Microbiome Diet

The Scientifically Proven Way to Restore Your Gut Health and Achieve Permanent Weight Loss


By Raphael Kellman, MD

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The groundbreaking program that connects the microbiome and gut health to healthy weight loss, complete with a three-phase plan and recipes.

Cutting-edge science has shown that the microbiome is the key to overall mental and physical health — and the secret behind healthy, sustainable weight loss. Drawing on nearly two decades of experience as a specialist in functional medicine and intestinal health, Dr. Raphael Kellman has developed the first diet based on these scientific breakthroughs.

Offering a proven program to heal your gut and reset your metabolism, along with meal plans and fifty delicious chef-created recipes, The Microbiome Diet is the key to safe, sustainable weight loss and a lifetime of good health.

“Dr. Kellman masterfully presents a life enhancing, actionable plan based on this emerging science in a way that is user-friendly, for all of us.” — Dr. David Perlmutter, New York Times bestselling author of Grain Brain







Robert just could not manage to lose weight.

He was a middle-aged man who was my patient about eight years ago. I was treating him for multiple health problems—heart disease, high blood pressure, high levels of insulin, and a blood sugar reading that I was very concerned about. But I knew that all of these issues would greatly improve—and perhaps even disappear—if we could just get Robert down to a healthy weight.

Before he had become my patient Robert had been on every diet in the book. Atkins, the Zone, low-carb, low-fat—you name it, Robert had tried it. But to his great frustration, none of these diets ever worked for him. He would starve himself for weeks, trying to stick to the rules he had been given, only to find that he could barely lose five pounds. Then, the moment he broke the diet even a little bit—a single forbidden baked potato when he took a client to a steakhouse, splitting a piece of chocolate cake with his wife on their anniversary—he would gain back even the little weight he had lost. By the time he came to see me, Robert had simply given up.

So for most of the time I had been treating him Robert was nearly fifty pounds above his ideal weight. He drank, he smoked, he ate all the wrong things, and I simply could not get him to adopt a healthy lifestyle.

“What’s the use, Doc?” he would always ask me. “No matter what I do, the weight doesn’t come off. So why bother trying?”

Now he was in the hospital with pneumonia. When I thought about the potential effect that might have on his weight, my heart sank. Robert had had previous hospital stays for different ailments, and he had always emerged five to seven pounds heavier. The combination of starchy hospital food and lack of movement exacerbated his tendency to gain weight, and I always dreaded the aftereffects of his prolonged periods of bed rest.

This time, however, I was treating Robert with a course of antibiotics. To counter the effects of the antibiotics I was also treating him with probiotics. Antibiotics kill the bacteria that make us sick, but they also kill the healthy bacteria that live throughout our bodies, especially in our intestinal tract. Probiotics counter the destruction that antibiotics cause—and sometimes, as we shall see, they have even more powerful effects.

I had also prescribed prebiotics for Robert. Prebiotics are foods and supplements that nourish healthy bacteria. Whereas probiotics help to replace the healthy bacteria that have been destroyed, prebiotics help to support the healthy bacteria that still remain.

So this time, instead of gaining weight, Robert lost seven pounds in two weeks—without making any effort at all. Why?

Trying to solve this mystery led me on a journey I never expected: the discovery of a new approach to diet and health that transformed my own understanding of weight loss and one that I hope will transform yours too. I believe that this book will challenge everything you know about the causes of obesity—and about the kind of diet that can successfully overcome it.

Thanks to Robert, I was able to develop a diet that benefited dozens of my patients, helping them lose weight quickly and to keep it off forever.

Patients who followed this new approach were able to lose pounds, inches, and body fat, especially around the stomach, waist, and abdomen.

They found that after years of struggling to lose those stubborn pounds they could never get rid of, all of a sudden the weight was coming off by itself.

They discovered that within a few days they began to lose their cravings for sugar, bread, baked goods, and other “forbidden foods,” such as macaroni and cheese, pizza, and ice cream, and within a few weeks those cravings were gone completely. For the first time they could remember they no longer felt like a prisoner of their own appetites, forever longing for foods they knew were not good for their health.

Best of all, once my patients had spent a few weeks on this diet they were able to drop to only 90 percent compliance. After a few more weeks on this diet they were able to maintain only 70 percent compliance—all while remaining at their healthy weight! My new approach to weight loss had enabled my patients to reset and reboot their sluggish metabolism so they could periodically indulge in an occasional rich food or sweet dessert without fear of developing the old cravings—or gaining back the old weight. And unlike the vast majority of dieters, who tend to regain all the old weight and more, the people on this diet continued to maintain a healthy weight for years.

What is the secret to this extraordinarily successful weight loss plan? What mystery had my patient Robert unlocked for me on his “accidental diet”? The answer lies in the microbiome, the mysterious but oh-so-important world that each of us holds within.



  90 percent of the cells within your body are not human—they are microbes and bacteria known as the microbiome.

  The microbiome is the key to revving up your metabolism and losing weight.

  You don’t have to count calories, fats, or carbs to lose weight; you just have to avoid the foods that hurt your microbiome and eat the foods that support it.

  After seven weeks you can maintain only 70 percent compliance, indulging in other foods up to 30 percent of the time.



What if I told you that 90 percent of the cells within your body are not human?

And what if I told you that this nonhuman 90 percent—an entire separate ecology within your own body—is the key to losing weight and keeping it off?

A series of scientific breakthroughs over the last few years has revealed that the key to fast, permanent weight loss is the microbiome—the trillions of tiny bacteria living within our intestines.

While millions of people have been struggling with all kinds of diets—and either failing to lose weight or gaining back all the weight they lost—a whole new paradigm has begun to emerge.

Cutting-edge science has shown that the microbiome is the secret to healthy, dramatic weight loss as well as significant improvements to your overall health, mood, energy, and mental function. Research reveals that when the microbiome goes out of balance, people often gain weight, even when they haven’t changed their diet or exercise. An imbalanced microbiome often dooms just about any diet to failure. When the microbiome is balanced, however, people often lose weight, even when they don’t make any other changes.

These microscopic organisms regulate the way calories are extracted from your food. They produce vital nutrients and help regulate your immune system. They exert enormous influence over your hormones, your appetite, your cravings, and even your genes. They also have a huge impact on your neurotransmitters, the brain chemicals that govern your mood, energy levels, and mental functioning.

Most important of all, however, is the way the microbiome affects your metabolism. When your metabolism is revved up and working at top speed, you lose weight and keep it off, effortlessly maintaining a healthy weight. When your metabolism is sluggish and cued to retain body fat, you will gain weight and hold onto those extra pounds even if you cut way back on the calories and ramp up the exercise.

Metabolism is the key to weight loss. And the microbiome is the key to metabolism.

The microbiome was the reason Robert had suddenly lost weight, effortlessly, after years of unsuccessful dieting. The microbiome was the reason Robert no longer craved sweets and starches, fried foods and fatty meats, potato chips and cheesecake. The microbiome was the reason Robert no longer felt hungry all the time and why he finally felt satisfied after he ate. Best of all, the microbiome was the reason Robert could occasionally enjoy that baked potato or chocolate cake—as much as 30 percent of the time.

Robert’s experience—and the knowledge I sought as a result—convinced me that supporting and balancing the microbiome can be the basis for a fast, effective, and long-lasting approach to weight loss. Supporting the microbiome might even be the solution to the worldwide obesity epidemic. So let’s take a closer look at this mysterious but crucial portion of your anatomy.


The microbiome is a miniature world made up of trillions of microscopic, nonhuman organisms that flourish within your gastrointestinal tract. These intestinal organisms—bacteria—digest your food, govern your appetite, control your metabolism, orchestrate your immune system, influence your mood, and even help determine how your genes are expressed. They have a major impact on whether your heart is healthy, whether your bones develop properly, and whether your brain feels sharp and clear or fuzzy and unfocused. They sustain the gastrointestinal tract so your food is properly digested and you get all the nourishment you need. They produce crucial vitamins and other nutrients. They even manufacture natural antibiotics.

Most amazing of all, these nonhuman organisms make up a whopping 90 percent of your cells!

Think about that for a moment. The vast majority of the cells within your body are not human. Within your intestinal tract lies a whole separate ecology that is inextricably involved with yours. When these microscopic organisms flourish, you flourish. When they struggle, you struggle. When they crave sugar, so do you. And when they operate at peak efficiency, so does your metabolism.

That is why balancing your microbiome is the key to eliminating food cravings.

It is the key to eliminating symptoms that you might never even have connected to your weight and the way you eat, such as fatigue, anxiety, depression, brain fog, headaches, acne, eczema, congestion, frequent colds and infections, joint pain, and muscle pain.

Balancing your microbiome is also the key to preventing and even reversing major illnesses, including diabetes, heart disease, metabolic syndrome, autoimmune disorders, autism, and other developmental disorders

I knew about the microbiome when I began treating Robert, but I didn’t know about its connection to weight loss. I had prescribed those probiotics and prebiotics for Robert as part of my effort to improve his intestinal health. The “invader” bacteria causing Robert’s pneumonia had also caused Robert’s microbial system to become even more imbalanced. The antibiotics I had prescribed to kill off the bad bacteria would help cure the pneumonia, while the probiotics and prebiotics I gave him helped Robert rebalance his inner ecology. As a result, Robert’s pneumonia was cured, and at the same time he lost weight, without even trying, simply because his microbial health had been restored.



Antibiotics can have a near-miraculous effect on many diseases, but they can also wreak havoc with the microbiome, as we shall see, creating multiple health problems and a greatly increased risk for weight gain. If you need to take antibiotics, be sure to also follow my Microbiome Diet recommendations for probiotics and prebiotics, on page 79. Probiotics are microscopic organisms that will replenish your microbiome. Prebiotics are foods and supplements that nourish the organisms already in your microbiome.


In fact, by themselves antibiotics don’t lead to weight loss but, instead, to weight gain—and for the same reason. Antibiotics are designed to kill the unhealthy bacteria within our bodies, but often, like a spray of gunfire, they wipe out innocent bystanders as well, destroying our good bacteria and throwing our microbiome out of balance. The underlying principle is clear:

                    Our metabolism, weight, and overall

                    health depend on the balance of microbial

                    life within our gastrointestinal tract.


Perhaps it’s because I have a four-year-old daughter, but when I imagine the microbiome I think of that old Dr. Seuss story Horton Hears a Who. If you recall, Horton the elephant had enormous ears that enabled him to hear tiny sounds that others missed. As a result, he was able to detect an entire civilization of microscopic organisms, called Whoville, situated on a minuscule speck of dust.

Because Horton’s neighbors could not perceive that microscopic world, they were skeptical and even angry when Horton tried to get them to acknowledge, respect, and protect it. In fact, they were ready to destroy the entire community of Whoville simply because they could not see it. “A person’s a person, no matter how small,” Horton kept repeating, but his respect for the miniature world he had discovered angered his neighbors even more.

Just as Horton’s neighbors could not perceive the tiny residents of “Whoville,” so do most of us remain unaware of the microscopic world within us. And just as Horton’s neighbors did not understand their responsibility for preserving that unseen community, so do most of us fail to understand our own responsibility for supporting our microbiome—with disastrous results for our weight, our metabolism, and our health.

I know it sounds like the stuff of fantasy, but we really do contain within our bodies an entire ecology of nonhuman organisms—bacterial flora and fauna living inside us in a symbiotic relationship. The ecology that lives within our intestines is dependent on us. And we, likewise, depend on it. Healing this ecology and keeping it in balance is the key to our overall health.

Scientists have known about the microbiome for a long time, but only recently have we begun to understand its importance. In 2008 the National Institutes of Health began a project to map the microbiome, triggering an enormous amount of exciting research. Cutting-edge studies reveal that in addition to helping us resist disease, depression, and anxiety, the microbiome is crucial to our metabolism, our hunger, our eating patterns, and our weight.

We used to think that all microbes were unhealthy bacteria determined to infect us with deadly diseases. Now we are beginning to understand that most microbes are actually helpful to us, performing so many important functions that, without them, we could not survive.

When we eat the foods that keep this inner world in balance, our metabolism runs at peak efficiency. Our bodies almost effortlessly maintain their ideal weight. We feel hungry only when we really need more food, and we feel full and satisfied when we have had enough. We lose the body fat that distorts our shape, regaining our healthy waistlines and relatively flat abdomens. We also feel more vital and energized than ever before; dispel our brain fog, sleep problems, depression, and anxiety; and develop healthy, glowing skin and hair. This is why I say that balancing our microbiome is the key to optimum weight and health.

By contrast, when we consume foods or medicines that throw this inner world out of balance, we put ourselves at risk for a host of diseases, from skin rashes to cancer. We feel tired, anxious, grouchy, depressed, or just plain “not ourselves.” We feel hungry much of the time—perhaps even all the time—regardless of whether we need the food. And, ultimately, we accumulate body fat, especially around the abdomen, gaining weight that is virtually impossible to lose and even harder to keep off.


Most of us tend to think of ourselves as separate, autonomous beings whose growth and development depend entirely on ourselves. But in fact, our health, our weight, and our very survival are inextricably dependent on our microbiome.

As soon as we pass through the birth canal we begin to become 90 percent microbe. The moment we come into this world we start the process of acquiring the trillions of bacteria that we need to achieve optimal health. In fact, the microbiome is so important to our survival that it has been dubbed “the forgotten organ.”

One of the first bacteria we encounter is called Lactobacillus johnsonii, a microscopic creature we acquire in the birth canal. This microbe digests milk and, therefore, helps us metabolize our mother’s breast milk.

Significantly, our mother’s milk itself contains oligosaccharides, a type of prebiotic that feeds our microbiome. As infants, we cannot digest this substance, but our microbes can. How important must our microbiome be to our survival if mother’s milk itself nourishes this nonhuman but crucial portion of our anatomy?

Scientists are just beginning to realize the importance of the microbes acquired during that trip down the birth canal, because babies who don’t have that initial access to their mother’s microbiome—that is, babies who are delivered by Caesarean section—are often prey to a number of immune-related disorders, such as asthma, allergies, celiac disease, and skin infections. Some studies suggest that babies born by C-section also face a higher risk of Type 1 diabetes and obesity—a further connection between the microbiome, metabolism, and weight. Likewise, many researchers now believe that when children are given antibiotics, which can devastate the microbiome, they face a higher risk of allergy-related diseases, inflammatory bowel syndrome, and, again, obesity.



If you’re prone to frequent infections in the vaginal area, an unbalanced microbiome might be the cause. Following the Microbiome Diet will help rebalance your microbiome and prevent further infections.


Although each microbe is small, those trillions of tiny organisms add up to a weight of about three pounds—coincidentally, what your brain weighs as well. Your “forgotten organ” occupies your digestive system, mouth, nasal passages, and lungs as well as living on your skin and in your brain. If you’re a woman, as we just saw, the microbiome also inhabits your vaginal canal. A healthy microbiome supports your health in each region, whereas an out-of-balance microbiome leaves you prone to infection, imbalance, and distress.

Scientists have come to believe that the more diverse your microbiome—the more species it contains—the healthier you are likely to be and the better you will be able to control unwanted weight gain. So far, researchers have identified about ten thousand species of bacteria that potentially occupy the human microbiome, but each person’s microbiome has its own unique combination. Even identical twins have been shown to have individual microbiomes.

At the same time, we tend to acquire bacteria from the people we live and work with and perhaps even from casual contacts in a crowded street or packed room. This is possible because your microbiome is extremely dynamic, able to change composition within twenty-four hours in response to stress, antibiotics, and illness and able to change within a few weeks or even days in response to diet, supplements, and exercise.

In fact, many scientists are concerned about the ways in which our microbiomes are changing, because those of us in the developed world seem to be losing microbial diversity with every generation. Those of us in the developed world tend to be treated with antibiotics frequently and to have relatively little contact with plants, animals, and soil. In addition, the Western diet includes a high proportion of refined foods, which also tends to kill off certain bacteria. As a result, our microbiomes tend to contain far fewer microbial species than people who grow up in developing nations. According to some scientists, the microbial diversity of developing nations is the reason for their lower rates of allergy and asthma: Diverse microbiomes are better at keeping the immune system in balance. To help respond to the various bacteria that it will encounter throughout your life, your immune system must be introduced to a wide variety of microbes.

Many scientists also believe that low microbial diversity correlates with weight gain. Some have even argued that the destruction of the microbiome is a prime mover behind the obesity epidemic. Martin J. Blaser, chair of the Department of Medicine and a professor of microbiology at the New York University School of Medicine, does not believe that bad eating habits are enough to cause our rapid and widespread explosion of obesity, and he’s tried to prove this by creating his own mini-obesity epidemic among the mice in his laboratory simply by administering small but steady doses of antibiotics. The antibiotics kill off many of the mice’s microbes, and the mice have gained enormous amounts of weight. Blaser believes a similar destruction of microbial diversity might help explain the worldwide obesity epidemic.

Other studies back up Blaser’s hypothesis, including one reported in the August 29, 2013, issue of Nature. The Pan European Meta HIT Consortium studied nearly three hundred Danish volunteers, both lean and obese, whom it examined over the course of nine years. Researchers measured the bacterial genes found in the volunteers’ stool along with weight gain and other markers of metabolic health, such as blood pressure, blood sugar levels, insulin levels, and inflammation, all of which can set you up for both weight gain and disorders like heart disease and diabetes.

And, indeed, the study discovered that for the volunteers who were already obese, a relatively low diversity in the microbiome correlated with significant weight gain over the course of nine years. Generally, low diversity correlated with higher inflammation, greater insulin resistance, and other danger signs of metabolic disorder.


I know it’s challenging to wrap your mind around the idea that there is a whole other ecology within your body, an ecology that is not human but nevertheless an essential part of you as well as a crucial aspect of your health.

And yet it’s true. The health of your microbiome determines the quality of your health, and without your microbiome you couldn’t survive. In fact, without your microbiome you would no longer be you, just as you would no longer be you without your brain or your heart.

A balanced microbiome regulates your immune system, three-quarters of which is located within your intestines. It nourishes and sustains your gastrointestinal tract. It produces crucial vitamins and nutrients, including various B vitamins and vitamin K. It lays the groundwork for optimal mood and brain function by influencing the production of your neurotransmitters, the hormones and biochemicals your brain needs to process thought and emotion. And it keeps you at your ideal weight by helping you digest your food, maintain an appropriate appetite, regulating the calories that enter your system, and keeping your metabolism working at optimal speed.

Every human and animal on the planet has its own unique microbiome. But as scientists have become interested in this “forgotten organ,” they wondered what might happen to animals who actually were raised without one. So they began breeding germ-free mice in sterile laboratory conditions to learn what happens when an animal is 100 percent itself instead of 90 percent microbe.

The results were startling. In the eloquent words of science journalist Moises Velasquez-Manoff, writing in Mother Jones in April 2013,

Animals raised without microbes essentially lack a functioning immune system. Entire repertoires of white blood cells remain dormant; their intestines don’t develop the proper creases and crypts; their hearts are shrunken; genes in the brain that should be in the “off” position remain stuck “on.” Without their microbes, animals aren’t really “normal.”


  • "Reset your metabolism and free yourself from food cravings and an uncontrollable appetite with Dr. Kellman's revolutionary diet, which shows us how to balance the gut's healthy bacteria. Lose weight and keep it off with this nonrestrictive plan."
    Natural Solutions

On Sale
Jul 1, 2014
Page Count
272 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