Harness the Power of Your Gut Bacteria to Boost Your Mood and Heal Your Body


By Raphael Kellman, MD

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A groundbreaking, medication-free, scientifically based approach to healing depression, anxiety, and brain fog by focusing on your “whole brain” — the brain, the gut, the microbiome, and the thyroid

There is a fundamental connection between the brain, the gut, the microbiome, and the thyroid: if any one part of this system is malfunctioning, it will impact the others–and this is where The Whole Brain comes in. Integrative health pioneer Dr. Raphael Kellman presents his revolutionary concept of “the whole brain” (a biological system made up of the microbiome, the gut, and the thyroid). Kellman then shares a completely new approach to curing depression and other mood problems by focusing on this interconnectedness, explaining how this system works in tandem to heal mood and mental disorders without drugs.

Based on Dr. Kellman’s decades of experience as a physician and his ongoing study of the latest science, the book offers a lively, accessible explanation of how the brain works and why, for optimal brain health, you need to heal the microbiome, the gut, and the thyroid. With a proprietary three-week plan (21 days of meal plans, featuring 50 original and simple recipes; a complete exercise program; and a program of daily meditations and affirmations). The Whole Brain program will benefit people diagnosed with depression and/or anxiety as well as those who just want to feel better.



Get Ready to Feel Better

Hey—how is your brain doing today?

Are you thinking well? Is your mood terrific? Do you feel as though your brain is functioning in peak condition, humming along the way it was meant to: concentrating easily, analyzing effectively, deciding confidently, and maintaining its focus? Is your brain making you feel calm, energized, and optimistic?

Or are you feeling anxious? Depressed? Foggy? Does your brain feel like an enemy you’re constantly battling—one creating anxious thoughts, mood swings, or a sense of misery and despair? Do you wonder if you need medication to sharpen your mind or improve your mood?

Or perhaps are you already taking medication that isn’t working as well as you would like. Maybe you’re wondering if you will ever be able to take your brain for granted—still waiting for that morning when you’ll wake up rested and full of energy, enthusiastic for the day ahead.

If you are one of the millions of Americans who feel that your brain just “isn’t working right”—that your ability to think clearly or maintain a balanced, happy mood has been lost long ago—take heart. The problem is not “in your head”—there are understandable scientific reasons for what’s gone wrong. And there are proven solutions that can help you—without medication, without frustrating side effects, without the constant fear that maybe your medications will stop working and what will you do then?

I’m a holistic and functional medicine MD who has spent the last two decades in private practice, treating thousands of patients with complaints like yours. I’ve developed an approach to brain health that goes far beyond conventional medicine—and beyond most functional and “alternative” practitioners as well. I’ve written this book to share my solutions with you, so that you, too, can feel calm, energized, clear, sharp, and optimistic—so that your brain functions at its very highest level, every day, all the time.

In this book, you’re going to learn about the latest cutting-edge science, because that science offers so much room for hope. When you understand how the brain works, you’ll understand that you have the power to make your own brain work better. Like many of my patients, you might have spent years going from one doctor to another, trying different medications, taking various herbs and natural remedies, struggling in therapy, and you may have become discouraged, even despairing—certain that there is no help for you. So, I want to say this loud and clear:

This approach can work for you, just as it has for thousands of my patients.

And when you understand the science behind it, you’ll know why it works, and why you can be helped.

In Part I, you’ll learn the basics of the new brain science and you’ll discover a powerful new concept that I call the Whole Brain. In Part II, you’ll learn about each aspect of the Whole Brain: brain, gut, and microbiome, as well as the thyroid, which powers the Whole Brain, and the will to wholeness, which activates it.

Then, in Parts III and IV, you’ll find your Whole Brain Protocol. I’ll tell you exactly what to eat and which supplements and probiotics can get your Whole Brain functioning at top capacity. The Whole Brain Protocol is your 4-week plan for getting your brain back on track, so that you can think clearly and feel terrific. If you’ve been taking medication, you may very well be able to work with your prescriber to wean yourself off of it. If you haven’t yet taken medication, you might never have to start.

So, read on. A whole new world of brain health is waiting. I can’t wait for you to experience the wonders of that world.

A Growing Crisis in Brain Health

Take a quick look at the waiting room of any doctor’s office, and you can see at a glance that we are facing a crisis in brain health. Rates of depression and anxiety are skyrocketing. More and more people struggle with cognitive decline: brain fog, failing memory, “senior moments.” Rates of ADHD, Alzheimer’s, autism, and neurodegenerative diseases are on the rise as well.

Unfortunately, the treatments we have—antidepressants; antianxiety medications; anti–attention-deficit medications, such as Adderall; and a host of other medications—represent an outmoded approach to treating the brain. They work to a degree, but not very well.

I see the hazards of the old type of treatment all the time. People come into my office with long histories of depression or anxiety or sometimes both, having spent years on one medication after another. Maybe their depression has gotten a little better. Maybe their anxiety is more under control. Or perhaps it isn’t—perhaps after offering a short-lived relief, their medication has stopped working and they’ve had to increase their dose, switch to another medication, or suffer through a return of the very same symptoms—which now, perhaps, are even more intense.

Even when the drugs actually work, they don’t accomplish nearly enough. In the best-case scenario, they might alleviate some symptoms. Even then, they almost always create punitive side effects—weight gain, sleep disturbances, brain fog, loss of energy, the diminishment or loss of sexual function. Worst of all, available medications rarely allow people to achieve optimal levels of enthusiasm, clarity, and joy—the zest and energy that make life truly worth living.

Fortunately, as this old era ends, a new one is beginning. We now understand the brain in a new way, which means that we can heal it in a new way. The first step in this exciting new approach to brain health is to understand that the brain is not merely the gray and white matter between our ears. Rather, the brain is part of a system that includes the gut and the microbiome, the community of bacteria that populate your digestive tract. That system—brain, gut, and microbiome—makes up what I call the Whole Brain. Your Whole Brain is powered by your thyroid, which means that if your thyroid gland is not functioning properly, your brain, gut, and microbiome won’t work well, either.

The Whole Brain Brain + Microbiome + Gut Powered by the Thyroid

This new view has profound implications for our approach to healing depression, anxiety, brain fog, and other types of brain dysfunction. Here’s the bottom line: If your gut is dysfunctional or your microbiome is degraded, you will feel as though your mind is deteriorating and your emotions are out of control. That is why when a patient comes to me with a “brain problem,” I look at the big picture: healing the Whole Brain.

If your gut is dysfunctional or your microbiome is degraded, you will feel as though your mind is deteriorating and your emotions are out of control.

When I treat the Whole Brain, the results are extraordinary. I have been able to help virtually all of my patients wean their way off antidepressants, antianxiety medications, and anti–attention-deficit medications. Patients with conventional diagnoses—anxiety, depression, brain fog—lose their symptoms and gain a whole new world of buoyancy, clarity, and focus. Patients whose symptoms evade diagnosis—the ones who tell me that they “just can’t think straight” or “their brain just doesn’t work right”—likewise regain the ability to think clearly and to enjoy a sense of optimism, energy, and calm.

It’s not just that people’s symptoms disappear. They also attain a whole other level of function—access to a kind of vitality and joy that they haven’t felt for a long time. Life regains its savor. As many patients tell me, “I finally feel like myself.” Many report major life changes: a richer, more satisfying marriage; the ability to feel compassion for their parents; a renewed interest in a beloved activity; a sense of engagement and enthusiasm. “It’s like I’m finally living the life I was meant to,” one patient said to me. “Like I’ve pushed the fog and misery out of the way and I can finally just live.

The Microbiome Revolution

The past century has seen many thrilling medical advances. The discoveries of antibiotics, vaccines, and advanced surgical techniques have had stunning effects on our lives and health.

Of all the medical breakthroughs of our lifetime, however, one of the most exciting of all has been the discovery of the microbiome: the community of bacteria that lives within each of us. This discovery is the key to a whole new type of medicine—and it’s the key to healing the Whole Brain.

That’s because the microbiome is a crucial component of the Whole Brain, working with the brain and the gut to create the biochemicals and other types of support on which your brain depends. The microbiome’s condition plays a role in whether or not you may develop anxiety, depression, and brain fog, as well as in many other conditions, including obesity, gut disorders, autoimmune disease, cardiovascular disorders, and perhaps even cancer.

Conventional medicine has barely grasped the true dimensions of the microbiome revolution, and if you ask your conventional doctor about the microbiome, he or she may not have much to say. But if you look at the scientific literature—and when I look at my own results with patients—I know that our new era of “microbiome medicine” can radically transform our treatment of both body and brain.

This revolution is all the more remarkable because for a very long time, we have seen bacteria solely as the bad guys. Ever since the inception of the germ theory in the mid-1800s, scientists and physicians have taken up arms against these microscopic villains, waging war against the evil germs that caused us to get sick. With the development of antibiotics, we seemed well on our way to winning that war. The discovery of penicillin was greeted by the medical community as the ultimate “secret weapon” in our efforts to conquer bacteria and perhaps even disease itself.

Now, as a physician, I certainly appreciate the positive role played by antibiotics. Before they were discovered, even a minor infection could turn into a life-threatening condition. I can understand why it seemed that antibiotics put a definitive end to the power of germs, radically limiting our vulnerability to illness, and, seemingly, to death itself.

However, the bacteria didn’t take this war lying down. As the use of antibiotics grew, an increasing number of bacteria developed resistance to them—a resistance that has grown stronger and stronger over time. The medications that once cut through our enemies’ ranks unopposed now began to work less and less well. This prompted the development of new antibiotics—and, in turn, the rapid evolution of new resistant bacteria.

In what I consider the greatest turnaround in the history of medicine, we are finally letting go of the idea that all bacteria are our enemies. Instead, we have come to understand that a great many are actually our friends—indeed, our greatest allies.

Suddenly, we found ourselves locked into a kind of medical arms race whose endgame does not bode well. The specter of an epidemic set off by antibiotic-resistant bacteria is not just the stuff of blockbuster disaster films. It’s every physician’s worst nightmare.

Luckily, the story now becomes vastly more hopeful. While antibiotics certainly have their place, we have begun to be aware of the dangers of overusing them. More important, a research revolution has given us a radically different perspective on the centillions of microbes with which we share the earth. In what I consider the greatest turnaround in the history of medicine, we are finally letting go of the idea that all bacteria are our enemies. Instead, we have come to understand that a great many are actually our friends—indeed, our greatest allies.

What we now understand is that bacteria rarely mean us harm—in fact, we literally could not exist without them. Bacteria enable us to digest our food, maintain our immune system, and cope with stress. They have a dramatic impact on our thyroid, heart, liver, bones, and skin. They are the key to new approaches to our modern chronic illnesses: obesity, autoimmune disease, cardiovascular disorders, and diabetes. They also play a vital role in optimizing our brain function—enabling us to think clearly, process our emotions, learn effectively, and remember accurately. In fact, along with the gut, I consider our community of bacteria to be an integral part of the Whole Brain.

We’re used to thinking of ourselves as autonomous creatures whose anatomies function as self-sufficient machines, much like the engine of a car. Sure, we need fuel, and water, and perhaps a little lubrication, but basically, the mechanism functions by itself.

Bacteria play a vital role in optimizing our brain function—enabling us to think clearly, process our emotions, learn effectively, and remember accurately. I consider our community of bacteria to be an integral part of the Whole Brain.

Nope. Not even close. Without our bacterial community, we are more like a wagon with two wheels on the left side only. If you want the wagon to roll, you’d better add two wheels on the right side, or you won’t get very far.

Of course, that crude analogy hardly does justice to the exquisitely complex interactions between billions of bacteria and our own biochemistry. But as you read this book, I want you to keep thinking of that wagon. You need your microbiome at least as much as your wagon needs those two wheels. And when your microbiome is in optimal shape, your mind is well on its way to being there, too.

The Whole Human

As a scientist, I’m thrilled by the new discoveries that are expanding our worldview. These breakthroughs are helping us to rethink health and healing. They are also transforming our very notion of what it is to be human.

We are used to seeing ourselves as discrete individuals, separate and inviolate inside our skin. Once we understand our relationship to the microbiome, however, this worldview changes profoundly. When you realize that your bacterial cells outnumber your human ones by as much as a factor of 10 to 1, you understand that you are not only one human individual—you are also a community of bacteria. For you to be happy and healthy, your bacterial community must thrive.*

Moreover, you, the human, are responsible for the health and well-being of that community. What you eat, your bacteria eat; when you are exposed to toxins, they are, too; when you are stressed, their population changes. And only when your microbiome is healthy can you be truly healthy. I tell each of my patients to think of themselves as a king or queen, responsible for governing the “kingdom” or “queendom” of their microbiome. Neglect that kingdom at your peril—your own health will suffer immediately, including the health of your Whole Brain.

Nor is your body’s microbial kingdom an isolated territory, separate within the boundary of your skin. Rather, you are always exchanging bacteria with your environment: through the food you eat, the people you live with, and the places you inhabit. Family members tend to have similar microbiomes—not through genetics (although there may be a genetic component) but because they live in the same house. If you get another set of housemates, your microbiome will begin to resemble theirs. One study even found that a woman’s roller-derby team shared common elements of their microbiome!

Thus, understanding the microbiome helps us forge a new definition of the Whole Human: not an autonomous individual but rather a diverse community formed of one human plus hundreds of different types of bacteria. We are not self-sufficient—we depend upon our bacteria for our very life. We are not impermeable—we are constantly exchanging bacteria with the plants, animals, and humans in our environment—even with the soil and sediment of our planet. And in fact, viewing ourselves in this way—interconnected with our loved ones, our community, our planet—is actually very healthy, with significant benefits for your immune system and your resilience, as well as your Whole Brain.

My Microbiome Journey—and Yours

My own discovery of the microbiome and its effect on the brain was a long, exciting process. I don’t really have an “aha” moment or a single dramatic incident to focus on. Rather, I began with a profound awareness of the importance of the gut to human health, an awareness that inspired my first book, Gut Reactions.

I can’t take particular credit for this—the gut was central to the worldview of many functional and holistic practitioners, including a rudimentary understanding of the microbiome. However, my imagination was seized by the vision of our community of microbes—the trillions of bacteria connecting us to the world of nature, the collective power within us to transform gut health and overall well-being. As I saw how powerful an ally the microbiome could be, I began to rely upon it more and more, first for gut healing, then for other aspects of health, and finally—most excitingly—for the brain.

I was thrilled to see microbiome medicine unlock for my patients a whole new dimension of brain function. As you will see many times throughout this book, treating depression, anxiety, and brain fog via the microbiome and the gut didn’t just make my patients feel a little bit better. It didn’t simply resolve a few symptoms or give them some partial relief. Rather, it transformed their brain function entirely, bringing them to a whole new level of vitality, clarity, and enthusiasm. People whose lives had been riddled with anxiety suddenly, perhaps for the first time, experienced calm. People whose lives had been shadowed with depression suddenly—often unexpectedly—felt hopeful, engaged, even buoyant. People who felt that their brains had “stopped working” or their memories were “full of holes” experienced a new level of clear-headed focus and concentration, as though, in the words of so many clients, “my brain is finally working the way it’s supposed to.”

This is the level of health I want for you, too, and I am 100 percent confident that you can attain it. If you are suffering from anxiety, depression, or brain fog, the Whole Brain Protocol can help ease your symptoms, bringing you significant relief—perhaps even total relief.

Although this book focuses on anxiety, depression, and brain fog, it also provides overall support for improved brain function. If you are struggling with other types of brain dysfunction—such as Alzheimer’s, ADD/ADHD, autism, multiple sclerosis, or Parkinson’s—you are also likely to find some relief from the Whole Brain Protocol, though you will almost certainly need additional support.

If you are currently taking medications for any type of brain dysfunction, please, do not stop taking any medication without the support of the person who prescribed it. You could create even more severe problems for yourself by abruptly stopping an antidepressant, antianxiety medication, or other brain-related prescription.

Treating depression, anxiety, and brain fog via the microbiome and the gut didn’t just make my patients feel a little bit better.… Rather, it transformed their brain function entirely, bringing them to a whole new level of vitality, clarity, and enthusiasm.

However, after several weeks on the Whole Brain Protocol, you might well be able to work with your practitioner to wean yourself from these medications. Likewise, if you’re taking Adderall or some other ADD/ADHD-related prescription, you must work with your practitioner to alter the dose or to stop taking the medication entirely, but with the Whole Brain Protocol, you may be able to do so.

Whether or not you continue taking medications—and certainly if you have never taken them to begin with—I want you to hear my faith in you loud and clear. No matter what you have heard in the past—no matter how many treatments you have already tried, whether medical, natural, or both—no matter how long you have been struggling with depression, anxiety, or brain fog—no matter how severe your condition—you can be well. I’ve seen it with thousands of patients—most of whom have come to me after two, four, seven doctors, many of whom have almost given up hope. I know you can do what they have done.

If you have been struggling for a long time, believing in me might require a leap of faith. From the bottom of my heart, I encourage you to take the leap. The results, I promise you, will make the entire journey worthwhile.

The Whole Brain Solution

In this book, you learn the latest cutting-edge science of the microbiome revolution. The microbiome is so powerful, it affects even the expression of your genes—partly because the microbiome has far more genes than you do, by a factor of 150 to 1.

You’ll also learn how the microbiome and the gut affect the brain, and how the thyroid powers the whole system. You’ll discover why the will to wholeness is an integral aspect of brain healing. Addressing gut, microbiome, thyroid, and your will to wholeness is an unbeatable combination, enabling you to achieve a whole new level of brain health.

No matter what you have heard in the past—no matter how many treatments you have already tried, whether medical, natural, or both—no matter how long you have been struggling with depression, anxiety, or brain fog—no matter how severe your condition—you can be well.

You can revitalize your own Whole Brain with my 28-day program of diet and supplements. You also have the opportunity to use specially designed meditations and visualizations that have helped my patients to achieve extraordinary success.

When my patients undergo treatment for the Whole Brain, they don’t just feel a little bit better. They don’t just get rid of a few symptoms, or become able to stumble through the day, foggy and depleted. Instead, they tap into extraordinary reservoirs of vitality, clarity, and joy. That is what I want for them—and I want it for you, too. Once the Whole Brain is functioning as it was meant to, you’ll be amazed at how good you can feel.


* Although some recent research suggests that the proportion might actually be 1:1, the microbiome remains a hugely important factor in the human anatomy.




What Is the Whole Brain?

Annette had struggled with mild depression ever since she was in high school. For much of her life, she managed to keep the symptoms at bay. But when she graduated from college and encountered the stress of her first job, she found herself facing more intense depression punctuated with panic attacks, bouts of insomnia, and fatigue. She also began gaining weight. By her late twenties, she was twenty pounds overweight and relying on over-the-counter sleep aids.

For several months, Annette resisted taking antidepressants, hoping to find relief when she finally settled in at work and resolved her stormy relationship with her boyfriend. Meanwhile, though, she developed a painful case of acid reflux, for which her primary care physician prescribed a proton pump inhibitor (PPI).

“That was a really hard time,” Annette told me as we were going over her case history. “I felt like my whole body was just falling apart. My stomach hurt, my heart hurt, my mind hurt. It was like my entire body had just turned against me, and everything I did to try and fix it only made everything worse.”

Unfortunately, by her early thirties, Annette’s depression had worsened, and she suffered frequent crying jags. She had finally agreed to take Paxil, an antidepressant, which helped a little—but not nearly enough. Her doctor also prescribed her some Xanax for her panic attacks, which helped as well. But Annette hated feeling dependent on drugs and she also worried about becoming addicted.

Meanwhile, despite the meds, Annette’s sleep problems continued, her reflux was barely under control, and, no matter how strenuously she dieted, she was 30 pounds over her ideal weight. She had also developed a raging case of acne that covered her back and chest. She felt exhausted most of the time and complained of being foggy all of the time, unable to focus or to motivate herself.

“Bad as it was before, it’s even worse now,” Annette said shakily. “Not being able to sleep makes me absolutely crazy—I can’t think straight at all. Even when I get a good night’s sleep, my brain doesn’t work right. And I can’t stand being so tired all the time. It’s like I’m just dragging myself through every minute of the day, waiting for it all to be over.”

By the time I saw her at age thirty-eight, then, Annette was on three different prescription medications: a PPI, Paxil, and Xanax. Her cluster of both brain and gut symptoms plus the prescription drugs she took to medicate them is not in the least unusual. Some 59 percent of all US adults are taking at least one prescription drug. Meanwhile, the percentage of Americans taking antidepressants—specifically, a type of antidepressant known as an SSRI (selective serotonin reuptake inhibitor) is rising rapidly—from 6.8 percent in 1999 to 13 percent in 2012, according to a study of nearly 38,000 people published in the Journal of the American Medical Association.1

The patients who come to see me have suffered for years, even decades, with depression, anxiety, fatigue, and, most distressingly of all, the sense that their brain “just isn’t working.” Their brains have begun to fail them in ways that defy conventional categories. Some feel that their personality mysteriously is being altered. Others wonder why they can’t remember clearly or why they can no longer make quick, powerful decisions. My patients have suffered a whole host of problems that evade diagnosis—but that make every day a misery. And they tell me the conventional medications they’ve been prescribed—the typical polypharmacy of two, three, five, seven prescription drugs—aren’t really helping.

True, these medications might alleviate some symptoms (although sometimes they fail to do even that). But they don’t come anywhere close to true healing. They frequently don’t fully eliminate anxiety or depression, don’t promote sustained mental acuity, and don’t even begin address the other health problems. They often produce upsetting side effects, which feel like a punitive trade-off for the improvement in mood. They certainly don’t create a deep, long-term sense of vitality, optimism, and purpose.


  • "After decades of treating patients for depression, gastrointestinal problems, low thyroid, and a multitude of other 'mysterious' ailments, pioneer in holistic and functional medicine Dr. Raphael Kellman has connected the dots between the brain, the gut, the microbiome, and the thyroid. The Whole Brain offers his groundbreaking plan to diminish anxiety and depression-and to give you more energy and vitality."—Izabella Wentz, PharmD, FASCP, #1 New York Times bestselling author of Hashimoto's Protocol
  • "Dr. Kellman is a rare kind of doctor. An innovative functional medicine physician? Indeed, he is that--but he helps his patients heal with the spiritual wisdom of a Rabbi. His latest book, The Whole Brain, connects the dots between your gut, microbiome, thyroid, and brain. Not only does it present actionable lifestyle remedies to help you heal physically and mentally it also offers a deeply spiritual understanding of the will to heal."—Donna Gates, M.Ed., ABAAHP, Author & Founder The Body Ecology Diet
  • "Dr. Kellman has identified an interconnected system of organs he calls 'The Whole Brain.' He teaches you to control your anxiety, depression, and chronic fatigue starting with the microscopic world and working your way up from there. The Whole Brain offers both a profound message and practical tools to own your mental states without medication. Highly recommended."—Dave Asprey, Founder and CEO of Bulletproof
  • "Dr. Kellman has long been on the cutting-edge of health and science. Now, he introduces his groundbreaking concept of The Whole Brain: If you want to improve brain function--if you want your mind to be focused, your memory to be sharp, and your mood to be hopeful--start with a healthier microbiome, heal your gut, and balance your thyroid. This book will show you how."—Dr. Terry Wahls, author of The Wahls Protocol: A Radical New Way to Treat All Chronic Autoimmune Conditions
  • "In The Whole Brain, Dr. Raphael Kellman shares his groundbreaking research, showing the intimate connections between the gut, microbriome, thyroid, and brain, and then offers a proven, holistic plan that doesn't rely on prescription medication."—Mark Hyman, MD, Director of Cleveland Clinic's Center for Functional Medicine, the Founder of The UltraWellness Center, ten-time #1 New York Times bestselling author
  • "If you're one of the millions of US adults experiencing anxiety or depression, and you're looking for natural solutions, you'll want to read The Whole Brain by Raphael Kellman, MD...[it] helps readers get started with healing from the inside out."—Taste for Life magazine
  • "In The Whole Brain, Raphael Kellman, MD shares strategies that nourish the gut to lift mood, ease anxiety and end brain fog-for life!"—Closer magazine

On Sale
Oct 31, 2017
Page Count
320 pages

Raphael Kellman, MD

About the Author

Raphael Kellman, MD, graduate of Albert Einstein College of Medicine, is the author of The Microbiome Breakthrough, The Microbiome Diet, and other books on health and healing. Dr. Kellman manages a thriving medical practice and lectures all over the world. He lives with his wife and two young daughters in New York City.

Learn more about this author