Gut Check: Unleash the Power of Your Microbiome to Reverse Disease

What if I told you that free will is an illusion but that instead of a vast, mysterious universe out there controlling our fates, there is actually a vast, mysterious universe within us that we are on the verge of being able to comprehend? By the end of this book, I hope to convince you that this is true, teach you how this universe was designed to guide and support you, and empower you with the ability to restore this universe—which we have unknowingly decimated—to heal anything that currently ails you.

Have you ever seen the movie Men in Black? In one scene, there’s a little alien named Frank the Pug who tells the main characters that the galaxy they are looking for is here on Earth: “The galaxy is in Orion’s belt.” The humans are understandably confused. They assume that he is referring to the well-known constellation Orion, which, first of all, is not on Earth, and second, whose belt is made up of three stars. Galaxies have an estimated one hundred million stars. How could three measly stars contain an entire galaxy?

As Frank goes on to explain, “You humans! When are you going to learn that size doesn’t matter? Just because something’s important, doesn’t mean it’s not very, very small!”

Over the course of the film, the protagonists come to understand, as I have, that whole galaxies can exist in unexpected places. And that was exactly what the little Frank the Pug was trying to communicate. It turns out that an unfathomably vast galaxy of stars, solar systems, and planets filled with beings is actually hanging off the collar of a cat named Orion. Get it? Orion’s belt.

Those characters made the same mistake as humans everywhere. But instead of looking up at the stars, we’ve looked in all the wrong places for answers about our health and longevity. We’ve focused our search externally, assuming that the most important things are physically big and therefore must live outside us, whereas in reality the most significant, far-reaching contributors to our well-being and health are actually the smallest. And to find them, we must look inward.

The truth is that inside your digestive system lives a galaxy made up of trillions of bacteria belonging to at least ten thousand different species, plus an as-yet-undetermined number of viruses, fungi, and other microbes. This is your gut biome. You also have an oral biome with seven hundred species of bacteria and a skin biome with a thousand different species. As I’ve written before, all these living microscopic creatures collectively make up your holobiome. Among them, these microbes contain more than three million genes, whereas the human genome contains a mere twenty-three thousand.

Take a moment to consider just how vast this thing is. There are somewhat more than eight billion human beings on this planet. That means there are 12,500 times as many bacteria in your own gut as there are humans on Earth. If you prefer plants to humans, consider this: it was recently calculated that there are approximately three trillion trees on Earth.¹ That’s more than seven times as many as experts previously believed, despite the billions that humans cut down each year. Even with that discovery, however, there are ninety-seven trillion more bacteria in your gut than there are trees on Earth.

When I was in medical school back in the Stone Age, we were taught that the human gut was basically a hollow tube. Food went in, digestion occurred, proteins, sugars, and fats were absorbed, and whatever waste was left over came out as feces. Now we know that our gut is akin to a teeming tropical rain forest with its own diverse ecosystem, communities, and multiple signaling devices, languages that single-celled organisms use to talk among themselves.

Quite startlingly, they also use these languages to tell your mind and body how to think, feel, and behave and how to maintain your skin, muscles, joints, organs, cells, and even the organelles within your cells to keep them healthy—or, conversely, to attack them with inflammation and disease. These billions of single-celled organisms manipulate and control us in unfathomable and downright shocking ways.

It’s been only six years since I wrote The Plant Paradox. I thought I knew a lot back then, and I’m pleased to say with the passage of time that I was on the right track. But in the time that has elapsed since the publication of that book, scientists have discovered a whole new world of information about the microbiome and the multiple languages its members use to interact with every part of our bodies, to communicate with one another, and, most important, to control the power plants in our cells, our mitochondria. Through these communication signals, they exert control over every aspect of our health, wellness, and longevity. And you are about to learn how to decipher this system and use it to your advantage.

Let me start with a small (literally) example of how these bugs can control us.

Many of us are familiar with the single-celled organism Toxoplasma gondii, which is responsible for the disease toxoplasmosis. Pregnant women are told to avoid close proximity to cat litter and to have their partner “scoop the poop” for the duration of their pregnancy because cats can pass along toxoplasma in their feces. If a pregnant woman becomes infected with toxoplasmosis, it can cause severe health problems in her unborn child. But of course, most of us don’t stop to consider how this single-celled creature came to live in cat litter to begin with.

Bear with me for a moment. I promise that whether or not you ever plan on getting pregnant or owning a cat, this relates to you in more ways than you can probably imagine.

Toxoplasma has two life cycles. There is a host that the organism ultimately wants to get to, and it uses an intermediary host before arriving at that final destination. In this case, the final objective is a cat. It can be a tiger, a house cat, any kind of cat. Toxoplasma can reproduce only in the gut of a cat—and, like all life-forms, its end goal is to reproduce and pass on its genes to the next generation.

To get into a cat, toxoplasma uses a rodent as its intermediary host. This makes pretty good sense. After all, rodents are famously cats’ favorite prey. Just look at Tom and Jerry, my favorite cartoon when I was a kid. It seems logical enough for toxoplasma to hang out in the rodent, hoping that it will eventually be eaten by a cat so it can end up in that feline’s gut.

But toxoplasma has evolved over millions of years so that it doesn’t have to just wait around; it can actually change the rodent’s behavior so that it’s far more likely to get eaten by a cat. What’s that? A single-celled organism can manipulate the actions of a mammal? Yes, it can, and if I teach you anything in this book, hopefully it’s that single-celled organisms are far more intelligent than we’ve ever considered—and that they not only are capable of controlling us but in fact are already doing it. Constantly.

Okay, then, you might be thinking, the toxoplasma must paralyze the rodent or something similar to make it easier feline prey. That would certainly make sense, but it actually chooses a much more complex and nuanced mode of manipulation than that. Unlike brave little Jerry, most rodents are innately afraid of cats. They are repelled by the sight of a cat or even the smell of cat urine. In fact, if you take a rodent that’s never been exposed to a cat (or its urine) in its life and expose it to the smell, it will run away. That fear and the associated stress response are hardwired into the rodent for its survival.

Toxoplasma undoes that fear response. It manipulates the fear pathways in the rodent’s brain to make it not only less afraid of cat urine but actually attracted to the smell of it. Now, instead of running away, the rodent will approach the cat urine. Sniff, sniff . . . hey, that smells pretty good! Uh-oh, here comes the tomcat! And now the rodent is much more likely to end up in its belly.

How does toxoplasma do this? In his lab at Stanford University, Robert Sapolsky, one of my heroes and a professor of biology, neurology, and neurosurgery, studied the brain chemistry of rats that were infected with toxoplasma. What he discovered was shocking.²

In both rodents and humans, the amygdala is the part of the brain associated with fear. Toxoplasma infiltrates the nervous system of the rodent, travels to the amygdala, and shrivels the dendrites, which are the branches through which neurons receive information from other neurons. This disconnects the fear circuits in the amygdala. But toxoplasma is even more precise than that; it leaves the circuits associated with other types of fear alone and disconnects only the ones associated with the fear of predators.

Now the rodent is no longer afraid of cat urine and will no longer exhibit a stress response and run away when exposed to its smell. That’s pretty good. But how do you get it to be attracted to the urine instead? It turns out that in its genome, toxoplasma has the necessary genes to produce the main enzymes found in dopamine, the neurotransmitter that’s all about pleasure, attraction, anticipation, and reward. And it produces that dopamine and sends it to the rodent’s brain, activating a different circuit this time: the one that’s associated with sexual attraction.

When the rodent smells cat urine now, it no longer experiences a stress response because the pathways associated with the fear of predators have been deactivated. Even better, it really likes the smell because the sexual attraction circuitry is activated instead. The rodent will now run toward danger in the form of cat urine instead of away from it, often leading to its own demise.

This brilliant single-celled organism has completely hijacked the brain chemistry and behavior of a mammal for its own selfish purposes. Pretty darn impressive, isn’t it? But these little buggers don’t stop with rodents. In 2022, field biologists noted that many of the gray wolves in Yellowstone National Park were infected with toxoplasma and wondered if the wolves’ behavior was also being manipulated. It turned out that wolves with toxoplasma were forty-six times as likely to become pack leaders^3,4 as wolves without toxoplasma. Obviously, pack leaders must be bold risk-takers, and toxoplasma infection was causing them to take more risks. But why is toxoplasma bothering with wolves? Because the main predators of gray wolves are cougars, aka mountain lions, aka cats.

By now you might be thinking back to the cat litter situation. What is going on with toxoplasma and humans? When humans become infected with toxoplasmosis, they can get very sick, but many remain asymptomatic while toxoplasma lives in the body. An estimated one-third of the population in developed countries is infected with toxoplasma. Those people are considered asymptomatic because they are not sick, but that doesn’t mean that they aren’t affected by it.

In fact, it is during this latent stage that toxoplasma begins producing the enzymes that make up dopamine. We may not become attracted to cat urine, but humans with toxoplasma do become a little more impulsive, tend to disregard rules, and are more likely to put themselves into harm’s way to save others! So all of those so-called heroes out there may just be acting as tools for toxoplasma.⁵ Humans with toxoplasma also have two to three times the likelihood of dying in a car accident due to reckless driving as do people without toxoplasma.⁶ That extra dopamine certainly makes us run toward danger.

There is also an interesting link between toxoplasmosis and schizophrenia.⁷ We know that patients with schizophrenia have altered dopamine levels in the brain. And if rodents that have toxoplasma are treated with the same drugs that are used to treat schizophrenia, they stop being attracted to cat urine. Pretty wild.

But why would toxoplasma want to mess with a human? After all, it can’t reproduce in our gut. In some parts of the world, humans and great apes have always been the main food choice of tigers and other big cats. Indeed, some researchers have looked at our closest relatives, chimpanzees, which are the prey of leopards. Lo and behold, chimps do in fact lose their aversion to leopard urine when they are infected with toxoplasma.⁸ And remember, toxoplasma isn’t picky about which breed of cats it lands in; it’s just as happy reproducing in the gut of a tiger or leopard as it is in Tom’s belly.

In other words, toxoplasma uses us (and our close chimpanzee relatives) in the exact same way it does rodents: it eliminates our fear and causes us to run toward danger so that we turn ourselves into easy prey. We think that we’re the highest-functioning organism on the planet and that our mind has complete control over our behavior, but in the hands of a simple single-celled organism, we are essentially nothing more than a giant lab rat.

Is this a mic drop moment or what? I assure you, there are plenty more to come.

The thing is, this is not a rare pattern. Like toxoplasma, the other single-celled organisms that use us as their hosts exert their control over us in a multitude of highly complex, sophisticated, intelligent ways.

As Frank the Pug asked, “You humans, when are you going to learn?” The truth is that there’s still a lot we don’t know about this microscopic galaxy. But we can’t afford to wait until we have the full picture to act. For too long, we’ve overlooked these microbes in favor of the relatively tiny number of cells that constitute what we think is human. Now we are paying the price. There is power in numbers, and those numbers tend to dislike being ignored.

Yet that is exactly what we have done. In fact, we’ve gone far beyond simply ignoring the majority; we’ve treated it with outright hostility. Over the past fifty years, we have introduced innovation after innovation that has overlooked, depleted, and destroyed our microbiomes. It’s no coincidence that in the same time frame there has simultaneously been a stark increase in major diseases, from obesity to the current mental health crisis to the autoimmune epidemic that I treat in my clinics every day.

In this book, you’ll see how each of these diseases, and many more, are directly tied to the ways that modern living has decimated the majority shareholders in our guts. It’s safe to say that these microbes are angry, and they’re not going to take it anymore. We are all in dire need of a Gut Check.

The good news is that the vast majority of the bugs living in our guts do not want us to run toward danger as toxoplasma does. Quite the opposite! They want us to stay healthy and thriving because it is in their own best interest. As far as these gut buddies, as I like to call them, are concerned, we’re the cat; they want to reproduce in our guts and pass on their genes.

Our relationship with these bugs is symbiotic. Your body is their home. Ever since the time of Louis Pasteur, we have been taught that these bugs are our enemies and mean us harm, or that at the very least we would be better off without them. But as we now know, we can’t live well without them. And if you treat them well, they will in turn take good care of you.

Hippocrates was 100 percent correct more than twenty-four hundred years ago when he said, “All disease begins in the gut.” He also believed that a physician’s purpose was to be a detective. He proposed that we all have within us (translated from Greek) a “green life-force energy” that provides perfect health. The physician’s job, he suggested, is to identify the factors that prevent our green life-force energy from flourishing and teach the patient to remove those causes with no further intervention.

At the risk of sounding a bit woo-woo, I believe that Hippocrates was right about our life force. No matter what is ailing my patients, I investigate until I discover the root cause, which without fail lies in their gut. As I’ve written elsewhere, once we restore the gut to a state of equilibrium, the disease often abates or even disappears. I don’t have to do anything except act as Sherlock Holmes. Our green life force is the galaxy of very, very small beings living behind your belt! And now that scientists are discovering the mechanisms behind these diseases, I propose advancing Hippocrates’ theory a step further to say that all diseases can be cured in the gut, too. And with the Gut Check program, that is exactly what you will be able to do.

So let’s get going. We’ve got a whole galaxy to explore.