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

Our guts are much more important to our overall health than most of us believe and understand. At least that is what The Microbiome Diet by Dr. Raphael Kellman tells us. This book reinforces the message I have received in The Good Gut, Missing Microbes and Let Them Eat Dirt. Kellman’s book is the first of these to present a detailed account of what we can eat to improve the health of our gut. As I have said in the past, the research into our microbiome is exciting and should provide new insights to weight control and improved health. I do not believe, however, that gut science is so advanced as to overturn most the basic knowledge we have of nutrition. As I did with The Angry Chef I will use the author’s words to guide us in understanding this book.

“Our metabolism, weight and overall health depend on the balance of microbial life within our gastrointestinal tract.” The preceding statement is the basic premise of The Microbiome Diet. The assumption is that all Americans, or at least those of us who are overweight, are living with an unhealthy gut. The symptoms of an unbalanced microbiome include abdominal pain, arthritis, difficulty focusing, headache and low energy. How many of us have exhibited at least one of these warning signals at one time or another? Are these and the other twenty-five symptoms listed controlled directly by our gut or are there other organs involved? Thus, even if we don’t have a major gut disorder, many of us appear to suffer from a subclinical case, or so the book suggests.

Remove—Replace—Reinoculate—Repair are the main steps of the plan. Kellman calls us to remove unhealthy foods. Although there is no need to count calories on this diet, we can count on a rapid loss of weight in phase 1. Such losses can be explained in conventional nutrition by depleting glycogen and losing water weight. The restrictive aspects of the diet make it impossible to gain weight and difficult to stop losing weight while following the plan. Next, we are urged to replace the unhealthy foods with superfoods, digestive enzymes & hydrochloric acid. The book is vague as to what form we are supposed to ingest the HCl (memories of Organic Chemistry labs haunt my thoughts at this point). I did find Betaine HCl available on along with digestive enzymes. I am not sure of the effectiveness of betaine HCl or the performance of such enzymes after passing through the natural HCl in our stomach.


Third, we should reinoculate with probiotics from fermented foods or supersupplements. One type of fermented product we should avoid completely in phase 1 and only add sparingly later is yogurt. Finally, we need to repair leaky portions of the gut. At this point I wonder just how we know if our gut is leaky. Leaky gut is not a clearly defined disorder within the medical community. It appears to be a problem in celiac and Crohn’s disease, but it is not clear that leaky guts are widespread in the American public. To learn such information in a book that proclaims to be “A Scientifically Proven Way” to weight loss and better health in its subtitle is disturbing.

“food is far more than a collection of chemicals and nutrients” The Microbiome Diet informs us that gut health goes beyond what we eat. Our food should be eaten in a stress-free environment. Love appears to be part of the diet’s success—love of others and love of ourselves. We are urged to develop a relationship with each food we eat and all the factors that nourished the raw materials. I have no doubt that our environment and social relations are important parts of our lives and mental health, but do these factors override a basic understanding of human nutrition? Maybe I am missing something, but foods are made up of nutrients and other chemicals while few of us commune with all aspects of food origins when we sit down to eat. Many of us live busy, hectic lives. A healthy diet may just not be enough to head off an imbalanced microbiome.


Reminder: Atoms are the building blocks of chemicals, and everything we put in our mouths is chemical.

“weight loss and health are not two separate issues—they are one and the same.” Two months ago, I reviewed The Angry Chef who stated that one of the problems with diet approaches today is that they equate weight and health. At the time I thought the Angry Chef was guilty of oversimplification, but the author of The Microbiome Diet supports his claim. A major theme in recent posts on this site has been about the BMI and whether it can serve as an index of good health. It is not clear that the BMI is a good indicator of a healthy weight, much less a valid index of overall health.  The book points to the direct role of an unhealthy gut in the development of the current plague of chronic diseases facing the modern world. I repeat my disclaimer that the microbiome has been underappreciated in disease etiology, but is it the cause of everything that can go wrong with us? Pardon my skepticism.

“Luckily, now that we understand the problem, we can solve it.” Kellmen provides an easy-to-understand theory of the microbiome’s role in development of diseases such as obesity and a detailed explanation of how it works. As someone who has criticized articles about a lack of mechanism, I was impressed. Then, I went tracking down many of the pieces of the author’s proposed mechanism. I confess to not being comprehensive in my analysis, but every aspect I tracked down in the scientific literature revealed some very interesting hypotheses, each supported by a few studies. There does not appear to be enough confirmation of the steps in the proposed mechanism to gain wide acceptance in the scientific community. Here we have, however, an advocate of very young science suggesting that almost everything we thought we knew about human nutrition has been disproven. I am not convinced that the science of the gut has solved the problems that the science of nutrition has not.

My basic takeaway from reading The Microbiome Diet is that the author has presented a very complex and detailed theory on how our gut controls most of the other functions of our body. He has accompanied his theory with an in-depth description of how and why the gut is in control and contrasts it with the principles of basic nutrition. Most of the positive results that we can expect by adopting this microbiome diet can be explained by an understanding of current nutrition. I have no doubt that adopting this diet will lead to significant weight loss, but I am not sure that it will provide sufficient nourishment. I cannot recommend either the diet or the book.

Next week: A view of the role of gut microbiota on obesity and health from a research scientist in the field.

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