one that includes ten or more types of bacteria) with several species of Lactobacillus and, especially, of Bifidobacterium. This latter organism is one of the most researched, showing health benefits in many areas. Most health- food stores have several good options. (Good to take probiotics in Week 3 as well.)

Healing the Gut Walls

After you get rid of the bad bacteria in your gut, you can take various foods, nutrients, and herbs to facilitate regeneration of the gut cells.

Cabbage-family foods are high in glutamine, a healing nutrient that helps repair the gut walls. Cabbage also contains sulforaphanes, which increase liver detoxification. Drinking one quart a day of the fresh cabbage (or sauerkraut) juice is so powerful, it even heals stomach ulcers. You can get bottled cabbage juice, but the best way to obtain it is to make your own using a juicer. Add one beet and two stalks of celery to one-quarter head of cabbage to make a half quart of cabbage juice. I prefer juicers that keep the fiber in the juice—and they are also easier to clean. Even if, like some people, you decide you really like the taste, I strongly advise that you only drink this amount of cabbage juice for the time that I recommend here. Cabbage has compounds that bind iodine in the gut. This is not a problem in the short term, but after a few months it can decrease iodine levels (which are already low in the majority of the population) and cause a lower level of thyroid hormone production.

If you are among the group who don’t like the smell or taste of cabbage juice, you can take glutamine,one of the key, gut-healing nutrients in cabbage, 500 mg, three times per day. I always prefer to use food whenever possible, so try the juice first: you may be amazed at how much you come to enjoy it. Surprisingly, gut regeneration doesn’t take long; it can be accomplished in the one week you will do this program—as long as you also stop damaging the gut as discussed below.

Taking 250 mg of quercetin twice a day helps quench inflammatory processes in the gut. If you want to obtain quercetin from a food source instead, add yellow onions to your diet. Quercetin is what gives them their yellow color.3

I recommend taking licorice in the form of DGL (deglycyrrhizinated licorice), 250 to 500 mg, three times a day, letting the lozenges dissolve in your mouth. Researchers have documented for decades the power of licorice root to heal the digestive system’s damaged mucous membranes. One study found a 52 percent reduction in symptoms using licorice compared with 24 percent in those receiving a sugar-candy placebo.4

Licorice is particularly effective for healing stomach ulcers and the mucosal damage caused by aspirin, as mentioned below.5 You can use cabbage and yellow onions or glutamine and quercetin supplements for as long as you want, but licorice can be used for only a few months, because some people develop high blood pressure from it. That’s why I prefer DGL, another form of licorice, which has the problematic blood-pressure molecule removed and can be taken as long as you want.

Licorice and "Singer’s Voice”

My late teacher Dr. John Bastyr, after whom I named Bastyr University, was for decades the favorite doctor of the Seattle Opera. When performers from that troupe suffered from “singer’s voice” and became too hoarse to perform, they turned to him, because his “secret” herb (licorice) was so effective. Because I now lecture so much internationally on toxicity and detoxification, I have learned to always have licorice fluid extract (more concentrated than the tincture) with me: as my voice starts to fade after three to four hours of lecturing, I can always count on it to give me another hour or two of voice.

As the gut heals, your health is radically improved.

 You reduce the amount of endotoxins in your blood.

 Inflammation calms down.

 You can absorb nutrients from food.

 Your gut cells now keep in the gut what belongs in the gut, protecting the rest of your body.

You are prepared to successfully detox.

All of these benefits await you, and to ensure that you are motivated, I want to reveal all that goes into an unhealthy gut—and it’s quite a lot!

The Dangers of an Unhealthy Gut

Why does The Toxin Solution emphasize gut health to the extent of devoting two full weeks to it? Because when the digestion is not working properly, the gut becomes too permeable—or, in common parlance, “leaky.” When the gut “leaks,” undesirable molecules, food antigens, bacteria cell parts, and so on get through the gut membrane. Leaky gut syndrome triggers many other undesirable biochemical activities. For example, instead of keeping allergic substances and other toxins confined to the gut, a permeable gutcell lining allows these to circulate through the body.

Since human gut contents can be either beneficial or problematic, Mother Nature wisely designed our bodies so that all the blood from the gut first goes through the liver, to be detoxified before it circulates through the bloodstream. The bad news is that when this process goes awry—with bad gut flora, leaky gut, and liver dysfunction (all extremely common)—this toxic mess ends up overwhelming the liver and entering the body. Although leaky gut therefore contributes to most chronic disease, you don’t have to have a diagnosed serious disease to be suffering damage from a leaky gut.

For all of these reasons, the condition of your gut is a primary factor in your health. Unfortunately, few doctors understand and use this key insight. And yet, research connects endotoxins with diabetes, heart disease, and mitochondrial damage, among other problems. For example, a research group in Germany followed 122 patients with chronic cardiac failure—an advanced case of heart disease. They found that after two years, those with the highest level of endotoxins had a dramatically higher rate of death, with one-half the patients dying.6 In other words, endotoxins contribute to—and compound—a wide range of health issues.

The two main problems with endotoxins are that they:

 Contribute to toxic overload.

 Prevent your body from detoxifying successfully.

There is still some debate about the primary mechanisms. The body contains around ten pounds of gut bacteria—there are ten times more bacteria than there are cells of the body. Some bacterial metabolites may be beneficial. Endotoxins clearly are not. One theory holds that gut endotoxins use up liver capacity so that there is less ability to detox other poisons. Another possible scenario is that fat buildup in the liver (due to endotoxins) causes progressive dysfunction such that the liver can less effectively detoxify the gut toxins, thus allowing more of them to pass into circulation. When left unchecked, these toxic gut chemicals increase damaging oxidative stress throughout the body. Whether either or both theories turn out to be most accurate, it’s best to address endotoxins.

How Gut Toxins Cause Specific Diseases

In this section, I will help you understand what the Two-Week Gut Protocol is designed to correct. Let’s first highlight just a few of the ways in which the wrong bacteria in your gut cause toxicity and damage, including the following:

 Production of inflammatory chemicals, which translates into increased risk for cardiovascular illness, diabetes, and other health concerns

 Conversion of nutrients to toxins, so that you are both nutritionally deprived and toxic

 Conversion of dietary polysaccharides to sugar, which results in increased absorption of sugar and increased production of fat from carbohydrates—all of which contribute to weight gain and diabetes. Obese people convert polysaccharides to sugar at a much higher rate than lean people due to the types of bacteria present in their guts.

 Poisoning of mitochondria, which support health and vitality. Twenty-five percent of the volume of the typical cell consists of mitochondria.

 Undermining of the liver’s detoxification processes

Gut toxins are also responsible for weight gain, obesity, and diabetes. If you have ever tried to diet, it’s important to understand this. Even if you carefully avoid sugar, the wrong gut bacteria will convert healthy complex carbohydrates, like those found in beans, potatoes, and pasta, to simple sugars, the same types of carbs found in sweets. Intriguing new research shows that obese people actually lose weight when given bacteria extracted from the guts of lean people—with no change in diet. Of course, if the obese people stay on their unhealthy diet, they will stimulate the regrowth of the same toxic bacteria.

Here’s another key finding: the higher the endotoxin level, the higher the insulin resistance. In insulin resistance, a precursor to diabetes, the body’s cells do not respond to the presence of insulin. As a result, insulin can’t do its job of getting sugar from the bloodstream into the cells so it can be converted into energy and instead is stored in fat. People with the highest levels of gut endotoxins (the top 25 percent) have a greater than threefold increased risk of diabetes, compared with those in the bottom 25 percent.7

In addition, as endotoxins increase, levels of the good HDL cholesterol go down.8 This leads to increased toxic overload. Why? Because HDL is the “garbage truck” that carries endotoxins to the liver for elimination. HDL also carries fat-soluble toxins—like the POPs mentioned in chapters 1 and 2—to the liver for detoxification. So the endotoxins act as a double whammy: they are directly toxic, and they make it more difficult to get rid of other toxins by filling up the HDL, which is then unable to transport them to the liver. One reason why people with high HDL levels have less heart disease may simply be that they are better able to get rid of the highly inflammatory endotoxins.

What’s worse is that the wrong gut bacteria can change normal, healthy food constituents into toxins. For example, the wrong bacteria convert choline—which you need for cell membranes and neurotransmitters—into the toxic compound trimethylamine (TMA), which in turn is rapidly converted to trimethylamine-N-oxide (TMAO). TMAO results in the accumulation of cholesterol, causing atherosclerosis (plaque in the arteries).9

And that’s not all. The wrong gut bacteria make people reabsorb the very toxins the liver works so hard to release! Here’s how: In a process called Phase II liver detoxification, the body excretes chemical toxins by binding them, through a process called conjugation, to other molecules that safely carry them through the bile and into the gut, where they are eventually excreted (or to the kidneys for elimination in the urine). But when you have the wrong bacteria and not enough fiber, the bacteria remove the conjugating molecule—the molecule that makes the substance nontoxic—leading to the toxins’ reabsorption. This is why almost everyone is toxic: when you eat too little fiber and have the wrong gut bacteria, you lack the ability to get toxins out of the body.

Figure 4.1. Conversion of dietary choline to toxic TMA by inappropriate gut flora

For all these reasons, eliminating endotoxins through the protocol in this chapter will prevent many different kinds of illnesses, improve your nutrition, and set you up for healthy detoxification.

The Heart and Blood Sugar

Research also connects endotoxins with heart disease. As endotoxin levels rise, so do all the indicators of cardiovascular conditions—such as waist size, waist-hip ratio, total cholesterol, serum triglycerides, serum insulin levels, and other health problems. These markers also signify increased inflammation throughout the body. The immune system is always on alert to defeat an invading virus, bacterium, or fungus. This is an important way the body protects us from infection and regenerates tissues. But when inflammation is chronic, the immune system is overactivated, causing unintentional tissue damage. This is a key reason that most diseases, especially chronic diseases, derive from excessive inflammation. And it is also why so many disease names end in -itis (a suffix denoting diseases characterized by inflammation) —rheumatoid arthritis, osteoarthritis, dermatitis, and so on. But many other diseases also have a strong inflammatory component—for example, asthma, atherosclerosis, and Alzheimer’s disease.

Figure 4.2. How gut endotoxins disrupt metabolism

Healing your gut is a must, because almost everyone with any type of chronic disease has a leaky gut. The conditions that are most closely linked to leaky gut are:

 Abdominal bloating

 Aphthous stomatitis


 Atopic dermatitis

 Blastocystis hominis

 Candida albicans

 Celiac disease

 Chronic stress

 Entamoeba histolytica

 Essential fatty acid deficiency

 Food allergies



 Inflammatory bowel disease

 Irritable bowel syndrome



Rheumatoid arthritis Type 1 diabetes Type 2 diabetes

When the levels of toxins from leaky gut get high enough, the health condition worsens even further— to a dangerous condition called metabolic endotoxemia (ME). Most people who are obese—which is one-third of the population—have ME. This means they have much higher levels of the chemicals that produce chronic inflammation and oxidative stress.10 ME is strongly associated with many diseases. It’s unknown how many people in the general population have ME. It’s present in diabetes, cardiovascular disease, and obesity—I’d estimate in 10 to 25 percent of cases. It can be diagnosed by measuring endotoxins in the blood.

John’s Story

John was sick all the time, feeling like he always had the flu. He had recently read an article about “hidden infections” and thought an undiagnosed viral infection was causing his problems. When he came into my office, his problem seemed pretty obvious, since this five-foot-eight-inch man weighed about 275 pounds. Nonetheless, because I wanted to be supportive of his taking control of his health, I drew several vials of blood and sent them to the lab for every then-available test for infection. All the results were negative for acute or chronic infection.

I gave him an Indican test (a urine test that measures toxins that come from the gut). The results indicated a lot of gut toxicity. I explained to him that a toxic gut produces many of the same inflammatory molecules released when we have a viral infection and that he likely had ME. John assumed that I would, like other doctors, simply tell him to lose weight. I surprised him by explaining that his toxic gut was far worse for his health than being overweight.

John immediately started on the gut-detoxification program. Every two weeks we reran his Indican test, and as his toxicity decreased, so, too, did his symptoms. After six months, his Indican test was normal and all his symptoms were gone. He had also lost twenty pounds—without trying to lose weight! As you’d expect, he was very happy with the results.

Diseases Associated with Metabolic Endotoxemia11

 Cardiovascular disease

 Chronic inflammation

 Diabetes (type 2)


 Insulin resistance

 Nonalcoholic fatty liver disease (NAFLD)



Most people would be surprised to hear that the normally strong relationship between obesity and diabetes disappears when a person has a low level of toxicity. And overweight individuals who regularly exercise do not have the expected increase in heart disease. I am not saying that obesity is good for you! What I am saying is that the toxicity and lack of exercise that typically cause the obesity are the problem. Decreasing toxins and engaging in healthy behaviors are more important than what the scale says.

As John’s case reveals, a toxic gut is worse than merely being overweight. Even if you don’t have full-blown ME, endotoxins send health in the wrong direction and increase the risk of getting these—and other—ailments. That is why it’s vital to repair your gut and address endotoxins now.

(As an aside, one of the challenges in medicine is the constant fads. Back in the 1980s, “hidden infections” were the rage, and a number of chronically ill patients sought my help in diagnosing them. With only two exceptions, every one of them was suffering from an unhealthy diet and lifestyle, not a hidden infection.)

The source of many common ailments is not always intuitively obvious when symptoms manifest themselves. And that is one of the reasons why, in this book, I provide a lot of scientific background to help you feel confident in following my suggestions. It’s important to both follow the program and understand why you are following the program. And it’s also extremely important, once you have completed these two weeks, to avoid disrupting your gut going forward.

Stop the Damage Going Forward

Now that you have repaired the past damage to your gut, you may be wondering how to stop future damage. What undermines gut integrity? Good question! Let me single out four of the most important things to avoid if you want a healthy gut:

1. Nonsteroidal anti-inflammatory drugs

2. Excessive consumption of alcohol

3. Consumption of high-fructose corn syrup

4. Food allergies (discussed in chapter 7)

Though widely ingested, each of these attacks cell-wall integrity. Let’s find out how they do this.

Nonsteroidal Anti-inflammatory Drugs

Aspirin and acetaminophen are the quintessential over-the-counter pain-management offerings. You may have heard the scientific term for them, which is nonsteroidal anti-inflammatory drugs (NSAIDs). (Yes, acetaminophen is not technically an NSAID, but they are typically grouped together.) Though convenient, and in wide use, these drugs cause far more harm than most doctors and users of them realize. Studies show that NSAIDs produce gut damage and gut permeability.12 Thirty million people take NSAIDs every day. When taken regularly, it’s been shown, NSAIDs both increase absorption of toxins and decrease absorption of the healthy nutrients your body gets from food—exactly the opposite of what you want. Instead of using NSAIDs to dial down your perception of pain and other symptoms, it’s far better to find and treat the causes of your symptoms. All NSAIDs increase gut permeability within hours of ingestion. NSAID-induced damage is estimated to significantly increase rate of death in users.

Table 4.2. Gut Damage from Regular Use of NSAIDs



Gut inflammation


Leaky gut




Mucosal ulceration


Blood loss and anemia


Other NSAIDs that increase gut permeability include ibuprofen, indomethacin, naproxen, Vioxx, and Feldene. I always recommend treating the causes, not the symptoms. Sometimes, of course, we need to decrease symptoms in the short run to allow time for healing to take place. But even then, I try to use natural therapies that support the body’s own efforts to heal rather than drugs that are yet another chemical that the body has to detoxify. For example, women having menstrual cramps will often find magnesium with pyridoxal-5-phosphate (P5P) supplements more effective than NSAIDs. This also helps those suffering migraine. If you have an inflammatory condition like allergies or asthma along with migraine, you’ll find the herb butterbur very helpful. Readers wanting to learn more about natural therapies for common diseases will find my Encyclopedia of Natural Medicine a helpful resource.

Excessive Consumption of Alcohol

In my early years as an extremely health-conscious new naturopathic doctor, I carefully avoided alcohol. My grandfather pointed out that all my long-lived forebears drank one or two full glasses of red wine every evening. I, of course, confident in my arrogance, was sure he was wrong. Well, wise sayings of yore endure because they contain a kernel of truth.

Let’s look at what alcohol does to gut permeability. The more alcohol a person drinks, the leakier the gut. Note in figure 4.3 that even three hours after alcohol consumption, excessive gut permeability persists.

When alcohol meets your gut cells, it activates an enzyme called cytochrome P450 2E1 (CYP2E1), which detoxifies the alcohol. This process releases free radicals, which can be neutralized by glutathione, a major antioxidant. But that can happen only if there’s enough glutathione available. Once glutathione gets depleted by alcohol consumption, the free radicals multiply and alcohol leaks into the body.

Figure 4.3. Alcohol increases gut permeability in a dose-dependent manner

When intestinal cells are damaged by alcohol, they also allow increased entry of endotoxins. In fact, some researchers now suggest that anxiety, depression, dementia, facial rash, and other symptoms associated with alcoholism may result from endotoxin damage, not just alcohol.

The research clearly shows that light to moderate alcohol consumption is healthful, while too much alcohol is quite damaging. But what constitutes healthful levels? The answer varies widely, based on genetics, nutritional status, and environmental toxin load.

For example, people deficient in vitamin D experience more leaky gut after consuming alcohol than those with adequate vitamin D levels. The majority of Americans are deficient in vitamin D. This deficiency makes gut permeability from other causes worse as well.

Bottom line: the safest approach is to follow the general guidelines of one or two alcoholic drinks per day for women and two or three per day for men.

Figure 4.4. Alcohol causes release of free radicals in intestinal cells, causing leaky gut

High-Fructose Corn Syrup

It used to be that only late-stage alcoholics suffered from fatty liver disease. But now nonalcoholic fatty liver disease (NAFLD) affects a stunning 31 percent of the U.S. population.13 (It was 18 percent in 1990 and 29 percent in 2000.) Even children now suffer from this terrible illness. Children with NAFLD have ten times more endotoxins than healthy children.14 The question is why?

It turns out that a few years before NAFLD was first seen, high-fructose corn syrup was introduced into our diets. Along with its well-known disruptive effects on blood-sugar regulation, high-fructose corn syrup (HFCS) raises endotoxin levels. Serious research now connects consumption of HFCS soft drinks and NAFLD.15 In figure 4.5 you can see that the number of soft drinks consumed correlates with higher levels of fatty liver disease and metabolic syndrome (MS). When fed to mice at levels now commonly consumed by foolish humans, HFCS causes an elevation of endotoxins in the blood and outright NAFLD.16

Figure 4.5. Correlation between soft-drink consumption per day and fatty liver disease

Going forward, to protect your healed gut from further damage, make sure to avoid consuming HFCS. It is not necessary to avoid fruit, which has fructose. The level of fructose in food is much lower than that found in soft drinks, and fructose in food is more slowly absorbed.

Food Allergens

Any kind of allergic response can cause gut-wall inflammation and leaky gut, increasing your risk for illness.


As you focus on healing the first pathway of detoxification—the gut and digestive function—you will accrue tremendous benefits. With a deeper understanding of the damage caused by a toxic gut, you can follow the four steps you need to take to heal it. To summarize:

Step 1. Eliminate the bad bacteria.

Step 2. Add fiber to bind the toxins and carry them out of your system.

Step 3. Introduce healthy bacteria and repair the gut walls.

Step 4. Stop the damage from recurring.

In chapter 7, I will offer other recommendations for increasing digestive health going forward.

You are now well on your way to improving your health and vitality and establishing the foundation for a disease-free life. There is nothing more important than a properly functioning intestine. Health starts with a clean gut with the right bacteria, well-functioning membranes, and effective digestion that completely breaks down foods so their life-dependent nutrients can be absorbed and toxins kept out.

As the gut heals, everything else gets better. And I truly mean everything. Endotoxins no longer poison you. Inflammation is calmed. The liver is no longer overloaded, so it can deal with the rest of the toxins. Nutrients can be better absorbed. All of this because the gut now works as it is supposed to.

Now, let’s get your next key detoxification organs—your liver and kidneys—healed and functioning, and able to detoxify successfully.

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