Q&A with Robynne Chutkan, MD

The author of The Microbiome Solution discusses why you should toss your hand sanitizer.

By Lena Huang featured image Photograph by Trevor Paulhus

What is the microbiome?
The microbiome refers to all the bacteria, viruses, and fungi that live in or on our body — over 100 trillion microbes, plus their genes. Our unique microbial footprint develops over our lifetime, and it reflects everything about us: how and where we were born, what we’ve eaten, where we’ve lived, our occupation, personal hygiene, past infections, exposure to chemicals and toxins, medications, hormone levels. The end result is a mix so distinctive that our microbiome is a more accurate identifier of us than our own DNA.

Why is the microbiome important to health?
Microbes are the worker bees that perform most of our important functions. They help to digest our food, train our immune system to distinguish between friend and foe, turn our genes on and off, synthesize important vitamins that we can’t make on our own, aid in detoxification, neutralize cancer-causing compounds, and do a host of other really critical things. So, our overall health is very closely tied to the health of our microbes.

You say that our gut bacteria may be more important than the genes we inherit. Why?
We have about 23,000 human genes and eight million microbial ones. Genes from gut bacteria play an important role in genetic expression: they provide instructions for essential functions like carbohydrate metabolism and enzymatic detoxification — instructions that are missing from our own human genome. Bacteria also turn various human genes on and off, which influences whether or not a disease that you’re genetically predisposed to actually develops. This may explain why inherited diseases don’t always afflict family members equally — even in identical twins, who have the same genes but different microbes.

How do antibiotics change our gut bacteria?
Antibiotics prevent death from serious infection every day, but in our current climate of overdiagnosis and overtreatment, they’re also used indiscriminately for a wide variety of minor, self-limited conditions that don’t require any treatment. Just five days of a typical broad-spectrum antibiotic destroys one-third of our gut bacteria — and there’s no guarantee those microbes will ever return.

How does gut bacteria affect obesity and weight gain?
We can predict obesity with 90 percent accuracy just by examining someone’s gut bacteria, and we can make skinny mice fat by inoculating them with microbes from obese mice. Studies show that overweight mice can actually extract more calories than their normal-size peers from exactly the same food. We see the same phenomenon in humans: If your gut bacteria are out of whack, you may be packing on pounds despite eating a diet identical to that of someone who’s not gaining weight.

What is dysbiosis?
Damage to the microbiome, which we call dysbiosis, is the root cause of a broad range of diseases — not just gastrointestinal disorders like Crohn’s disease, ulcerative colitis, and irritable bowel syndrome, but autoimmune diseases like hypothyroidism, multiple sclerosis, and type 1 diabetes. Studies have demonstrated an altered microbiome in children with autism, in certain types of cancer, obesity, and even heart disease. These “modern plagues” have emerged over the last century in parallel with the assault on our microbiome from our super-sanitized lifestyle.

You propose the “Live Dirty, Eat Clean” plan. Briefly explain what you mean by “live dirty.”
Live dirty refers to the process of “rewilding” yourself in order to reestablish the critical balance between good and bad bacteria that’s essential for good health. It ranges from simple things like throwing out the hand sanitizer and opening a window to let some microbes in, to more specific guidance on which ingredients to avoid in personal care products, and how getting a pet can help you avoid antibiotics.

And how do we “eat clean”?
Eat clean introduces a whole new way of looking at food that emphasizes the nutrients you need to grow a good gut garden. It combines the best of how our ancestors ate with microbe-boosting, plant-based strategies, and it has helped thousands of my patients with dysbiosis recover and heal. Using food as the nourishing medicine that it’s meant to be will optimize your microbiome, help you achieve and maintain your ideal weight, boost your energy levels, and improve your overall health.

Why did you write this book?
I wanted to write this book because of my amazing daughter, Sydney. I shared her saga of antibiotic misadventure in my first book, Gutbliss. Since then, I’ve seen many patients with stories similar to hers, and I’ve become even more convinced that damage to the microbiome is at the root of many of our current health problems. Figuring out how to undo that damage has become a focus of my medical practice and a personal journey in our household. As a physician, I’m mortified that many of our medical practices are actually creating illness rather than curing it, and I feel a personal obligation to share what I know about the microbiome and its importance for overall health with as many people as possible.