Dr. Perlmutter: Brain Maker, Fecal Transplants, and How to Heal Your Gut with Real Food

Dr. David Perlmutter Brain

It’s my pleasure to have Dr. David Perlmutter on the show again– the author of the number one book in America on brain health after being out for just six days on Amazon. His cutting-edge new book, Brain Maker, essentially validates Dr. Perlmutter’s other wildly popular book—Grain Brain.

On the show, you will learn:

  • What makes a good microbiome go bad
  • How antibiotics, wheat, and C-sections effect gut bacteria
  • Understanding the link between your microbiome and your brain
  • And so much more!

I just wanted to share our review of the week. This one is for the podcast—and if you’re someone who just jumped on board, or if you’ve been with us for over 150 podcasts, I hope you stop by and leave a review. I read them all, and they help shape the show.

5 Stars – LOVE Abel by CagTagMomma

Always makes me smile and I truly appreciate that he offers up great information in a positive way. I’ve stopped listening to the podcasters that feel they need to bash other people and their protocols. You won’t get that here and I’ll be a loyal listener forever. REALLY glad he’s back by the way. No more going off the grid, Abel!

You betcha, it’s good to be back. Plenty more shows and fun to come in the weeks ahead.


The Brain Maker shares with us some powerful information about the gut microbiome, something that wasn’t really talked about much at all until just a few years ago, but is now seen as something really important to our health. So, what is it?

“I’m a neurologist—a brain specialist,” says Dr. Perlmutter. “Pretty much in the field until quite recently it was a scenario of diagnose and adios. Then, we had very little to offer patients. That has changed.”

He goes on to explain that there are 100 trillion plus bacteria living in the human gut, and they are absolute symbionts. They modulate our metabolisms and determine the set point for inflammation, regulate our immunity, manufacture nutrients for the brain and regulate levels of serotonin.

Dr. David Perlmutter on the Fat-Burning Man podcast with Abel James“The bacteria in the gut are changing your genetic expression.”

This is a leverage point of controlling your own DNA expression.

“It’s time to start to respect our microbiomes.” Their health plays a huge role in your health, and they eat what you eat. They determine inflammation, the cornerstone of coronary heart disease, autism, multiple sclerosis, diabetes, Alzheimer’s, Parkinson’s, and even cancer.

The problem is, we’ve been trained to fear bacteria. In the 14th century, the bubonic plague wiped out a third of Europe… so that fear was valid. But 100 years ago, they discovered a probiotic aspect to bacteria—this bacteria clustered in the intestines controls our physiology, and this is very exciting!

We are finally paving the way in terms of keeping the brain healthy. Preventative medicine in the arena of the brain and recognition that brain health aligns itself so much more with preventative medicine than any other organ of the body—this is remarkable.

“The fire has been lit and there’s no going back.”

What is the state of our gut health?

It’s become very clear that the sad state of health of our Western cultures relates back to the sad state of health of our gut microbiome. And that is strongly influenced by our environmental choices, mostly the food we eat.

In 2011, a scientific study characterized the difference between gut bacteria in kids in sub Saharan Africa to those of children in Europe. Those kids living in rural primitive population centers actually had a high degree of diversity of gut bacteria compared to kids in Europe eating a Western diet.

Changes we see in comparison of the two populations is quite vast: The two major groups of bacteria (making up 80% of the total gut bacteria) are Firmicutes and Bacteroidetes. In this study, it was found that the African subset has far less of Firmicutes as compared to the Bacteroidetes.

Why is that important? Higher levels of the Firmicutes are associated with obesity, diabetes, inflammation, and activating maladaptive gene pathways from our own DNA.

The tragic state of our gut health, on a standard American diet, is leading to higher rates of these inflammatory diseases.


How you were born has a huge role to play in the microbiome that you do or do not acquire.

Vaginal delivery allows the baby to pass through the birth canal, where lives a whole host of life- sustaining bacteria, and that will inoculate that child with bacteria. It’s a microbial baptism that children undergo at birth that allows their immune system to develop, it helps to heal the gut lining right off the bat. It also allows them to digest breastmilk. So, it’s really very important that newborns have this microbial baptism in the process of being born.

Children born by C section to not have that microbial baptism. C sections are important if they’re necessary, if there’s a complicated delivery. But right now, 1/3 of all American births are caesarian section. We don’t have a higher rate of complication than other countries… but caesarian delivery is chosen as a matter of convenience.

When a baby is born caesarian, it deprives a newborn of a very powerful event in terms of their immune system and overall health. Autism, ADhD, celiac disease, type 1 Diabetes, and adulthood obesity are strongly related to being born by caesarian section.

Following delivery, it’s important that women breastfeed if possible. Bacteria on the skin of the breast that the child imbibes will become part of his or her healthy microbiome… and thus breastfeeding helps protect the immune system and help prevent inflammatory diseases like those mentioned above.


Could over-use of antibiotics lead to autism? What’s the connection between antibiotics and obesity?

We are seeing a substantial over-usage of antibiotics in children… and in adults as well! Click To Tweet

Kids gets a cold or sore throat and Mom and Dad walk out of the clinic with a powerful broad spectrum antibiotic in spite of the fact that the American Medical Association is telling doctors that we shouldn’t do be prescribing them for colds and sore throats.

But people gotta get back to work. Kids gotta get back to school. Never mind that the sore throat will go away in a week with antibiotics, or in seven days without them.

Dr. David Perlmutter on the Fat-Burning Man podcast with Abel James“We are substantially overusing antibiotics. These antibiotics have a huge impact on the health and the diversity of the microbiome.”

According to a collection of data published in the American Journal of Medicine, there’s a correlation between women who take more antibiotics and a higher risk of developing breast cancer.

The microbiome is changed by antibiotic exposure, and the microbiome is important in detoxification and immunity. So, then when you see a study like that, you begin to wonder. I just want my readers to simply wonder— this is published by the American Medical Association?!

It’s good to avoid antibiotics unless they’re necessary: They can be life-saving, but shouldn’t be abused.

The World Health Organization has characterized antibiotic resistance as one of the top two health concerns world-wide. The more we use antibiotics, the more we create superbugs– infections for which we have no treatment. This includes such infections as MERSA, something that was unheard of when I [Dr. Perlmutter] was in medical school.

In America, 75% of antibiotics we use go into raising livestock, creating a scenario for developing antibiotic-resistance organisms. Think about it: 3 times as many antibiotics as used by people are used in animals. Why is it that farmers give the livestock antibiotics?

The answer is simple: Since the 50’s, it was widely known that when you give the animals antibiotics, they get fat.

In a book called Missing Microbes, Martin J. Blaser expresses concern about the relationship between obesity and food kids are eating, and changes in microbiome based on exposure to antibiotics. When you create a microbiome that thinks you’re starving, you are going to extract more calories from your food, and you’re going to get fat.


Five or six years ago, researcher Michael Gordon transplanted the microbiome of an obese person into a laboratory rat, and the lab rat got fat. Even though they didn’t change the food, and the cage mate was fine.

Recently, a woman received a fecal transplant for the treatment of a bacteria of the gut. Since fecal material would be transplanted into her colon, she decided to use her daughter as a donor, knowing that her daughter was healthy. Right away after the transplant, she was cured… but she got fat, remarkably overweight. This was because, at the time of the transplant, the daughter was remarkably overweight.

“These bacteria living within us control our destiny. The truth of the matter is that 99% of the DNA in Abel James’ body is not from your mom and dad, it’s contained in the bacteria that live in your intestine.”

It’s a game changer.


When we understand that so many of our most challenging brain disorders, even depression, are at their core inflammatory—we now fully understand that markers of inflammation correlate with levels of depression. Where is inflammation coming from? The gut.

Pointing the finger at the gut. Why hadn’t we found the answers to autism, depression, and Alzheimer’s? Because we were looking in the wrong place.

That’s the central thesis of Brain Maker.

The second brain.


So what makes a good thing go bad? Environmental toxins like glyphosate (or Roundup) that permeates our foods. Chlorinated water. And much more.

The gut lends itself wonderfully to being rehabbed. The most aggressive treatment is taking healthy fecal material and transplanting it into the colon of someone who is sick or has a sick microbiome. This is called a fecal transplant. By and large people don’t need to consider that.

In one study out of Amsterdam, Dr. Max Nieuwdorp looked at the relationship between problems with the microbiome and becoming metabolically unstable (diabetic). If this is the case, what would happen if we reprogrammed the gut bacteria? Dr. Nieuwdorp treated over 250 patients with type 2 diabetes with fecal microbial transplants.

The patients with healthy stool donors had reversal of their diabetes.

The University of Arizona has just recruited children with autism to treat with fecal transplants. Autism is an inflammatory disorder and autistic kids have massive gastrointestinal issues—even as infants. Just the fact that such a reputable university is looking into the link between microbial health and autism is exciting and promising!

In Brain Maker, I [Dr. Perlmutter] presented a case of an autistic 10 year old patient of mine who underwent a fecal transplant. I was in Frankfurt giving a lecture, and I got a video sent to me by his mother—it was of him talking and interacting with her, becoming socially intact, by having fecal transplant. The story is on drperlmutter.com.

We also have a case of a man with MS who couldn’t walk, and now walks without a cane after fecal transplant. I’m not saying that it’s a cure for MS. It’s a treatment.

Pushing a Reset on Gut Bacteria: Fermented Foods to Heal the Gut

“This is the future, and how cool for Abel James Fatburning Man, to be right on the vanguard of this information!” [What a kind compliment.]

Within our community, we’ve been talking about it a lot.

A lot of people want to avoid the conversation of fecal transplants, says Perlmutter. “I say bring it.”

A year or two from now we will get together and go, “Wow, look how far we’ve come?”

We have to recognize that we can very quickly repopulate the gut with great health-supportive probiotic bacteria by choosing to eat fermented foods. Things like kombucha and Kimchi explode with good probiotic bacteria. Also try cultured foods like yogurt, fermented eggs, meat, fish, vegetables, and sauerkraut.

Do you think the food industry is looking at this? I know that they are– in a very very big way.

Probiotic foods and prebiotic foods that are rich in fiber enhance the growth of the good bacteria in you.

Dandelion greens, jicama, Jerusalem artichoke, onions, leeks, and garlic are rich in inulin. Inulin amps the growth of the good bacteria that then go on to do all the wonderful things they do. They maintain the integrity of the gut lining, and that is critical for health.

Healing Leaky Gut to Treat Autism, Alzheimer’s, Depression

We have a one cell barrier from the esophagus throughout the rest of the digestive system. That’s the gatekeeper between what’s in the intestine and what’s in our systemic circulation. When it’s leaky due to in imbalance of bacteria, then things in the gut get into the bloodstream, leading to inflammation and immunity issues.

LPS (lipopolysaccharide), needs to stay in the gut, but when it gets into your bloodstream it powerfully amplifies your inflammation and plays havoc with your immunity. In the book, we have graphs that show much higher levels of LPS in autism, Alzheimer’s, Lou Gehrigs disease, and depression.

This demonstrates a relationship between leaky gut and inflammatory diseases.

Dr. David Perlmutter on the Fat-Burning Man podcast with Abel James“We look upon depression as an inflammatory disease that looks back at the gut in terms of the balance of organisms.”

When we target the gut bacteria and overall inflammation, that’s when we are going to see powerful changes in terms of mood. We rehab their [patients suffering from depression] gut bacteria as an intervention for depression. Who knew gut bacteria could change a person’s perception of the world?

In the Journal Gastroenterology, there’s a study wherein one group got a probiotic yogurt, one regular yogurt, and one a placebo. After 4 weeks, the groups were shown photos of threatening faces and given a Functional FMRI (views areas active of the brain that are active). The probiotic group had a lesser response.

What does it mean? Consuming foods with certain strains of bacteria changed how these people responded to the world around them.


How has this changed your plate?

It’s now going past eating low carb and gluten free with added amounts of good fat to the diet—now in addition, we add in the probiotic enriched foods: kimchee, fermented foods… you can make a gallon of kombucha in about a week with just a little bit of starter. You put in tons of sugar— don’t worry, it gets fermented, the sugar is gonna be gone by the time you drink it.

Last night I [Dr. Perlmutter] was home alone, so I had to cook dinner. I grabbed a wok and I threw in a lot of kale, a bunch of dandelion greens (rich in inulin), free range chicken and olive oil. Low carb, good fat, fiber rich meal. Spice it up with a little bit of kimchi and you have a great gut-healing meal.

The trick to a healthy gut is to get that fiber back in your diet. Click To Tweet

We are now treating brain disorders, dementia, autism, skin issues, asthma—all by targeting the gut and gut bacteria.


Treating obesity by changing the gut bacteria and supplying bacteria that will extract less calories per given meal. This is new territory. It’s like discovering the new world!

How did you make that shift into the topic of your current book and connecting the gut to the brain?

While I was writing Grain Brain, we knew that low carb high fat works, but I wanted to explore more deeply “why?” What is happening mechanistically here?

When sugar binds to protein, that leads to inflammation—and this glycation of proteins leads to increased free radical activity.

High sugar levels changes gut bacteria, which leads to inflammation and gut permeability. Glycated proteins increases the leakiness of the gut.

Usage of antibiotics, gluten, and glycated proteins are powerful factors that lead to gut permeability and therefore enhance inflammation, leading to every bad thing you don’t want to get.

With Brain Maker, Grain Brain is fully validated. The two books work together.

Six weeks ago, the Unites States Dietary Advisory Committee came out and said the issue isn’t dietary fat and cholesterol, it’s the carbs!

It’s been estimated that our hunter gatherer forbearers consumed 145 grams of prebiotic fiber a day. The typical American gets only 5 grams.

People have been fermenting foods for over 7,000 years. When food goes bad it is fermenting and people didn’t have the luxury of throwing things out.

These books work in tandem, but the cornerstone here is that what you eat is fundamentally important in terms of our gut bacteria—they eat what we eat.

Will your child have autism or not? Are you going to succumb to neurodegenerative disease, or not?


By and large today, people are digestive enzyme deficient for a number of reason, and there’s a good place for good natural enzyme supplementation with enzymes that break down protein, fat and carb as well.

The first activation happens upon eating food is with the stomach acids, but people are killing it using the acid-blocking drugs with the mistake that they think it’s the acid hurting them. They’ll force the issue, eat the bad food, and pop a couple of acid-blocking drugs.

Aside from the enzyme issue, acid blocking drugs play havoc on the microbiome. And we’ve got to recognize that. They are associated with the C Diff that affects more than half a million Americans and kills over 30,000 of us right now.


How easy is it to get started fermenting at home?

I can do it. Enough said.

My wife is a great cook and I have deferred that to her because it’s in my best interest. It works well. That said: making kimchi is really straight-forward. Making kombucha is super easy. All the recipes in my book are tested and very, very easy.

I want you to look at your food in terms of not just how it tastes (great and satisfying), but I also want your viewers (podcast listeners) to recognize that your food is talking to your gut bacteria and that is your most important leverage for your health today, as well as your disease-resistance for tomorrow.

Fermented eggs, kombucha, kimchee, and you can buy these things in a health food store… it’s all about the gut. Hippocrates was right all along.

As a brain specialist, I now spend all my time talking about the gut… up until now, they’ve [neurologists] been concentrating on the smoke and not the fire.

Empowering news: What do you do? How do you push that reset button? How do you get back in the game? The word doctor doesn’t mean “healer,” it means “teacher.” Sure there may be some criticism, but if there weren’t criticism, then I wouldn’t be out on a limb, and that’s where the view is fantastic.


Find him on his website, drperlmutter.com, and on Facebook at David Perlmutter, MD. Check out Brain Maker wherever books are sold.

What do you think of the gut-brain connection? Let us know in the comments below.


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  1. great interview! I have read recently that many of the probiotics on the market contain some amount of gluten, even the ones labeled gluten free. Any recommendations for a good probiotic free of gluten?

  2. PghPammy (aka CagTagMomma) says:

    So thrilled to hear you read my review from iTunes, you made my day Abel (btw, Cag Tag stands for Congo African Grey and Timneh African Grey – my feathered kids)! Another fabulous podcast… lately I seem to be developing the habit of listening at least twice, to make sure I get everything. This podcast was full so much information! I have BrainMaker on Audible (not finished yet) and I LOVE pickled eggs, so I’m really locking forward to this recipe (no doubt it’s not like my grandma used to make). I would particularly like to know about soil based probiotics.

    • Hey there – I’m so glad you came by to say that you heard it! I love getting feedback from you guys – couldn’t do any of this without you. 🙂

  3. Pete Kang, MD says:

    Awesome podcast! As a physician, I was fascinated to hear about the fecal transplants, and excited to hear that there’s so much yet to be discovered about our relationship with our gut microbial community, our bodies, and our genome. As a Korean-American, it made me think more about the traditional foods of Korean culture: Kimchi, doenjang, gochujang… how traditionally the know-how to make these things have been passed down from generation to generation, transmitting not only the processes but the gut microbes down the centuries! Perhaps getting away from the traditional foods to a more Western diet is contributing to the rise in obesity among South Koreans. Perhaps not making these things at home, as it is traditionally done (I have fond memories of those days when mountains of cabbages were delivered to each house for making kimchi), but buying store-bought fermented products may dilute some of the beneficial effects. The podcast gave me a lot of food for thought, as I went to my parents’ house for Sunday dinner tonight, and I tried to gobble up much of the microbes as I can with each bite of kimchi!

    • Rock on, Dr. Pete! In researching for my book, I became convinced that you’re exactly right – moving away to traditional foods robs us from habits that were keeping us lean and healthy for centuries. Time to get back to our roots (especially if that means eating delicious kimchi!)

  4. This was a fascinating podcast. Aside from the generic probiotic tablets available at most stores, is there a strain (or group of strains) that are specifically useful for weight loss?

  5. Michelle Miller says:

    What if your microbiome is so out of whack that taking probiotics makes you sick? What if you suffer from IBS, or have a FODMAP sensitivity (and fructoligosacharrides are exactly what you need to avoid)? This is all great (not news, really if you’ve been following nutrition science), but I’m waiting for medical science to catch up and figure out how to get me from where I am to normal and healthy gut microbiome. It’s not there yet. Any time I drink Kombucha, probiotics, or prebiotic fiberous foods, it makes me very ill.

    • Michelle, it sounds like you have a histamine problem? There is something called the histamine diet. Google Trudy Scott, CN.

      • Yvonne! Thank you so much for catching on to that and mentioning it. In ALL of my HOURS of research and trying pretty much every possible elimination diet there is, seeing multiple doctors, specialists, and a naturopath, NO ONE has ever even mentioned this as a possibility! (I even thought maybe it was something vague like sulfites, and so eliminated all my chemical-filled cleaners and skin care products etc.). I don’t have any allergies of any kind that I know of, but reading up on histamine intolerance it sounds like this could still be a legit explanation. You may have just solved the mystery I’ve been puzzling over for years. THANK YOU!!!!

  6. Michelle Miller says:

    Also, my gastro said that over the counter enzymes are a complete waste of money, that if your pancreas is not secreting sufficient enzymes, you will really know it, as that is a serious problem. Although I do want a second opinion, when he said that, it did make sense.

    Lastly, I will have to do more research, but off the bat, I’m taking serious issue with the whole “changing your bacteria will make you absorb less caloreies from a meal.”. As I understand it, most nutrients are absorbed in the small intestine. There *should* be no bacteria in the small intestine. Our gut bugs live in the large intestine. If they migrate into the small intestine, you have a problem. So, how is it proposed that these bacteria control our absorption? Via a genetic/hormonal pathway?

    I’m not trying to be a negative Nancy, Abel. I just think it’s important that people are fully infirmed befire they run out and add probiotics and fiber to their diet. It won’t work for everyone. There are oodles of caveats.

    • Thanks Michelle, I hear you. Medical conditions always make these topics especially challenging to cover in just one show, but I’ll be talking more about the pros/cons of fermented foods in shows coming up.

      I think the important thing that’s happening right now is that more people are paying attention to gut health (especially doctors), and the more research and work we do in the area, the better off everyone is.

      • Hi Abel! Thanks for the response. Yes, indeed it is very clear that gut health is pretty much the Holy Grail of overall health, and when you think about that scientifically (I’m a biologist) that makes total sense. I completely agree that turning our attention to it is the right thing to do. It is just so frustrating when everyone has a “fix” or diet that supposedly leads to better health – to try them all and still have issues is very frustrating. I am really intrigued by what Yvonne mentioned, and I see you’ve since added a couple posts specifically targeted at histamine sensitivity – off to check those out next. Thanks for having an awesome blog/podcast and spreading the paleo gospel! 😉

  7. Robert Noel says:

    What an amazing video and interview you did. I have primary progressive MS so I watch a lot of health related videos and this one was very educational. I just bought Dr. Perlmutter book off Amazon. If anyone knows if they perform that fecal transplant surgery in America please let me know. my email is robertn31 @ yahoo . com. Also if you or he would allow me to call or email him a question or two I would appreciate that too. Even pay if I have to., Thanks Abel.

  8. I have recently been diagnosed with MS. I would also be interested in some in depth information in regards to the fecal transplant surgery. Ive done some research on the Stem Cell treatments. I guess I just cant accept that there is nothing that can be done.

  9. Taymount clinic in London and Nassau, Bahamas have FMT. I am going in March and hoping it will have an effect on my parkinsons.

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