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Dr. Robynne Chutkan: Rewilding Your Microbiome, How to Recover from Antibiotics, & High Octane Poop

Did you know that even occasional use of antibiotics, hand sanitizers, and other germ-killers can wreak havoc on your long-term health? Watch the Interview here: http://bit.ly/rewildmicro

These days, many of us pop antibiotics like Tic Tacs.

But did you know that even occasional use of antibiotics, hand sanitizers, and other germ-killers can wreak havoc on your long-term health?

Evidence is mounting that this new germophobic clean craze – our obsession with antibiotics, hand sanitizer and sterile environments – is actually making us sicker.

Why? Because our bodies were perfectly designed to have a symbiotic relationship with bacteria, protozoa, fungi, and even viruses. When you wipe all of those “bugs” away, your immune system turns on itself.

This week, we’re here with Dr. Robynne Chutkan, a leading expert in the world of gut health and one of the most recognizable gastroenterologists working in America. She has a B.S. from Yale and an M.D. from Columbia, and teaches in the gastroenterology department at Georgetown University Hospital.

On this show, you’re going to learn:

  • How being afraid of germs is actually making us sick
  • Why you should reconsider using hand sanitizer
  • How to rewild your microbiome
  • Why doctors are suspicious of healing with food
  • And much more…


Abel: The importance of the human microbiome is finally getting attention from mainstream science and medicine. But what’s at the root of our germaphobia?

This idea of cleanliness has gone out of control. You walk into a hospital where everything is antiseptic and that’s important if you’re going to have surgery, but it’s trickled into our everyday lives. Kids are scrubbed clean and there’s hand sanitizer everywhere.

But those microbes you’re scrubbing away from your skin and depleting from your gut are part of your body. They’re essential to your “ecosystem” and they help keep you healthy.

But those microbes you’re scrubbing away from your skin and depleting from your gut are part of your body. They’re essential to your “ecosystem” and they help keep you healthy.

Abel: One thing that has helped my overall health tremendously is understanding my body not as a single unit, but as an ecosystem.

“We are host to 100 trillion microbes—mostly bacteria, but also viruses and fungi and protozoa. It’s helpful to think of ourselves as their host, like the planet with animals. If we’re good to them, they’ll be good to us.”

I wasn’t much of an eco biologist when I wrote this book. But 1,000 animal species are going extinct per year, much faster than should happen naturally. The same thing with the gut biome. If we look at gut bacteria, we have about ⅔ the species as someone in the Amazon, someone who hasn’t been exposed to the Western environment.


Abel: But wait a second, I thought all these creepy crawlies were bad for us! 🙂

I did too. The Center for Disease Control (CDC) claims that about ⅓ of Americans have been exposed to or have a parasite. Our immediate reaction is: Ew! But there’s an incredible symbiosis between some of these organisms, including some of the parasites.

The protozoa, bacteria, fungi, and even some of the parasites in and on our bodies are training our immune systems.

It’s vitally important that we’re exposed to some of the good, bad, and ugly so our immune system learns how to distinguish between friend and foe.

It needs to know how to deal with a common cold and then say, “Whoa, here comes Polio. That’s a really big deal and I need to make antibodies.”

This training of the immune system begins shortly after birth. Living in a western society, most of us don’t get exposed, and our immune systems get confused. This creates a situation where the body starts to react to itself—and that’s autoimmune disease:

  • Crohn’s Disease
  • Psoriasis
  • Joint pain and arthritis
  • Skin problems like acne and eczema
  • Gut issues

We need germs because they are a part of our balanced ecosystem.


Abel: One thing that fascinated me in your book was the description of the way you were raised compared to your daughter. She’s growing up in a society that’s so trigger-happy about killing everything with antibiotics. How did your upbringing differ?

“There are two kinds of doctors: Those who’ve drunk the koolaid—who really believe in better living through chemicals and prescriptions, and the ones who have one eyebrow raised.”

My dad is an orthopedic surgeon. He sees a lot of people applying for disability for back pain, and a lot of these things are really difficult to know for sure. His standard answer is to go lie down and you’ll feel better in the morning.

That’s how I was raised.

When I was a kid, I was running on a dock barefoot and I stepped on a nail. I ran to my parents and was told, “Go lie down and you’ll feel better.” I was up to date with tetanus and all my shots… and I still have the foot.

My parents took a hands off approach. We were not over-medicated. Back then, kids got measles and chickenpox and things they don’t get now. There wasn’t this running to the doctor at the slightest cough or the constant check to make sure they were pristinely clean.

I recall having pinworm from running in the sugarcane fields as a little girl. I’m not advocating getting worms, but some hookworm therapy shows promise for crohn’s and other things…

The hookworm dampens down the immune system—sort of how pregnancy does so the mother’s body doesn’t reject the fetus. Pinworm and hookworm are reemerging as therapy for autoimmune diseases.

Abel: If you’ve gone to a foreign country where the people are living long happy lives while being exposed to all sorts of crazy diseases, germs, and bugs, you realize that you’re the one getting immediately sick. How can we get a little bit closer to being antifragile?

It’s really interesting to observe how our dog Hugo does things. He does not wipe his feet on the front mat—there’s not this obsession to be clean all the time. A lot of what he’s doing when he’s sniffing other dogs and their poo is important for his immune system.

If we look at how kids play when left to their own devices, they’ll get sweaty and dirty and we reel against it and we whip out our hand sanitizer. Their impulse is to be on the ground and get dirty and stick a finger in their friend’s mouth. You see how close that is to the animal kingdom.

We have traveled way too far from our roots. Scrubbing everything away is not natural, and it’s downright harmful. Watch the Interview: http://bit.ly/rewildmicro

“We have traveled way too far from our roots. Scrubbing everything away is not natural, and it’s downright harmful.”

So, look at the animals to get an idea how to rewild yourself.


Abel: What about hand sanitizer?

If you are a hand sanitizer user you falsely believe that diseases are caused by basic germs you come into contact with everyday, and that’s just false.

Do you know someone who always gets sick, or never gets sick? There’s not a big difference between the germs they’re exposed to, but there’s a difference in their immune systems. The idea is not to scrub away the germs, it’s to have a healthy immune system so you can fight them.

There’s no ebola on the playground.

The big problem with hand sanitizer is that it contains a host of chemicals, including triclosan. Triclosan is an endocrine disruptor, so it can cause thyroid issues and a lot of other problems—and it’s also really toxic to microbes.

Triclosan is in household cleaning products and building materials and as a result, most Americans have levels of triclosan in their bloodstream. This is a big problem for the microbiome.

A little bit of dirt getting into your mouth versus triclosan getting into your mouth—I’d take the dirt.

Sure, if you’re visiting someone who’s sick or it’s flu season, it’s a good idea to wash your hands with soap and warm water.


Abel: The chemicals in our environment today can damage the microbiome. Now we’re starting to understand that we need to repopulate our microbiomes with good bacteria. Can you talk about the concept of feeding your ecosystem?

HMO’s (Human Oligosaccharides) in mother’s milk feed the baby’s bacteria, and they’re not found in baby food.

The microbiome really starts to develop in utero—there are even some viruses present in newborns… but don’t get out the Lysol!

Birth is the most crucial aspect of the development of our own microbiome because that’s when we swallow a mouth full of microbes. The baby turns posterior to the mother’s rectum because there are a lot of microbes there for swallowing. I never heard this until about a decade ago.

What? Passing through the vagina is a crucial thing? That’s why we don’t have a zipper across our abdomens.

Marty Blaser is the head of infectious diseases at NYU. He and his wife have done some amazing research, which you can find more about in his book “Missing Microbes.” They looked at the rising rates of cesarean delivery in South and Central America. When you’re born by cesarean, you don’t get the benefit of being bathed in the vaginal microbes.

Their solution was to take a simple gauze pad and swab the newborn in the mother’s vaginal juices. It’s so simple. You could even lay the newborn (by cesarean) between the mother’s legs. But what do we do here? We sanitize the baby!

We think of a cesarean as a modern medical thing and we have a positive association with it. And yes, it can be lifesaving—but one in three cesareans in the U.S. are not for medical reasons.

I had my daughter ten years ago, before my awakening. There was a moment where I had an intrauterine monitor, external monitor, an IV, a catheter for epidural, and I thought… I’m healthy, this seems like a lot.

When you’re part of the medical community, you’re biased to think everything you do is helpful. There’s a lot of evidence behind it. It’s a loss of faith to find out that might not be the case. Too much of what’s being done in medicine is done for commerce, for hospitals and the pharmaceutical industry.

I was lucky to be trained by people who were amazing mentors, who had the patient’s best interests at heart. It’s been a slow, steady evolution for me. I can’t tell you what’s the right thing to do, but I want to arm you with information.

I can’t tell you not to take the antibiotic for your sinus infection—but after five days on antibiotics, your gut bacteria will be wiped out and it could take years to come back. Watch the Interview: http://bit.ly/rewildmicro

“I can’t tell you not to take the antibiotic for your sinus infection—but after five days on antibiotics, your gut bacteria will be wiped out and it could take years to come back.”

That’s the amazing thing about people like you (Abel) and the do-it-yourself approach to health—we’re giving information and education. We’re saying, here are the short and long term effects on your health and your baby’s health…

Abel: Going to the doctor is like going to the mechanic. If you come to the hospital without information about your health, it’s like going to the mechanic without knowing anything about your car – and you get hosed. What can we do to practice preventative medicine so we don’t get over-medicated by traditional Western Medicine?

There is this great divide. I was trained at conventional places—Columbia, Mt. Sinai, Georgetown… these are all terrific institutions. Part of the problem is when you’re a doctor being told that the antibiotics you’ve been prescribing are not only unnecessary, but creating real disease—swapping colds for Crohn’s, psoriasis, eczema, and MS—you feel like the villain.

Now you’re presented with evidence saying we’re villains. It’s difficult for a physician to acknowledge that the very foundation of their education could be wrong or shaky. It’s much easier for average layperson to say “that makes sense” when you’re telling them microbes play an important role. They don’t really have a horse in the race.

The people I’ve had the hardest time convincing are my physician colleagues. I was there once, too. I’d have patients say, “I’ve healed my colitis with diet, by removing junk food and eating more plants.” I was skeptical because we were taught you heal colitis with this drug.

There is a role for prescription therapy because some people just don’t respond to alternatives. But as doctors, we are in this either/or situation. I choose both.

It’s not that medical prescriptions and procedures are bad, it’s just that they’re overused.

Abel: I haven’t taken antibiotics in years at this point since I’m doing my best to protect my gut microbiome. This seems especially critical when you look at recent mouse experiments that show transplanting gut bacteria can actually induce obesity in mammals!

The mouse studies are really key. As you said, we’re able to create obesity in mice by transferring the microbes of an obese mouse to a lean mouse. We are also able to produce anxious behavior in normal mice by transplanting microbes from an anxious mouse.

Of course, there may be more factors involved in humans—genetic predisposition, for example. But microbes are an important environmental trigger of these genes. We see identical twins with exact genetic material where one may develop Crohn’s and the other not. The difference is in the microbiome.

In Washington DC, we have a huge international population. I might be doing a screening colonoscopy for someone who’s sixty, and if they’re from the U.S. usually the list of meds is startling: antidepressant, anti-anxiety, asprin prohpolatically, sleep, blood pressure, cholesterol, restless leg. In the list I see mostly lifestyle issues. I see all these things, mood disorders to heart disease, that can really be fixed through lifestyle changes.

Then I see people from Asia and Eastern Europe and they’re on no drugs and they look amazing. The people from these countries have had limited access to the medical community. Access to medicine is great if you’re really sick, but it has to be the right access, not just pharmaceuticals and medical procedures. It has to be judicial access.

These people from the blue zones are not at Soul Cycle, but they’re walking, gathering wood, fetching water, eating a simple diet—plant based and local—and it’s night and day in terms of health. These are the things we need to pay close attention to.


Abel: Let’s talk about how you can nurture the good bacteria in your gut.

Food is key. I can give you 900 billion bacteria a day but if you’re not feeding them, they’re not going to repopulate your colon.

The idea is that they stick around enough to reproduce and start to repopulate. What’s the right stuff? Poorly digestible plant fiber—green bananas are fermented by bacteria in the colon, so they’re great. Also eat foods high in inulin—leeks, artichokes, asparagus, and oats. Then add fermented foods like sauerkraut and kimchee.

When you put the cabbage and salt in a jar and let it sit on the counter to make sauerkraut, lactobacillus grows on it. You get the fiber from the cabbage and the extra bacteria that have grown in fermentation process.

Abel: Stool transplants are all the rage these days. Can we talk about that?

Fecal Microbiota Transplant is what that’s called. Think of stool as a super probiotic—it’s 70% – 80% bacteria and contains the majority of bugs in our gut. When we create a probiotic, we can look at stool and see, say lactobacillus and streptococcus. We then take those strains and amplify them and grow them and put them in a probiotic.

But there’s a whole bunch of other stuff in stool that we can’t identify, but we think it’s beneficial. So when we transplant stool, we’re transplanting the whole kit and caboodle. The problem is, we’re also transplanting any harmful microbes and viruses.

This isn’t what to do if you have an obese microbiome and you’re overweight. You do it because you have a serious autoimmune illness and there’s enough studies out there to show it’s going to help you.

Your transplant is only as good as the donor it comes from. You don’t want to get a transplant from your family member that’s been hanging out at fast food restaurants and taking antibiotics. You need high octane stool, preferably foreign born.

There’s a lot of press about C-Diph. It can propagate our gut after being on antibiotics and leach a really serious infection into the colon and even lead to death. There’s an epidemic of death from C-diph in the U.S. from overuse of antibiotics. Stool transplant is one effective cure for C-diph.

What I think we’ll be seeing in the near future is the ability to remove your own stool, analyze it, pull out the best microbes, and amplify them outside your body to give you back your own stool but better. Your own higher octane stool.

Abel: Before we go, one thing I want to talk about is water. My wife and I have become water snobs… can you talk about the danger to your microbiome from consuming a lot of chlorinated tap water?

It boils down to microbes. Modern sanitation has done a lot for us, but not only have they removed some of the healthy microbes, but the water also kills microbes when digested.

I live in DC. I don’t want to drink from the creek in Rock Creek Park… again we’re kind of stuck between wanting to really live in a way we feel is more in sync with nature or healthier, but a lot of our options are polluted. One way to fix the water thing is to get a chlorine filtration system or get good natural spring water source that hasn’t been chlorinated.

Abel: Then again, even if you have it for drinking water, it’s getting in your skin and hair and disrupting your microbiome there. So, how can we live a little closer to the our roots?

Getting a water filter for tap and shower is a big bang for your buck. They’re inexpensive and make a huge difference to your health.


Dr. Robynne Chutkan’s new book is The Microbiome Solution: A Radical New Way to Heal Your Body from the Inside Out. Part 1 is about the microbiome, part 2 is how we mess it up, and part 3 is about how to live dirty and eat clean to fix it.

You can find Dr. Chutkan on her website at www.gutbliss.com, and follow her on Facebook and Twitter at @DrChutkan.


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I want to share a couple of success Tweets and a pic of one of our Tribe members doing her 7 minute Wild workout!

If you’ve changed your body and life and want to let me know, go ahead and leave a review on iTunes. You can also drop me a line at abel@fatburningman.com to share your story. Always love hearing from you. http://twitter.com/fatburnman

If you’ve changed your body and life and want to let me know, go ahead and leave a review on iTunes. You can also drop me a line at abel@fatburningman.com to share your story. Always love hearing from you. http://bit.ly/1M9Rt8F

If you’ve changed your body and life and want to let me know, go ahead and leave a review on iTunes. You can also drop me a line at abel@fatburningman.com to share your story. Always love hearing from you.

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