Acknowledgments Introduction: Live Dirty, Eat Clean MY HUSBAND ISN''T completely on board with my plan to sell our house in the city, move to a farm, raise animals, and grow our own food. But since much of what''s available in the supermarket is full of chemicals and devoid of any real nutrients, taking control of what we eat and making sure it comes from nature, not a factory, strikes me as a good idea. I''m fortunate to live in Washington, D.C., where farmers'' markets and community supported agriculture (CSA) shares are plentiful, so moving to an actual farm may seem a little extreme. My real motivation is that I want my daughter to grow up dirty, literally--as in easy on the soap and shampoo, heavy on the mucky animal chores. I shared her saga of antibiotic misadventure in my first book, Gutbliss . Since then, I''ve seen hundreds of patients with stories similar to hers, and I''ve become even more convinced that damage to the microbiome--the trillions of organisms that call our digestive tract home--is at the root of many of our current health problems.

Figuring out how to undo that damage and "rewild" ourselves has become a focus of my medical practice and a personal journey in our household. Living a little dirtier and eating a little cleaner is definitely part of the fix. Unwilding Ourselves Our ancestors had a symbiotic relationship with their microbes that evolved over millions of years and served them well. They were benevolent hosts to a dense jungle of microscopic creatures, including worms and other parasites that actually contributed to their health. Large predators and the absence of food were their main threats, not the hundreds of diseases that afflict us today. The irony is that as we''ve "unwilded" our bodies and our environment in an effort to become healthier, we''ve actually become a lot sicker in some important ways. Urbanization and modern medicine have undoubtedly improved our lives, but they''ve also introduced practices--overuse of antibiotics, chlorination of the water supply, processed foods full of chemicals and hormones, microbe-depleting pesticides, increasing rates of Cesarean sections--that have ravaged our microbiome, diminishing the total number of organisms as well as the diversity of species. The result is an increase in a wide range of modern plagues, including asthma, allergies, autoimmune diseases, diabetes, obesity, cancer, irritable bowel syndrome, anxiety, and heart disease.

The rise of these diseases is inextricably intertwined with the full-on assault on our microbiome resulting from our super-sanitized lifestyle. A decade ago, who knew that every antibiotic dispensed during cold and flu season was potentially bringing us one step closer to a diagnosis of Crohn''s disease, or making us fatter? None of us doing the prescribing realized that we might be paving the way to real illness in our well-meaning attempts to cure the sniffles. The prevailing wisdom was--and to some extent still is--that germs are bad and we should get rid of them, and antibiotics are good and we should use them. And use them we have: the average American child will receive more than a dozen courses of antibiotics before reaching college, primarily for minor illnesses that require no treatment at all. Despite the tremendous amount of research in the last few years connecting the dots, many physicians and their patients remain in the dark, blaming each manifestation of microbial discord on bad luck or bad genes, never questioning or understanding the root cause. Less Is Often More My own understanding came only after my daughter was treated with antibiotics at birth and throughout infancy, setting off a series of events that, a decade later, continue to affect her health. I had been trained at world-class institutions and practiced gastroenterology at a leading teaching hospital, but, like most physicians, I had no idea that the antibiotics I thought were so helpful were actually creating illness by decimating her microbiome at a time when it was most vulnerable, making her more susceptible to infection and inflammation. I wish I had known then what I know now and what I continue to learn every day: that illness is often the result of a decreased, not increased, bacterial load, and that less is sometimes more when it comes to medical intervention.

Rehab for Your Microbiome Every day in my gastroenterology practice I see patients with the telltale signs of a disordered microbiome: bloating, leaky gut, irritable bowel, gluten intolerance, Crohn''s disease, ulcerative colitis, eczema, thyroid disorders, weight problems, fatigue, and brain fog. It''s a veritable epidemic of "missing microbes," as infectious disease specialist Martin Blaser, MD, describes it. The symptoms vary, but the history doesn''t: overzealous use of antibiotics, often accompanied by a highly processed Western diet low in indigestible plant fiber--the preferred food of gut bacteria. Repopulating the microbiome can be a challenging process, but the good news is that most people do get better. Your microbes are constantly changing and evolving, and even if they''ve been severely damaged by medications, infection, or diet, paying attention to what you put in and on your body can yield huge improvements. The microbiome you have today isn''t the one you were born with, nor is it the one you''ll have next year or even next week. It''s highly dynamic, constantly changing and adjusting in response to your internal and external environment. In medical school, I was taught how to eradicate people''s germs.

A quarter-century later, I''m teaching my patients how to restore theirs: which foods to eat, how to care for their bodies and their homes without stripping away their microbes, what questions to ask when their doctor recommends an antibiotic, and whether a probiotic or even a stool transplant might be of benefit. These, I believe, are the new and essential survival skills for thriving in our super-clean era. You''ll find them all in the Live Dirty, Eat Clean Plan at the end of this book. When Dirty Children Grow into Clean Adults--My Rewilding Journey I spent my early childhood in the tropics, eating food from my grandfather''s farm grown in rich soil fertilized by a herd of goats (which we sometimes also ate) instead of chemicals. We lived in the hilly suburbs and roamed around outside with our dog after school, exploring gullies, picking mangoes and oranges from the fruit trees in our backyard, and acquiring the occasional case of pinworm as a result of our barefoot explorations. In our household there was lots of attention paid to schoolwork and athletics, but shoes, showers, and shampoos were more or less optional. My father was an orthopedic surgeon whose great fear was that his children would grow up to be hypochondriacs, so his medical advice for whatever ailed us--from the flu to a sprained ankle--was always the same: go lie down and you''ll feel better in the morning. We were vaccinated for the big stuff (polio and smallpox) but didn''t sweat the small stuff (whooping cough and chicken pox).

My daughter had more visits to the doctor before she was in preschool than I''ve had in my entire lifetime. So, despite my dirty childhood filled with organic, homegrown food, protective parasites, lots of time outdoors, and limited contact with an overzealous medical system, how did I end up in adulthood with not one but three manifestations of microbial discord: eczema, rosacea, and yeast overgrowth? It took a while. I managed to weather potent microbial disruptors like the antibiotics prescribed in college for acne and twenty years of birth control pills (we''ll talk about this more in Chapter 5) with no ill effects. But as life got more complicated, unrelenting stress and the cookies, cakes, and candy I consumed to combat it were my ultimate undoing. A Western diet high in sugar and fat promotes growth of the wrong types of bacteria in your gut, and a lifestyle that leaves literally no time to go outside and smell the roses can be the straw that breaks the camel''s back, particularly if you have additional risk factors, as I did, such as significant antibiotic use. Disease Begins in Your Microbiome My firsthand experience with how poor nutrition and stress can unmask the effects of a damaged microbiome and lead to a multitude of symptoms is representative of what most of the patients I see in my office have experienced: a decline in overall well-being characterized by seemingly unrelated conditions that appear out of nowhere, leaving them scratching their head and wondering what''s going on. Microbial disruptors are everywhere--in the food we eat, the water we drink, the products we use, and the medications we take--and the clinical manifestations of a disrupted microbiome are varied and show up in people of all ages and stages. Chances are there''s someone in your family with asthma, allergies, eczema, thyroiditis, diabetes, arthritis, or any of the many disorders that we''re now discovering have the same root cause.

A damaged microbiome isn''t the only reason people develop these conditions, but it''s often a major contributor that interacts with genetic and environmental factors to create a perfect storm of disease. That''s why it''s more important than ever to understand the complex and critical role bacteria play in our health, so that if and when yours is compromised, you can connect the dots and start to heal yourself. The solutions you''ll find in this book are based on clinical trials in our own patient population at the Digestive Center for Women, data from other scientific studies, published papers, trial and error, anecdote, patient testimonials about what''s worked for them, and careful observations accrued over almost two decades of taking care of people with all kinds of ba.