The TIGER Protocol

An Integrative, 5-Step Program to Treat and Heal Your Autoimmunity


By Akil Palanisamy, MD

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Prevent and heal autoimmune diseases and live the life you want through this groundbreaking, integrative protocol.

After working with patients in his two decades of practice, Harvard-trained Dr. Akil Palanisamy was inspired to develop The T.I.G.E.R. Protocol, an integrative treatment approach combining his work as a functional medicine practitioner with his training in Ayurvedic medicine. He has since used this simple protocol to successfully treat thousands of patients with autoimmune diseases. The protocol works to address the root cause of your autoimmunity instead of treating just the symptoms. 

Through the T.I.G.E.R. protocol, you will:
·         Address Toxins
·         Heal Infections
·         Improve Your Gut Health 
·         Learn to Eat Right
·         Consciously Rest and Rebalance
In the United States, autoimmune diseases affect an estimated 25 million people–it is the fastest growing category of disease. That’s a staggering number of individuals struggling with conditions like type 1 diabetes, celiac disease, lupus, and other issues like allergies and eczema. So many autoimmune patients feel confused, hopeless, or uninformed about their diagnosis and face poor quality of life despite conventional therapy; it can take three years and visits to four different health professionals to receive a formal, correct diagnosis of autoimmunity — even though that is the best time for early intervention in which holistic treatments can lead to major benefits. Learn how to prevent and reverse autoimmune diseases through this groundbreaking, holistic protocol.




Autoimmune disease has become a silent epidemic in modern times. Unlike COVID-19, autoimmune disorders have insidiously expanded to huge levels without attracting much attention. In just the past 10 years, some autoimmune diseases have increased by 300 percent. Others have risen up to 5,000 percent in the past few decades.

One out of every five Americans suffers from some form of autoimmune condition. Hundreds of millions of people worldwide are struggling with autoimmunity. The prevalence and cost of autoimmune disease are greater than heart disease, cancer, and diabetes—combined.

There are more than 100 autoimmune conditions affecting people today, including Hashimoto’s disease (also known as Hashimoto’s thyroiditis), type 1 diabetes, multiple sclerosis, and rheumatoid arthritis. Sadly, the list continues to grow. Recent research has even shown that irritable bowel syndrome, the most common digestive disorder, is autoimmune in nature.


Patients with autoimmune diseases are at a disadvantage in our current medical system. Conventional medicine excels at treating acute illnesses and injuries, but is ill-suited to tackle chronic diseases.

Such patients are often prescribed powerful immunosuppressive drugs that can subdue their symptoms—but this comes at a cost. These drugs can have serious side effects and unintended long-term consequences. More importantly, they only treat the symptoms and do nothing to address the underlying causes of autoimmune illness.


From my own three-plus decades of clinical experience, I know people are seeking natural alternatives to help them feel better and regain a healthy immune system. I have seen the frustration and despair that autoimmune patients experience. The TIGER Protocol is the comprehensive guidebook they have been waiting for—the solution that can transform their lives.

This book offers a revolutionary approach to healing. It introduces Dr. Akil’s innovative five-step TIGER Protocol to reverse autoimmunity by addressing the root causes of disease. The program is broken down into actionable and manageable steps that are easy to follow—providing a detailed road map to health.


My friend Dr. Akil is a unique “triple threat” in the field of integrative medicine. He combines expertise in Functional Medicine with extensive training in Ayurveda and an understanding of the paleo diet and ancestral lifestyles.

On top of that, he has compassion and empathy because he has gone through a serious disease himself. As he detailed in his outstanding first book, The Paleovedic Diet (which combines a plant-based Paleo diet with Ayurvedic medicine), he overcame a mysterious illness that forced him to halt his medical training. He emerged with firsthand experience of the power of integrative medicine.

With this background, Dr. Akil is eminently qualified to give you the most accurate and reliable information on autoimmunity. I have the utmost confidence in his approach and the content he has put together.


Functional Medicine, which seeks to detect and treat diseases by addressing root causes (as opposed to conventional medicine’s penchant for managing symptoms), is a movement I have been at the forefront of for decades. I am delighted to see Dr. Akil, one of the world’s top experts in Functional Medicine, sharing how this powerful approach can be used to treat autoimmunity.

In addition, Dr. Akil has combined the best of leading-edge research and insights from Functional Medicine with the ancient wisdom of Indian Ayurveda to offer a complete healing plan for patients with autoimmune disorders.

Ayurveda has a great deal to offer in our modern fight against autoimmune ailments. There is a reason why it has survived for over 3,000 years! In this book, Dr. Akil has seamlessly integrated this ancient wisdom with modern science.


Although not widely known, there is an extensive body of research in integrative medicine. (For example, there have been over 50,000 papers published on the microbiome in the past decade alone.) Dr. Akil has read tens of thousands of research papers on these topics and brought together their essential points into a single, user-friendly source (with 800-plus references!).

In other words, Dr. Akil has “climbed the mountain” of autoimmune research so you don’t have to.

In addition, he has treated thousands of autoimmune patients over a career spanning more than two decades, so you can trust that the recommendations he makes in this book are clinically proven and tested. You’d be hard-pressed to find another book in which all these medical advances and insights are compiled in a single, accessible place.


As a Functional Medicine practitioner, I always believe it’s best to treat the root causes of health issues. Dr. Akil will teach you his TIGER Protocol to help you identify and address each of the key root causes of all autoimmune conditions: toxins, infections, gut microbiome, eating right, and rest (or lack thereof).

Right off the bat, this is an important insight into autoimmune diseases. Although there are over 100 different varieties of autoimmunity, the root causes are the same and lead to the same basic dysfunction of the immune system. The particular autoimmune condition you end up with depends on what your “weak link” is, based on genetics and lifestyle.

This news is empowering for patients because they can understand what is causing their autoimmunity and learn what they can do about it.


I truly believe this book can revolutionize our approach to all those on the autoimmune spectrum, whether they are suffering from inflammatory symptoms like fatigue, joint pain, rashes, or digestive issues, or even if they are dealing with full-blown autoimmune disease.

In fact, I would argue that the diet plan outlined in this book, with its emphasis on building gut microbiome diversity with prebiotic and fermented foods, offers the healthiest, most well-rounded approach to eating out there—one that all people should follow.

We know that a diverse microbiome—which depends largely on your diet—is one of the most important factors in living a long and healthy life. The TIGER Protocol provides you with the most up-to-date understanding of the dietary approach that can best achieve this, including specific foods, recipes, and meal plans to try.


The section on the microbiome is one of the many gems in this book. The insights Dr. Akil offers about the microbiome are among the most advanced and sophisticated I have seen in any book. Yet he has conveyed these complex concepts in ways the average person can easily understand and implement.

One of the hallmarks of autoimmune disorders, and most modern afflictions, is a loss of gut bacteria diversity and an imbalance in the microbiome. The trillions of bacteria living inside of you have been linked to many autoimmune diseases—but also to such disparate conditions as allergies, asthma, diabetes, eczema, obesity, heart disease, fibromyalgia, and migraines.

It is absolutely crucial for those suffering from autoimmune conditions, or any other chronic illness, to restore and boost the diversity of their gut microbiome. I would go one step further and say that this should be a top priority for all people because the hallmark of the modern Western microbiome is a significant loss of diversity compared to the robust microbiome of our ancestors.

Dr. Akil gives you a detailed plan on how to achieve this. He explains in depth which foods contain each of the key classes of prebiotics necessary to strengthen your gut microbiome—inulin, resistant starch, polyphenols, oligosaccharides, and more. He teaches you to leverage herbs and spices for maximum benefit. And his tables on the top polyphenol-containing foods are eye-opening! You will find these and many more strategies on how to improve your microbiome in The TIGER Protocol.


Dr. Akil argues that toxins are overlooked in their impact on autoimmune disease; I couldn’t agree more. I have seen repeatedly in my own practice how discovering and eliminating toxins can have a profound impact on patients dealing with autoimmunity.

In my own case, I suffered from undiagnosed mercury toxicity. This led to debilitating chronic fatigue syndrome. But by using the principles of Functional Medicine, I was able to clear out the mercury, heal my gut, and recover completely.

Dr. Akil shines the spotlight on toxins as one of the key unrecognized drivers of autoimmunity and helps you begin your healing journey by addressing toxins first inThe TIGER Protocol.


Other books on this topic have various concerning issues. Some of them are not written by physicians and give you dangerous advice, like telling you to stop your medications abruptly. (Like Dr. Akil, I believe that any tapering of medications should be done gradually under the supervision of your physician.) Other books present diet plans that are too extreme or try to upsell supplements or programs created by the author.

The TIGER Protocol has none of these flaws. It is unbiased and free of commercial interests. The diet plan it offers is moderate and balanced. The program it recommends is a sage middle ground that is effective without being draconian. It is written by a globally renowned doctor who is a widely respected authority in the field of Functional Medicine.


I believe every patient with autoimmune or inflammatory issues would benefit from reading this book.

Dr. Akil provides readers with a powerful action plan to prevent, treat, and even reverse autoimmune disorders. The TIGER Protocol is packed full of evidence-based guidelines, case studies, and practical tools to help you take charge of your health. It is filled with pioneering new ideas and groundbreaking insights. And best of all, it’s exceptionally well-written and enjoyable to read.

You don’t have to settle for anything less than feeling your best and having the optimal quality of life—regardless of what your diagnosis is. The TIGER Protocol is an unrivaled guide that will empower you with information and strategies to take charge of your health and thrive. The knowledge and tools are in your hands now; it’s up to you to take advantage and start feeling better!

—Mark Hyman, MD




Overview—Immune Systems Gone Haywire

A nurse at her local hospital, forty-four-year-old Brenda was diagnosed with Hashimoto’s disease, an autoimmune thyroid condition, after experiencing otherwise unexplainable fatigue, weight gain, and hair loss. She had two young children and her symptoms were making it hard for her to manage her family’s busy schedule and demanding job. Her thyroid hormone levels were suboptimal but still technically normal, indicating that the attack on her thyroid gland was not yet critical.

She saw her doctor, who told her that because her thyroid hormone levels were not out of the normal range, she did not qualify for a prescription and there was nothing he could do—eventually her immune system would destroy her thyroid and she should return at that time to be prescribed thyroid replacement hormone. An independent thinker, Brenda was used to finding her own solutions to problems and believed that there had to be another approach.

Does this sound familiar to you? Perhaps for years you have been struggling with similar symptoms, but none of the diagnoses you have received feel appropriate, and the medications you have been prescribed do not help, or else they cause unwanted side effects.

We will come back to Brenda’s case later in the chapter, to illustrate that there is often a lot you can do even when you have been told that “there is nothing you can do.” But first, let me tell you more about how common challenges with autoimmunity are, and teach you about the basics of the immune system.

As discussed, autoimmune disease rates are skyrocketing, making it the fastest growing category of disease. The incidence of type I diabetes has increased fivefold since 1950 in certain countries.1 Rates of celiac disease, an autoimmune disease exacerbated by exposure to wheat, have also risen about fivefold in the past 50 years.2 The growth of autoimmune diseases in children is especially worrisome, with some conditions growing tenfold in the past few decades.3 Almost all varieties of autoimmune conditions, numbering more than 100, are increasing.4

But why are autoimmune disease rates rising so steeply? To answer this question, we have to understand the perfect storm of risk factors that have come together to create this raging epidemic. But first, you need to know a bit about the basics of your immune system.


We live in a sea of microbes. They are within our body, outnumbering our human cells, and all around us, and your immune system is a sophisticated network of defense systems that protect you from these microbes. When your immune system is underactive, you become at risk for serious infections. When it is overactive, your risk of autoimmune diseases develops.

Your immune system is distributed throughout your entire body, including your thymus (a gland located in the upper chest), lymph nodes, spleen, bone marrow, liver, blood, and cells that sweep through and scrutinize every organ.5 At a basic level, it can be divided into the innate and adaptive components. The function of the immune system is incredibly complex; what follows is a simplified explanation so we can explore a few key concepts.

Innate vs. Adaptive

While there is often much interaction between them, the innate and adaptive branches can be thought of as the two main components of the immune system. The innate immune system is the first responder—it consists of white blood cells and all the proteins and messengers that trigger an immediate reaction when your body decides that it needs to defend itself against an invader. This response is instant and powerful, but nonspecific, and sometimes damages surrounding normal tissues in its haste.

The adaptive branch, a hallmark of more evolved animals, is slower but more targeted and precise; although its reaction may take days to weeks, it ensures a more accurate response, and preserves memory so that the immune system can respond more quickly the next time it encounters a specific pathogen.6 Memory from these immune cells can last for years or decades.

The adaptive response includes B cells and T cells, including a subtype of T cells called T regulatory cells. Considered the master regulators of the immune system, these cells are crucial for “keeping the peace” within the immune system and play a major role in the development of autoimmune disease, as we will see later.

Molecular Mimicry

The first mechanism through which autoimmune disease occurs involves a case of mistaken identity called molecular mimicry, in which a foreign protein—found on a bacteria, virus, or food—resembles a protein found within the human body. Our immune system generally produces antibodies, which, to review, are proteins that bind specifically to foreign proteins and mark them for attack and breakdown by immune cells.

Antibodies are used by the immune system to distinguish foreign invaders from the body’s own cells and should never bind to your own cells or tissues. However, the same antibodies produced against a foreign protein could mistakenly bind to a protein on one of your cells if there is a strong similarity between them—thus triggering the immune system to attack and destroy human tissues, while mistakenly thinking that it is attacking invaders. To use a military analogy, it is a case of “friendly fire.”

For example, a common virus known as Coxsackie B virus is implicated in type I diabetes. This is a condition in which the body attacks and destroys cells of the pancreas known as beta cells, which produce insulin necessary for regulating blood sugar. The virus contains a protein that strongly resembles an enzyme found in the pancreatic beta cells; when the immune system produces antibodies against the viral protein they may instead bind to the beta cells of the pancreas, triggering an immune system attack that is considered part of the process by which type I diabetes develops.7

Another example is Guillain-Barré syndrome, a disease affecting the nerves which causes weakness of the muscles and even paralysis in severe cases. Most of the time, a preceding infection is identified that triggers this condition. The most common offender is a bacteria called Campylobacter, which is the most common cause of bacterial diarrhea in the United States.8 Proteins in the outer cell wall of Campylobacter have a striking similarity to those found in human nerves, and the cross-reactivity of these antibodies is known to be one of the major causes of Guillain-Barré syndrome.9

Many such examples exist. However, it is important to know that the susceptibility of the individual makes a big difference. Not every person who gets Coxsackie B virus or Campylobacter will develop the associated autoimmune conditions. This illustrates the several-step process needed to develop an autoimmune disease, and why it is necessary to intervene with a multi-pronged approach to reduce autoimmunity, as we will be discussing in this book.

Bystander Effect

The second model of autoimmune development involves a case of “collateral damage” known as bystander effect.10 In this scenario, the immune system works hard to eradicate and destroy a foreign invader that has entered the body. However, in its overzealous efforts to destroy the pathogen, it may damage and destroy some of the surrounding human tissue as well.

If your immune system identifies a group of virus-infected cells, it recruits a strong inflammatory response and brings large white blood cells known as macrophages to the affected area. These cells release toxic compounds that kill the virus-infected cells but also damage the uninfected neighboring cells in the area.

The bystander effect is also thought to be one of the mechanisms by which toxins such as heavy metals trigger inflammation and autoimmunity, as we will discuss in chapter 2.11

T Regulatory Cells

This type of immune cell plays a key role in the development of autoimmune disease; instability in these cells has been linked to increased risk of autoimmunity.12 Conversely, interventions and factors that lead to improving the number and function of these cells are beneficial in autoimmune disease. They are the key regulators of the immune system, and they help to ensure normal activity and prevent autoimmunity.

This is one of the themes that we will be returning to frequently as we discuss strategies and treatments that favorably impact T regulatory cells. Emerging therapies that seek to reprogram T regulatory cells to treat autoimmune conditions are currently in clinical trials, as I will explain in chapter 12.


As you learn more about autoimmune disease, you will learn how fundamental the gut is to autoimmunity and, in fact, all chronic diseases. That’s why a focus on the gut is foundational to my approach. In terms of the immune system, the majority of it is actually located in what is called the gut-associated lymphatic tissue (GALT). It is estimated that upward of 70 percent of your body’s total immune system is present in GALT.17 This is because our gut, apart from our skin, is our primary source of exposure to the outside world and foreign material and microbes, and thus the highest level of surveillance is necessary there.

The Microbiome

Older estimates put the number of bacteria in humans at 100 trillion versus an estimated 10 trillion human cells, hence the inaccurate but often repeated slogan that we are only 10 percent human and 90 percent bacterial. Newer, more precise estimates are that human beings have around 38 trillion bacteria and about 30 trillion human cells—still, you are more bacteria than human.18 Anaerobic bacteria (which do not require oxygen for growth) may comprise more than 90 percent of the bacterial species, as we will discuss in detail in chapter 4.

We know that the microbiome (also known as “microbiota”—I will use these terms interchangeably) is complex and may contain hundreds (or even thousands) of different species in the average individual.19

A recent global study of people from 32 countries identified nearly 5,000 genetically distinct species that can be present in a human microbiome, with many of these species yet to be named; data from European and North American populations is plentiful, but South American, Asian, and African data is underrepresented and growing slowly (Data from these regions usually leads to the discovery of new species when included).20 Our understanding of the microbiome is still in its infancy, although it is rapidly developing. There is much that is undiscovered and still unknown.

We know that gut bacteria play a critical role in many processes, including digestion, synthesis of vitamins and nutrients, metabolism, maintaining the health of intestinal cells, enhancing immune function, and protecting against pathogenic organisms. In addition, gut flora imbalance is implicated in various chronic illnesses including obesity, insulin resistance, and cardiovascular disease.

Some of the most exciting microbiota research involves autoimmune diseases. One of the key metrics to determine the health of the microbiome is diversity—tracking the number of different types of species in the ecosystem. Several distinct imbalances have been identified in the microbiome in various autoimmune disorders, but one of the most common findings is loss of diversity.21

In fact, studies show that the hallmark of the modern microbiome in almost all people today compared to the microbiome of our ancestors is a loss of diversity. Scientists have studied well-preserved stool samples from >1000 years ago and discovered dozens of bacterial species that are not found in modern microbiomes.22

This loss of diversity and important bacteria from our microbiota is thought to be one of the key factors behind the dramatic rise in almost all chronic diseases in modern times.23 A lack of diversity in the microbiome has been associated not only with autoimmunity but also systemic inflammation, obesity, diabetes, insulin resistance, elevated cholesterol, allergies, and asthma—so it has wide-raging health implications for most modern chronic illnesses.24 This will be one of the central themes of this book, as I teach you how to improve the health and diversity of your microbiome, and heal your gut in order to address autoimmunity.

Loss of Diversity

Several factors have been shown to contribute to this reduction in diversity. These include reduced breastfeeding rates, the rise of C-sections, low-fiber diets, increased consumption of processed foods, widespread use of antibiotics, emotional stress, and environmental toxins. Over the years, increased use of antibiotics in livestock, overprescribing of antibiotics by physicians, sterilization of our drinking water, reduced exposure to farm animals and microbe-rich environments, increased use of antibacterial soap and cleansers, and improved sanitation of the environment have all led to dramatic decreases in the microbial diversity that we are exposed to while growing up.

This phrase “while growing up” is key because it appears that the exposure to key bacteria in the microbiome during the first few years of life is critical to the normal maturation and development of the immune system. Our gut bacteria play a key role in educating our immune systems during childhood. There is a key window of opportunity during the first year of life, especially during which breastfeeding and exposure to the right microbes can induce lifelong positive changes that reduce the risk of immune-mediated disorders.25 A lack of this proper training of our immune cells by the microbiota can have long-term negative consequences for our health.


  • “A holistic and clinically proven approach to treating autoimmune disease that can help millions of people afflicted by this epidemic.”—Dr. William Li, MD, New York Times bestselling author of Eat to Beat Disease and Eat to Beat Your Diet
  • “Dr. Akil Palanisamy combines his extensive clinical experience with leading-edge research to create a detailed roadmap to health for those with autoimmune or inflammatory conditions. Filled with the most up-to-date, evidence-based information on the microbiome, environmental toxins, and the mind-body connection, The T.I.G.E.R. Protocol is a must-read for anyone serious about optimizing their immune health and vitality."—Dr. Andrew Weil, world-renowned integrative medicine physician
  • “So often we are led to believe  we can rid ourselves of our common ailments with the latest breakthroughs in pharmaceutical science. As so many have experienced, this approach generally disappoints. Dr. Akil provides us with foundational information, empowering the reader with a straightforward action plan to reverse disease and pave the way for optimal health. We need to take his teachings seriously as they are a gift.”—David Perlmutter, MD, New York Times bestselling author of Grain Brain and Drop Acid
  • “What if there is a much better way to get to the root of autoimmune disease so that you can either halt it in its tracks or reverse it?  Dr. Akil Palanisamy provides a revolutionary integrative medicine approach that does just that!”—Victoria Maizes, MD, Executive Director, Andrew Weil Center for Integrative Medicine at the University of Arizona
  • “Autoimmune disease has increased in prevalence over the past 40 years and is now poised to be one of the leading causes of both shortened lifespan and quality of life. Unfortunately, the accepted strategies to manage these conditions are not infrequently as concerning as the disease itself. Fortunately, Dr. Akil has developed an approach to address the many factors contributing to autoimmunity. If you or someone you love suffers from autoimmunity, this book revolutionizes our understanding of autoimmune diseases.” Robb Wolf, New York Times bestselling author of Wired to Eat
  • "1 in 6 Americans now suffer from autoimmunity, and conventional treatment is focused on suppressing symptoms with drugs. The T.I.G.E.R. Protocol offers a natural and effective "root cause" approach to healing autoimmune disease based on Dr. Akil's unique blend of functional medicine, ayurveda, and ancestral nutrition. I recommend this book to anyone seeking a more holistic approach to autoimmune disease."—Chris Kresser, New York Times bestselling author of The Paleo Cure
  • “In The T.I.G.E.R. Protocol, Dr. Palanisamy has created a fantastic, groundbreaking guidebook for treating autoimmune disease that empowers readers with science-backed actionable tools to optimize their health and well-being.”—Michelle Tam, New York Times bestselling cookbook author and creator of Nom Nom Paleo
  • "The Tiger Protocol is an invaluable evidence-based guide to the current state of knowledge about autoimmune disease and is designed to empower patients in living well with chronic illness. It is also a state-of-the-art resource for professionals who want the newest perspective on autoimmune disease and wish to effectively improve the quality of life of their patients. I strongly recommend keeping this unique clinical resource close at hand on your bookshelf.”—Rachel Remen, M.D., New York Times best-selling author of Kitchen Table Wisdom

On Sale
May 9, 2023
Page Count
320 pages

Akil Palanisamy, MD

About the Author

Dr. Akil Palanisamy, MD, is an integrative medicine physician and author of The Paleovedic Diet.  He blends his Western medical training with functional medicine and Ayurveda, the traditional medicine of India.

"Dr. Akil," as he is known, studied biochemistry at Harvard University, received his medical degree from the University of California, San Francisco, and completed his residency at Stanford University. He also completed a fellowship in integrative medicine with Dr. Andrew Weil at the University of Arizona, and is certified by the Center for Mind-Body Medicine at Georgetown University. He practices integrative medicine in the San Francisco Bay area, and travels worldwide to speak.

Learn more about this author