As you know, we’ve been doing a great deal of writing about our standards and practices to help explain why and how we do the things we do. This week, we’re opening up the discussion to include our circle of advisors and educators. Instead of sharing a long research piece this week, we’re giving you a glimpse of some of the current thinking about optimal health from our friend, Doctor Tom O’Bryan.

Tom O’Bryan is a speaker and workshop leader specializing in the complications of non-celiac gluten sensitivity and celiac disease. He has been on the faculty of the Institute of Functional Medicine for 8 years and recently hosted “The Gluten Summit,” a gathering of 29 of the world’s experts on gluten-related disorders.

We sat down with Doctor Tom to learn more about functional medicine, the gut, and learning why we need to start asking the question, “Why?”


(Note: Interview has been edited for length and clarity)

Mission: Heirloom: We hear the term “integrative” medicine a lot these days. Is it the same thing as functional medicine? What’s the difference?

Tom O’Bryan: Integrative medicine refers to an outlook of merging different concepts and treatment protocols. You ‘integrate’ different approaches to find the most effective protocol to achieve your result with a patient. Functional medicine is not about treatment of symptoms, it is primarily about getting a ‘big picture’ overview of the patient who comes in to you with a particular set of symptoms or concerns.

Take this analogy, for example: If you’re in an airplane and you’ve got a window seat. You look out the window and the only thing you can see is the plane at the gate next to you and the baggage claim guys throwing your bag up on the conveyor. And you can’t see much else. You’ve got a limited view. The plane gets pushed away from the gate, and you’re looking out the window and you say, “Oh look the trees are changing color out there.” You’ve got a little bigger picture and you can see a little more. The plane starts to taxi out to the runway and you say, “Oh look the whole runway’s lined with trees!” You see a little more. The plane starts to take off and you say, “Oh that’s not a row of trees, that’s a forest! Isn’t that pretty. Oh there’s a lake. Oh look there’s the skyline.” And all of a sudden you’ve got a 30,000 foot view of the airport that you were just at. You get the big picture. And when you get the big picture, you can determine the clearest path to your destination. Functional medicine is about determining where you need to go with whatever symptoms a person presents with.

So it’s not about figuring out how to treat migraines or how to treat recurrent miscarriages. It’s not about asking, “What’s the protocol?” In functional medicine, you have to get the big picture of a person — their health and their life history. You have to ask: What was it like in utero for their mother? Were there any complications? Did you have a natural birth? Were you c-sectioned?

MH: Where do those questions lead?

TOB: In the last trimester of pregnancy, the bacterial colonies in the vaginal tract change completely to where there’s a very high count of prevotella [bacteria]. Most of the time, there are practically none that are measurable in the vaginal tract at all. Why the change in the last trimester? Because when the baby’s coming down the birth canal, it gets coated in prevotella. Prevotella migrates through the nasal cavity through the mouth, gets down into the GI tract, it turns on the genes in the baby’s digestive tract, and says, “Okay, this is the mammal that is going to start feeding you. Here are the codes for the protein that’s about to come to you for food.” So then the baby’s digestive tract starts turning on the digestive enzyme production capability for the specific proteins that are encoded in the prevotella bacteria that the baby just got from mom. Isn’t that cool?

So what happens if a baby is c-sectioned? The concentration of colonies in their gut are strep and other skin bacteria from the skin and air at the time of the C-section. Then the GI tract thinks strep is normal. There’s no evidence that they will ever have a healthy GI tract in their life, ever, without putting attention on it regularly. Doctors won’t know any of this unless your new patient questionnaire says, “Were you born by natural childbirth or c-section?” And that question makes a huge difference! That’s the functional medicine approach.

Integrative medicine integrates a whole lot of different therapies to find what therapy will likely work best for this person. It’s a good thing. Functional medicine asks, “Where did all of these problems come from?” That’s the pathway that we want to address with whatever integrative approaches we’ve brought from our own clinical practice.

MH: In other words, a lot of what the result would be in terms of treatment from a functional medicine perspective would be similar to a treatment from an integrative background, but the overall vision is different.

TOB: Yes. Functional medicine is about understanding what might be going on for a patient, and thus finding what direction we want to go in with our treatment protocols. That’s what comes from your diagnostics. Functional medicine is all about diagnostics. Isn’t that cool? I think that everyone should have a functional medicine practitioner as part of their team. Everyone. Functional medicine doesn’t advocate particular vitamins or that everyone should be Paleo. It doesn’t even advocate a particular diet. What it advocates taking a step back and showing patients their health history. Doctors [that I’ve worked with at the Institute for Functional Medicine] say this all the time: when they apply this concept, many patients at the end of the first visit start crying. They say, “No one has ever asked these kinds of questions before. No one has ever taken the time to figure out what’s really going on for me.” They feel like they’ve finally found someone who’s listening. The person has hope at that point that the solution is not just another drug.

MH: What is your focus?

TOB: I talk about the gut, how critical the gut is, and why. There are 10 times more cells of bacteria in the gut than all the cells in the human body put together — all your bone cells, muscle cells, skin cells, organs. Add them all up, and you’ve still got 10 times more cells of bacteria, and that bacteria has a 100-200 times more genes than the human genome.

All genes control and determine function. Having genes like the BRCA genes for breast cancer doesn’t mean you’re going to get breast cancer, it means you’re highly vulnerable to getting breast cancer. If you turn that gene on, you got a problem, but if you turn that gene off, you’re like everybody else and you’re okay.

How do you turn the gene on or turn the gene off? Perhaps you’ve heard that broccoli seems to have some anti-cancer benefits? One of the reasons is because the sulforaphanes in broccoli turn off the BRCA genes and turn on anti-inflammatory and anti-cancer genes. That’s why the compounds can be anti-carcinogenic.

We have 23 to 25 thousands genes in the human genome completely mapped out. There are over 3 million genes that have been identified in the bacteria in our gut. So we have over a hundred times more genes that turn on function and turn off function located in our gut bacteria.

A whole new science was developed in 2007 called enteric neuroscience, which studies how the environment of the gut affects the nerves in the brain. Now there are hundreds and hundreds of studies that document that the bacteria in the gut control the production of your nerve hormones (neurotransmitters). So depression, anxiety, schizophrenia, and any psychoses that people have now are being directly associated with an imbalance in the gut bacteria.

So genes turn on hormones production and genes turn off hormone production in your brain. An earthworm has 23 thousand genes. So how is it that humans have around the same amount of genes as a worm? What makes us so different? Well it’s because of what happens around the genes. It’s just so different. That’s why humans are so advanced as a species on the planet. Our epigenome is more advanced than any other. The neural networks we have allow for our microbiome to determine which genes get turned on and which genes get turned off. … In other words, what happens around the genes turns genes on, turns genes off. That’s what’s happening in our bodies all of the time.

One of my basic messages is that every forkful of what you put into your mouth, every forkful, is either inflammatory or anti-inflammatory. There are no neutrals, except healthy water. So are you turning genes on for inflammation? The way I see it that when you pull at a chain, the chain breaks at the weakest link — your heart, your brain, your liver, wherever weak link is — you’ll break it.

MH: Do you have an example?

TOB: Yes! A friend asked me if I could help figure out why her 11 year old girl had developed seizures. So we ran Cyrex 2, 3 and 4. In her number 3 test [for gluten peptides and tissue transglutaminase] she’s got the alpha-17, both IgG and IgA, out of range, and she’s got wheat germ agglutinin out of range. And this little girl has the most sensitive marker of the mechanism of celiac disease, which is when gliadin, the protein in wheat, binds to transglutaminase in your intestines. That is the celiac mechanism, and she’s got elevated levels of IgA antibodies to that. This is celiac. You don’t need to do a biopsy, which is traumatic to the kid anyway. This is a card-carrying person on the celiac spectrum, whether she has total villous atrophy or not, it doesn’t matter. It doesn’t matter at this point in terms of justifying a gluten-free diet.

MH: So how many of these things show up if you were to get a blood test for celiac at a regular doctor?

TOB: None. They don’t check for this. She’s been to 3 pediatric neurologists, and they just want to give her more drugs. The only one they check for is the alpha-33 gliadin IgG and IgA. Hers are normal. So if they do the blood test for celiac disease, it would come back normal. And they’d do an endoscopy and most likely the endoscopy would come back normal because she’s 11, and she probably hasn’t had enough time for her microvilli to completely atrophy. So they would say, “The endoscopy is fine and you’re okay to eat wheat.”

To get the diagnosis of celiac, your microvilli have to be completely worn down. If your microvilli are not completely worn down, you don’t have celiac. And I wrote to a number of the authors of these papers, said, hey doctor, did you include patients that had partial villous atrophy or just the inflammation before the atrophy begins?  No. Celiac disease is total villous atrophy. With celiac [most researchers are] looking at the end stage of the degenerative process. And it’s actually more dangerous, double the mortality risk, when you just have inflammation.

MH: Why is that? Because my understanding is that the biggest danger with celiac is nutrient loss, which happens when you have total villous atrophy and you can’t absorb nutrients. You’re going to get very sick from that.

TOB: Yes, that is a complication, leading to things like osteoporosis, anemia, failure to thrive. It’s very true. My father died from that. Unknown to us. But he had a B-vitamin deficiency from undiagnosed celiac disease.

The reason the mortality is double with just inflammation is because no one checks for inflammation. No one treats it. Inflammation is the mechanism that causes intestinal permeability, the leaky gut. That’s what takes people down. Leaky gut is the gateway to the development of autoimmune disease.

Autoimmune disease is the number one cause of getting sick and dying in the world — number one. We used to think that cardiovascular disease was number one, followed by cancer, and then autoimmune disease. But there are many papers now saying that atherosclerosis is autoimmune. So if cardiovascular disease is autoimmune, what’s really the number one mechanism that causes morbidity and mortality in the industrialized world? It’s your immune system attacking your own tissue, and intestinal permeability is the gateway to getting autoimmune disease.

MH: So what’s the link between gluten and autoimmune disease?

TOB: Well as Alessio Fasano documented in his studies, no human can digest gluten. No human can break down the proteins completely into their individual amino acids. We don’t have the enzymes to do that. It’s not in our nature. There’s no question that wheat has saved millions and millions of lives. There’s no question. When there’s famine in third world countries, we ship boatloads of wheat over there and people stay alive. They’re fed and and they grow and they build new muscle, but you create intestinal permeability and the development of autoimmune diseases. It might just take 20 years or 30 years to take them down. They’ll have a heart attack or Alzheimer’s or diabetes or cancer. But the mechanism that causes many of those is not being able to digest gluten.

Dorland’s Medical Dictionary defines health as “optimal physical, mental, and social well-being — not merely the absence of disease and infirmity.” So if you don’t have optimal physical, mental, and social well-being you’re not healthy! At some point people ask the question, “Why am I not healthy?” But usually they have to cross a threshold of being sick enough before they start asking the question. Depending on who you talk to, you’ll get information like, “You need more vitamin C” or “You need more calcium.” Well, that may be, but why do you need more vitamin C? I’m eating good food, so why do I need more vitamin C?

51 403 biopsy reports remained in 287 586 unique individuals (celiac disease: 29 148; inflammation: 13 446; and normal biopsy: 244 992)

The Journal of the American Medical Association published a study in 2009 where they looked at the biopsy reports of 351,000, about 46,000 of which had [gastrointestinal problems]. They divided [the ones with gastrointestinal problems] into 3 groups: those that had total villous atrophy, those that had no villous atrophy but positive blood work for transglutaminase, and those that had inflammation in their guts. What did they find? Those that had total villous atrophy, celiac disease, had a 39% increased risk of dying early in life, compared to non-celiacs. Those that did not have villous atrophy, but had positive blood work, had a 35% increased mortality. And the third group, those that just had inflammation, had 72% increased mortality — double!

MH: That’s impressive.

TOB: Yeah, when I saw that paper, I got fired up. I thought, “I’ve got to get this message out there.” And now we have Cyrex, which finally is giving us accurate blood work.

MH: So say that a person had optimal health, at least to the extent that they have no signs of leaky gut. No markers, nothing. If they’re not running the risk of having gluten leak out because their gut is healed, is it okay if they eat sourdough bread sometimes?

TOB: The fastest growing cells in your body are the cells in your intestines. Every three to seven days, you have a complete new lining of your intestines. So when you have toast for breakfast, you create tears in the lining of your intestines. Now larger molecules can get through. But it heals. You have a sandwich for lunch, and you tear the cheesecloth. But it heals. You have pasta for dinner, and you tear the cheesecloth. But it heals. Every time you have an exposure to gluten, you get intestinal permeability within 36 hours, but it heals. But then one day you get intestinal permeability, and it doesn’t heal. You cross an imaginary threshold, which you can’t feel. Now you have pathogenic intestinal permeability and the whole cascade begins.

Now should everyone give up gluten? Being an opinion leader, I can’t say that — it sounds too fanatical. But I don’t know why anyone would eat something that’s definitely going to tear away at their body.

MH: So once you have pathogenic intestinal permeability, what do you do?

TOB: People need to live an anti-inflammatory lifestyle. Stop throwing gasoline on the fire. The first thing you do when you don’t have health is clean up your diet. Always. What does that mean? I don’t know what that means for you. Maybe you’re sensitive to bananas. Whatever it is, you’ve got to find it out.

There’s no cookbook for health. Everybody wants a cookbook. They say, “I’ve got lactose intolerance, what would you do?” Or “I’ve got PMS, what do I take?” The United States is ranked second by the WHO in overall quality of health, second, from the bottom. We’re the second worst in the world. And we spend more per capita in health than any other country in the world. The system doesn’t work. The thinking doesn’t work. [What we need] to focus on is always coming from the big picture. Always. The big picture is: Why is this happening?

MH: Have you heard about Rishi Manchanda? He has a clinic in LA, and his work is about being what he calls an “upstreamist.” His philosophy is very similar; it’s a big picture idea. What he does with his patients is, they have a very long intake procedure and they talk about, their on environment. Is there mold in your house, for example? Do you work 20 hours a day? Questions like that. So how does that relate to the idea that the gut is the source of health? When there are these external factors is this solution always to heal the gut?

TOB: That is exactly the approach of an accomplished Functional Medicine Practitioner. The trilogy in the development of autoimmune disease includes an environmental trigger, a genetic vulnerability, and intestinal permeability. And what the papers show is that you can arrest the development of autoimmune disease by healing the gut. You arrest Hashimoto’s thyroid disease. You arrest Lupus. You arrest rheumatoid diseases by healing the gut. So my message is that you can’t do anything about genes, that’s the weak link in your chain. You’ve got to deal with environmental triggers. The most common environmental trigger is the food that we eat. That’s the most common, that’s why your work here is so critical. And then you’ve got to heal the gut. So you can’t not heal the gut. To heal the gut, you’ve got to ask “why?”