Brain Maker

The Power of Gut Microbes to Heal and Protect Your Brain for Life


By David Perlmutter MD

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The bestselling author of Grain Brain uncovers the powerful role of gut bacteria in determining your brain’s destiny.

Debilitating brain disorders are on the rise-from children diagnosed with autism and ADHD to adults developing dementia at younger ages than ever before. But a medical revolution is underway that can solve this problem: Astonishing new research is revealing that the health of your brain is, to an extraordinary degree, dictated by the state of your microbiome – the vast population of organisms that live in your body and outnumber your own cells ten to one. What’s taking place in your intestines today is determining your risk for any number of brain-related conditions.

In Brain Maker, Dr. Perlmutter explains the potent interplay between intestinal microbes and the brain, describing how the microbiome develops from birth and evolves based on lifestyle choices, how it can become “sick,” and how nurturing gut health through a few easy strategies can alter your brain’s destiny for the better. With simple dietary recommendations and a highly practical program of six steps to improving gut ecology, Brain Maker opens the door to unprecedented brain health potential.


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Bug Alert: You've Got Company

Death begins in the colon.

—ÉLIE MECHNIKOV (1845–1916)

SEVERAL TIMES A WEEK THROUGHOUT my career, I've had to tell a patient or caregiver that there's nothing left in my arsenal to treat a grave neurological disease that will inevitably shatter the patient's life. I've surrendered because the illness gained too much control and no quick fix or drug existed to even decelerate the swift march of the affliction to the end. It's a heart-wrenching place to be, one that you just don't get used to no matter how many times you go through it. What gives me hope, however, is a burgeoning area of study that's finally affording me revolutionary approaches to relieving the suffering. Brain Maker is about this dazzling new science, and how you can take advantage of it for your own health.

Take a moment to think about how much has changed in our world over the past century, thanks to medical research. No longer do we worry about dying from smallpox, dysentery, diphtheria, cholera, or scarlet fever. We've made huge strides in lowering the death rates of many life-threatening maladies, including HIV/AIDS, some forms of cancer, and heart disease. But when you consider brain-related diseases and disorders, the picture is vastly different. Advances in preventing, treating, and curing debilitating neurological ailments across the life cycle—from autism and attention deficit hyperactivity disorder (ADHD) to migraines, depression, multiple sclerosis (MS), Parkinson's, and Alzheimer's—are virtually nonexistent. And, sadly, we are quickly losing ground as the incidences of these conditions are increasing in our society.

Let's consider a few numbers. In the ten wealthiest Western nations, death from brain disease in general, which largely reflects death from dementia, has risen dramatically over the past twenty years. And the United States leads the way. In fact, a 2013 British report showed that since 1979, death due to brain disease increased a breathtaking 66 percent in men and 92 percent in women in America. In the words of the study's lead author, Professor Colin Prichard, "These statistics are about real people and families, and we need to [recognize] that there is an 'epidemic' that clearly is influenced by environmental and societal changes." The researchers also noted how this surge, which is affecting people at younger and younger ages, is in sharp contrast to the major reductions in risk of death from all other causes.1

In 2013, the New England Journal of Medicine published a report revealing that we spend about $50,000 annually caring for each dementia patient in this country.2 That amounts to approximately $200 billion a year, twice what we spend on caring for heart disease patients and almost triple what we spend on treatment for cancer patients.

Mood and anxiety disorders are also on the upswing and can be equally as crippling to quality of life as other neurological conditions. About one in four adults in the U.S.—more than 26 percent of the population—suffers from a diagnosable mental disorder.3 Anxiety disorders afflict more than 40 million Americans, and nearly 10 percent of the U.S. adult population has a mood disorder for which powerful drugs are prescribed.4 Depression, which affects one in ten of us (including a quarter of women in their forties and fifties), is now the leading cause of disability worldwide, and diagnoses are growing at a startling rate.5 Medications like Prozac and Zoloft are among the most often prescribed drugs in the nation. Mind you, these drugs treat symptoms of depression, not the causes, which are flagrantly ignored. On average, people with severe mental illness, such as bipolar disorder and schizophrenia, die twenty-five years earlier than the general population.6 (This is partially due to the fact that these individuals are more likely to smoke, abuse alcohol and drugs, and be overweight with obesity-related illnesses in addition to their mental challenges.)

Headaches, including migraines, are among the most common disorders of the nervous system; nearly half of the adult population wrestles with at least one headache per month. And they are more than an inconvenience; they are associated with disability, personal suffering, damaged quality of life, and financial cost.7 We tend to think of headaches as being inexpensive nuisances, especially since many drugs that treat them are relatively cheap and easy to access (e.g., aspirin, acetaminophen, ibuprofen), but according to the National Pain Foundation, they cause more than 160 million lost work days each year in the U.S. and result in about $30 billion a year in medical expenses.8

Multiple sclerosis, a disabling autoimmune disease that disrupts the nervous system's ability to communicate, now affects an estimated two and a half million people worldwide, with close to half a million in America, and is becoming increasingly more prevalent.9 The average lifetime cost of treating someone with MS exceeds $1.2 million.10 Mainstream medicine tells us that there is no cure in sight.

And then there is autism, which has surged seven-to eight-fold just in the past 15 years, making this truly a modern-day epidemic.11

To be sure, hundreds of millions of dollars are being spent on these and other enfeebling brain-related ailments, yet we are seeing precious little progress.

Now for the good news: New, leading-edge science coming from the most well-respected institutions around the world is discovering that to an extraordinary degree, brain health and, on the flip side, brain diseases, are dictated by what goes on in the gut. That's right: what's taking place in your intestines today is determining your risk for any number of neurological conditions. I realize this may be difficult to comprehend; if you were to ask your doctors about a known cure for autism, MS, depression, or dementia, they would throw up their arms and say none exists—and may never exist.

It is here that I part company with most, but gratefully not all, of my colleagues. We as neurologists are trained to focus on what goes on in the nervous system, and specifically in the brain, in a myopic way. We automatically end up viewing other bodily systems, such as the gastrointestinal tract, as discrete entities that have no bearing whatsoever on what goes on in the brain. After all, when you have a stomachache you don't call a cardiologist or neurologist. The entire medical industry is characterized by distinct disciplines divided by body part or individual system. Most of my colleagues would say, "What happens in the gut stays in the gut."

This perspective is grossly out of touch with current science. The digestive system is intimately connected to what goes on in the brain. And perhaps the most important aspect of the gut that has everything to do with your general wellness and mental health is its internal ecology—the various microorganisms that live within it, especially the bacteria.


Historically, we've been taught to think of bacteria as agents of death. The bubonic plague, after all, wiped out nearly one third of the population in Europe between 1347 and 1352, and certain bacterial infections are still worldwide killers today. But the time has come to embrace another side of bacteria's story in our lives. We must consider how some bugs are not detrimental but fundamental to life.

The Greek physician and father of modern medicine, Hippocrates, first said in the third century B.C.E., "All disease begins in the gut." This was long before civilization had any proof or sound theory to explain this idea. We didn't even know bacteria existed until the Dutch tradesman and scientist Antonie van Leeuwenhoek looked at his own dental plaque through a handcrafted microscope in the late 17th century and spied a hidden world of what he called "animalcules." Today he is considered the father of microbiology.

In the nineteenth century it was the Russian-born biologist and Nobel laureate Élie Mechnikov who made a stunningly direct link between human longevity and a healthy balance of bacteria in the body, confirming that "death begins in the colon." Since his discoveries, made at a time when bloodletting was still popular, scientific research is bringing more and more credence to the notion that up to 90 percent of all known human illness can be traced back to an unhealthy gut. And we can say for sure that just as disease begins in the gut, so too does health and vitality. It was also Mechnikov who said that the good bacteria must outnumber the bad. Unfortunately, most people today carry around more bad, pathogenic bacteria than they should, lacking an abundant and diverse microbial universe within. No wonder we suffer from so many brain disorders.

If only Mechnikov were alive today to be a part of the next medical revolution that he tried to start in the nineteenth century. This one is finally under way.

Right now, your body is colonized by a multitude of organisms that outnumber your own cells by a factor of about ten (luckily, our cells are much larger, so those organisms don't outweigh us ten to one!). These roughly hundred trillion invisible creatures—microbes—cover your insides and outsides, thriving in your mouth, nose, ears, intestines, genitalia, and on every inch of your skin. If you could isolate them all, they would fill up a half-gallon container. Scientists have so far identified some 10,000 species of microbes, and because each microbe contains its own DNA, that translates to more than eight million genes. In other words, for every human gene in your body, there are at least 360 microbial ones.12 Most of these organisms live within your digestive tract, and while they include fungi and viruses, it appears that the bacterial species that make their home inside you dominate and take center stage in supporting every conceivable aspect of your health. And you interact not only with these organisms but also with their genetic material.

We call this complex internal ecology that thrives within us and its genetic fingerprint the microbiome (micro for "small" or "microscopic," biome referring to a naturally occurring community of flora occupying a large habitat—in this case, the human body). Although the human genome we all carry is almost the same, give or take the small handful of genes that encode our individual characteristics like hair color or blood type, the gut microbiome of even identical twins is vastly different. Research at the leading edge of medicine is now acknowledging that the state of the microbiome is so key to human health—with a sweeping say in whether or not you live robustly to a ripe old age—that it should be considered an organ in and of itself. And it's an organ that has gone through radical changes over the past two-plus million years. We have evolved to have an intimate, symbiotic relationship with these microbial inhabitants who have actively participated in shaping our evolution since the dawn of humankind (and indeed, they lived on the planet for billions of years prior to our emergence). At the same time, they have adapted and changed in response to the environments we have created for them within our bodies. Even the expression of our genes in each and every one of our cells is influenced to some degree by these bacteria and other organisms that live within us.

The importance of the microbiome motivated the National Institutes of Health (NIH) to launch the Human Microbiome Project in 2008 as an extension of the Human Genome Project.13 Some of America's best scientists have been charged with exploring how changes in the microbiome are associated with health and, conversely, disease. Moreover, they are studying what can be done with this information to help reverse many of our most challenging health problems. Although the project is investigating several parts of the body that host microbes, including the skin, the most extensive area of research is focused on the gut since it's home to most of your body's microbes and, as you're about to discover, a center of gravity of sorts for your entire physiology.

It's now undeniable that our intestinal organisms participate in a wide variety of physiologic actions, including immune system functioning, detoxification, inflammation, neurotransmitter and vitamin production, nutrient absorption, signaling being hungry or full, and utilizing carbohydrates and fat. All of these processes factor mightily into whether or not we experience allergies, asthma, ADHD, cancer, diabetes, or dementia. The microbiome affects our mood, libido, metabolism, immunity, and even our perception of the world and the clarity of our thoughts. It helps determine whether we are fat or thin, energetic or lethargic. Put simply, everything about our health—how we feel both emotionally and physically—hinges on the state of our microbiome. Is it healthy and dominated by so-called friendly, beneficial bacteria? Or is it sick and overrun by bad, unfriendly bacteria?

Perhaps no other system in the body is more sensitive to changes in gut bacteria than the central nervous system, especially the brain. In 2014, the U.S. National Institute of Mental Health spent more than $1 million on a new research program zeroing in on the microbiome-brain connection.14 Although many things factor into the health of our microbiome and therefore the health of our brain, nurturing a healthy microbiome today is easier than you think. I've taken all the guesswork out with the recommendations presented in this book.

I've seen dramatic turnarounds in health using simple dietary modifications and, on occasion, more aggressive techniques to reestablish a healthy microbiome. Take, for instance, the gentleman with such a horrid case of multiple sclerosis that he required a wheelchair and bladder catheter. After treatment, not only did he say goodbye to his catheter and regain the ability to walk without assistance, but his MS went into total remission. Or consider Jason, the 12-year-old boy with severe autism who could barely talk in full sentences. In chapter 5 you'll read about how he physically transformed into an engaging boy after a vigorous probiotic protocol. And I can't wait to share with you the countless stories of individuals with myriad, enfeebling health challenges—from chronic pain, fatigue, and depression to serious bowel disorders and autoimmune diseases—who experienced a complete vanishing of symptoms following treatment. They went from having an awful quality of life to getting a second chance. Some even went from harboring thoughts of suicide to feeling content and vivacious for the first time. These stories are not outlier cases for me, but by standard measure of what might typically be expected, they seem almost miraculous. I witness these stories every day, and I know that you too can positively change the fate of your brain through the health of your gut. In this book, I'll show you how.

Although you may not have extreme and unrelenting health challenges that require pharmaceuticals or intensive therapy, a dysfunctional microbiome could be at the root of your bothersome headaches, anxiety, inability to concentrate, or negative outlook on life. Drawing on scholarly clinical and laboratory studies, as well as extraordinary results I've seen over and over again or heard about at medical conferences that attract the finest physicians and scientists from around the world, I'll tell you what we know and how we can take advantage of this knowledge. I'll also offer highly practical and comprehensive guidelines to transform your gut health and in turn your cognitive health so you can add many more vibrant years to your life. And the benefits don't stop there. This new science can help all of the following:




Allergies and food sensitivities

Chronic fatigue

Mood disorders, including depression and anxiety

Diabetes and cravings for sugar and carbohydrates

Overweight and obesity, as well as weight-loss struggles

Memory problems and poor concentration

Chronic constipation or diarrhea

Frequent colds or infections

Intestinal disorders, including celiac disease, irritable bowel syndrome, and Crohn's disease


Painful joint inflammations and arthritis

High blood pressure


Chronic yeast problems

Skin problems such as acne and eczema

Bad breath, gum disease, and dental problems

Tourette syndrome

Extreme menstrual and menopausal symptoms

And many more

In fact, this new knowledge can help virtually any degenerative or inflammatory condition.

In the pages that follow we will explore what makes for a healthy microbiome and what makes a good microbiome go bad. The quiz here will clue you into the kinds of lifestyle factors and circumstances that relate directly to the health and function of the microbiome. And one thing you'll grasp quickly is that food really does matter.


The idea that food is the most important variable in human health is not news. As the old adage goes, "Let food be thy medicine and medicine be thy food."15 Anyone can change the state of their microbiome—and fate of their health—through dietary choices.

I recently had the opportunity to interview Dr. Alessio Fasano, who currently serves as visiting professor at Harvard Medical School and Chief of the Division of Pediatric Gastroenterology and Nutrition at Massachusetts General Hospital. He is recognized as a global thought leader in the science of the microbiome. We spoke about factors that alter gut bacteria, and he stated clearly to me that, hands down, the most significant factor related to the health and diversity of the microbiome is the food we eat. And what we put in our mouths represents the biggest environmental challenge to our genome and the microbiome.

What a massive endorsement for the notion that food matters, trumping other circumstances in our life that we may not entirely be able to control.

As I described in my previous book Grain Brain, the two key mechanisms that lead to brain degeneration are chronic inflammation and the action of free radicals, which for now you can think of as byproducts of inflammation that cause the body to "rust." Brain Maker takes a new look at these mechanisms and how they are influenced by gut bacteria and your overall gut health. Your intestinal flora in fact has everything to do with inflammation and whether or not you can combat free radicals. In other words, the state of your microbiome determines whether or not your body is fanning the flames of inflammation or squelching them.

Chronic inflammation and free radical damage are concepts that lie front and center in neuroscience today, but no pharmaceutical approach can come anywhere close to a dietary prescription for managing your intestinal bacteria. I'll explain that prescription step by step. Thankfully, the gut's microbiotic community is wonderfully receptive to rehabilitation. The guidelines outlined in this book will change your body's inner ecology to enhance the growth of the right kind of brain-sustaining organisms. This highly practical regimen includes six essential keys: prebiotics, probiotics, fermented foods, low-carb foods, gluten-free foods, and healthful fat. I'll explain how each of these factors plays into the health of the microbiome for the benefit of the brain.

Best of all, you can reap the rewards of the Brain Maker protocol within a matter of weeks.


I have absolutely no doubt in my mind that by embracing this information, we will completely revolutionize the treatment of neurological illnesses. And I can't express in words how honored I feel to be able to present these revelations to the public, exposing all the data that's been quietly circulating in the medical literature. You're about to appreciate how your microbiome is the ultimate brain maker.

My recommendations in this book are designed to treat and prevent brain disorders; alleviate moodiness, anxiety, and depression; bolster your immune system and reduce autoimmunity; and improve metabolic disorders, including diabetes and obesity, which factor into long-term brain health. I'm going to describe aspects of your life that you might never have guessed take part in your brain health. I'll discuss the significance of your birth story, of your nutrition and prescribed medications as a child, and of your hygiene habits (for example, your use of hand sanitizers). I'll explore how gut bacteria are different in populations around the world and how these differences are caused by dissimilarities in diet. I'll even take you through what our ancestors ate thousands of years ago and how this relates to new research about the microbiome. We will consider the notion of urbanization: how has it changed our internal ecological community? Has sanitized city living led to increased rates of autoimmune disease? I trust that you'll find this discussion equally illuminating and empowering.

I will show you how food-borne prebiotics—nutrient sources of fuel for the beneficial bacteria that live within your gut—play fundamental roles in preserving health by maintaining balance and diversity of intestinal bacteria. Foods such as garlic, Jerusalem artichoke, jicama, and even dandelion greens, as well as fermented foods such as sauerkraut, kombucha, and kimchi open the door for heightened levels of health in general, and brain function and protection in particular.

Although probiotics have now become commonplace in many food products and can be found in regular grocery stores, it helps to know how to navigate all the options—especially when you're confronted with "good for the gut" advertising. I'll help you do just that, explaining the science behind probiotics and how to choose the best ones.

Of course, other lifestyle habits factor into the equation, too. In addition to exploring the interaction between the microbiome and brain, we'll be getting to know a new discipline: epigenetic medicine. This science examines how lifestyle choices such as diet, exercise, sleep, and stress management influence the expression of our DNA and play directly and indirectly into brain health. I will also share with you the role of mitochondria in brain disorders, from the perspective of the microbiome. The mitochondria are tiny structures within our cells that have their own DNA separate from the DNA in the nuclei. The mitochondria can in fact be considered a third dimension to our microbiome; they have a unique relationship with the microbiome in our guts.

Parts 1 and 2 will provide the foundation you need to embark on my brain maker rehab program in part 3. I've given you a lot of information in this introduction. I hope I've begun to whet your appetite for learning about and embracing this whole new area of medicine, a fresh approach to maintaining brain health. Nothing but a stronger, brighter, healthier future awaits you.

Let's get started.


What Are Your Risk Factors?

WHILE THERE'S NO SINGLE TEST available today that can accurately tell you the state of your microbiome, you can gather clues by answering a few simple questions. These questions can also help you understand which experiences in your life—from your birth to today—may have impacted the health of your gut.

Note: Although microbial testing kits are starting to emerge on the market, I don't think the research is there yet in terms of knowing what the results truly mean (healthy vs. unhealthy) and which risk factors you bear. In the future I have no doubt we'll be able to establish evidence-based parameters and defined correlations between certain microbial signatures and conditions. But for now this is tricky terrain; it's still too early to know whether certain patterns being studied in the gut microbiome that are related to illness X or disorder Y are part of the cause or the effect of those conditions. That said, these kits can be useful for gauging the diversity and general composition of your microbiome. But even then, it can be difficult to say that a certain microbial makeup identifies you as "healthy." And I wouldn't want you to try to understand the results from such tests on your own without proper guidance from trained medical professionals who are experienced in this domain. So for now, I'd press pause until further notice about these kits. The questions below will arm you with plenty of personal data that can help provide a sense of your risk factors.

Don't be alarmed if you find yourself answering yes to most of these questions. The more yeses you have, the higher your risk might be for having a sick or dysfunctional microbiome that could be impacting your mental health, but you are not doomed. My whole point in writing this book is to empower you to take charge of your gut's health and, in turn, your brain's health.

If you don't know the answer to a question, skip over it. And if any particular one alarms you or prompts you to ask further questions, rest assured I will answer them in the upcoming chapters. For now, just respond to these questions to the best of your ability.

1. Did your mother take antibiotics while she was pregnant with you?

2. Did your mother take steroids like prednisone while she was pregnant with you?

3. Were you born by C-section?

4. Were you breast-fed for less than one month?

5. Did you suffer from frequent ear and/or throat infections as a child?

6. Did you require ear tubes as a child?

7. Did you have your tonsils removed?

8. Have you ever needed steroid medications for more than one week, including steroid nasal or breathing inhalers?

9. Do you take antibiotics at least once every two to three years?


  • "Dr. Perlmutter's book is among those rare and exciting exceptions: information so empowering, so enlightening, and presented so clearly and concisely that the reader emerges far better off for the reading experience. Put this book on your short list of must-reads for health and nutrition."—William Davis, MD, author of Wheat Belly
  • "The single most important medical innovation in the 21st century is making the link between the gut and the little bugs that live there and nearly every chronic disease - from autism to depression, from asthma to autoimmune disease, from diabetes to dementia. Brain Maker is a game changer. For the first time, this brilliant scientist doctor connects the dots and teaches us why we need to tend our inner garden (our microbiome) and provides a radical but simple plan to reset, reboot, and renew your microbiome. This book shouldn't be called Brain Maker, it should be called Health Maker."—Mark Hyman, MD, author of The Blood Sugar Solution
  • "Thanks in large part to dramatic and ongoing increases in understanding the brain-gut-microbiome connection, there is new hope for the treatment of many neurological conditions, from autism to Alzheimer's to multiple sclerosis. David Perlmutter is a leader in this burgeoning field, and his new book, Brain Maker, is a landmark contribution."—Dale E. Bredesen, MD, professor and director of Alzheimer's Disease Research, UCLA
  • "In this revolutionary new book, the nation's leading integrative neurologist, David Perlmutter, gives you a powerful program to heal your gut and optimize your brain. I will recommend it to all of my patients and friends."—Daniel G. Amen, MD, founder of Amen Clinics and author of Change Your Brain, Change Your Life and Healing ADD
  • "Bravo! Dr. Permutter's latest paradigm-shifting book shows us how to manage our health, and especially our brains, through the new frontier of science, the microbiome. By connecting the dots from our gut to our brain, he explains how we can avoid disease, age well, handle stress, and manage our moods. With revolutionary ideas and practical advice, he gives us a fighting chance against brain decline. I love this book!"—John Ratey, MD, author of Spark and coauthor of Go Wild, Clinical Professor of Psychiatry, Harvard Medical School
  • "Dr. Perlmutter engagingly explains the hope-generating power of the new gut microbiome-brain science, motivating you to regenerate your brain health with his powerful and practical program."—Martha Herbert, MD, PhD, Assistant Professor of Neurology, Harvard Medical School

On Sale
Apr 28, 2015
Page Count
464 pages
Little Brown Spark

David Perlmutter MD

About the Author

David Perlmutter, MD, is a board-certified neurologist and a Fellow of the American College of Nutrition. He was the recipient of the Linus Pauling Award for his innovative approaches to neurological disorders. With his books now published in twenty-seven languages, Dr. Perlmutter is setting new standards for what healthy lifestyle means around the world.

He is the author of the New York Times bestsellers Grain Brain, The Grain Brain Cookbook, and Brain Maker, as well as The Better Brain Book and Raise a Smarter Child by Kindergarten. He lives in Naples, Florida.

Learn more about this author