Category: Science


The Secrets Revealed by Teeth

So much is now being written that connects many of our modern day health issues with changes in the microbiome, the hundred trillion organisms that live within us. Indeed, this was the impetus behind the human microbiome project that began in 2008.

What scientific research has clearly identified is a dramatic shift in the makeup of the population of gut bacteria living within individuals who reside in Western cosmopolitan situations, in comparison to people living in more rural environments. In addition, more recent research has revealed that the bacterial populations living within the gut of individuals from non-urbanized areas, with less emphasis on sanitation, much more closely emulate the good bacteria of our ancestors.

Now, you might wonder how we could possibly know what the gut bacteria were like in our distant relatives. As it turns out, scientific research has developed techniques that can actually fully characterize the gut bacteria from humans living thousands of years ago. Though it may sound somewhat distasteful, researchers are able to analyze the genetic signature of bacteria in fossilized human fecal material called coprolites.

Even more intriguing is new research that actually uses the dental calculus from ancient humans to characterize the state of their microbiome. In a recently published study from researchers at the University Oklahoma, entitled “Ancient Human Microbiomes“,  researchers described this fascinating technology. Further, they raised the question as to what specifically defines a “normal” microbiome, and framed this question with the notion that changes in food dramatically impact the gut bacteria, stating:

Although considerable effort has been invested in characterizing healthy gut and oral microbiomes, recent investigations of rural, non-Western populations have raised questions about whether the microbiota we currently define as normal have been shaped by recent influences of modern Western diet, hygiene, antibiotic exposure, and lifestyle. The process of industrialization has dramatically reduced our direct interaction with natural environments and fundamentally altered our relationship with food and food production. Situated at the entry point of our food, and the locus of food digestion, the human oral and gut microbiomes have evolved under conditions of regular exposure to a diverse range of environmental and zoonotic microbes that are no longer present in today’s globalized food chain. Additionally, the foods themselves have changed from the wild natural products consumed by our hunter-gatherer ancestors to today’s urban supermarkets stocked with an abundance of highly processed Western foodstuffs containing artificially enriched levels of sugar, oil, and salt, not to mention antimicrobial preservatives, petroleum-based colorants, and numerous other artificial ingredients.

The authors then explain the implications of the changes in the microbiome in terms of the role of gut bacteria in various aspects of human physiology including digestion, vitamin production, and energy liberation. To this list we can also add immune function, and regulation of inflammation.

These are fundamental processes that, when functioning appropriately, pave the way for good health. However, with disturbances of balance related to gut bacteria, our health is threatened. And it is this relationship that serves to underpin the explosive amount of research now being generated that correlates changes in the gut bacteria to such disease conditions as coronary artery disease, type II diabetes, autism, neurodegenerative conditions, mood disorders, inflammatory conditions, autoimmune disorders, and even cancer.

Exploring the microbiome of our ancestors using this novel technology is clearly going to provide us with very valuable information. Genetically, we have changed very little in tens of thousands of years. But when you understand that 99% of the genetic material in human body is bacterial, and not the 23,000 genes that we inherited from mom and dad, it tends to reframe our understanding of the role of our bacterial symbionts in terms of who we are. As we have changed our environment, including our food choices and exposure to medications like antibiotics, we have impacted the health and diversity of our microbiome. As the authors stated:

There can be no doubt that modern behavior and dietary changes are altering the microbial ecology of humans. While some of these changes could be beneficial, others are disruptive and may be a driving force behind the rapidly increasing rates of chronic inflammatory diseases in developed countries. Common medical interventions, such as antibiotic therapy, have dramatically reduced infectious disease burdens worldwide. However, rather than being targeted strikes against harmful bacteria alone, such therapies can also act as weapons of mass microbial disruption.

Clearly, important migratory and technological events in our past have had a dramatic impact on who we are, far beyond our day-to-day health. But researchers, like this group from the University of Oklahoma, are now looking at these events from the perspective of the microbiome. As the authors concluded:

Our goal now should be to discover if and how each of these pivotal moments in human history and prehistory reflect moments where our relationship with microbes was changed. Fortuitously, substrates such as dental calculus appear to preserve well and are nearly as ubiquitous as the skeletal material itself, with globally diverse distributions through time. There is now a wealth of ancient human microbiome information available to us, which is providing a more complete picture of human biology and evolution. The future for ancient microbiome research is very bright indeed.

For more information, pre-order your copy of Brain Maker today and join Dr. Perlmutter’s email list.

  • Lynn Dell

    I had a scheduled dental cleaning recently. This was the third one since starting this dentist and changing eating habits. This last time I had a new hygienist. She looked at my records and said I had a lot less plaque accumulation than the previous two records indicated. I have not changed my oral care routine, so I attribute the better results to diet, and possibly ramping up timed release vitamin C.

  • agbinsgrief

    For about 2 years, I ate a fully ketogenic diet and had almost zero plaque in my teeth. After having major energy crashes, I started slowly incorporating carbohydrates back into my diet and the plaque has come back concordantly with carb intake. I have suspected gut dysbiosis is the culprit, as when other symptoms I have had flare up, I get more dental plaque, but that is pure speculation.

  • agbinsgrief

    For about 2 years, I ate a fully ketogenic diet and had almost zero plaque in my teeth. After having major energy crashes, I started slowly incorporating carbohydrates back into my diet and the plaque has come back concordantly with carb intake. I have suspected gut dysbiosis is the culprit, as when other symptoms I have flared up, I also get more dental plaque, but that is pure speculation on my part.

    • janet

      I am a registered dental hygienist. carbohydrates do affect the amount of plaque that is formed on your teeth. initially a clear protective biofilm is formed and the bacteria in our mouth attaches to the clear protective biofilm. in the plaque film are bacteria and the endotoxins from the bacteria. it is interesting to note that there are 4 different types of bacteria that cause decay on 4 different surfaces of the teeth. each bacteria has a preference to the area. the cavity is produced by the acid that is formed from the endotoxin excreted by the decay causing bacteria. in order for the bacteria to survive it needs carbohydrates. as a hygienist I also noticed that I have barely any fuzzy plaque on my teeth while eating ketogenic and my colleague who is eating the same way as me, noticed the same thing. I would also like to point out that the honey bear is one of the only animals that gets decay in the wild. I believe that you are on target with your speculation of carbohydrates and dental plaque, it is scientifically proven. no one wants to hear that though because they want to eat what they want to eat. I also believe that gut bacteria plays a major role in our overall health and speculate that it could have effects in our oral cavity also

      • janet

        I would like to add that in addition to developing caries, plaque can cause gingivitis (reversible inflammation of the gums) and because of a dense bacteria laden plaque can lead to periodontal disease, which is when bone loss occurs, causing us to lose teeth. so not only does the plaque affect our teeth it also affects our gum health. so the less carbs the better. we were not designed for the extent that we eat them.

  • TechnoTriticale

    I suspect that where we’re headed is that dental biome is going to become a topic of its own, with a spectrum of optimal critters that is different from gut biome.

    Almost no one will turn out to have optimal dental critters, due both to the same factors that impair gut biome, and separate factors that nuke dental biome.

    It requires considerable effort, for example, to find a toothpaste that is not contaminated with antibiotics and other needless junk adverse to dental biome, if not your gut and endocrine systems too. The list likely includes non-native halogens like fluorides. (Getting glycemic carbs out of the diet is essential. Fluoride in toothpaste or municipal water can’t compensate for poor diet, and is probably unwise for other reasons.)

    If your toothpaste contains the antibiotic triclosan, for example, throw it away right now. You’re better off just using spring water and a brush.

    • Pamela Rosalynde

      Thank you for your thoughts, I can most certainly recommend the toothpaste made by “Young Living Essential Oils”., obtainable only through the website or representatives. You may like to check out this site for the list of ingredients I have used this toothpaste now for four years and have only once needed a filling. (and I’ve improved my diet a la Perlmutter..

  • Lena Smith

    Weston Price is the man. Please explore his work which is beautifully preserved and promoted by the Weston Price Foundation.


    It has changed my life and I embrace it in healing my husband who has Parkinsons. All this information is dove-tailing in ways that clearly demonstrate how losing our primal and wild connection to Nature is devastating to not only our health but our survival.

    Bless you Dr. Perlmutter.

  • This is very exciting info and we’d like to share it with our readers. Thank you Dr. Perlmutter

  • Anne Kahlbaugh

    This is timely indeed as I wanted to inquire with Dr. Perlmutter what his thoughts were in regards to teeth. The reason behind my curiosity is when my mother was diagnosed with Alzheimer’s her teeth were very dark and yet, years before that they were newly bonded by the dentist and very light in color. As the years progressed closer to her diagnosis, her teeth became very dark and she blamed it on the coffee she drank ( 2-3 cups/ day of instant coffee ;-( – should of been organic) and we never gave it much more thought. Now the I am in the process of reading “Brain Maker” my suspicions are now even more confirmed with my mother’s gut bacteria balance. Both my father and brother have Parkinson’s and my mother passed away in 2014 of Alzheimer’s. I am thrilled that Dr. Perlmutter is changing the thinking in the medical field towards these and other diseases!

  • Maria

    Amazing article, thanks Dr. P.
    Recently I started making our own toothpaste and after reading this article I wonder if the NEEM POWDER I add to the toothpaste is harmful or beneficial to good bacteria in the mouth.

    • Janice

      I would think the Neem powder is okay. I use a neem toothpaste I purchase from vitacost.com

  • ri

    I would love to see food products at my local grocery store with your name and stamp of approval on them Dr Perlmutter especially toast that’s gluten free but not the gluten free kind we find in sections of our grocery store already. There is something I really miss about toast spread with butter and some jam I think its nostalgia growing up and eating that for breakfast but now when I eat regular toast I get this nagging cough that wont go away so that tells me a lot! is this a business venture you might consider?

  • Ri

    Hi All! I just finished reading the chapter in Grain Brain about mood disorders and other neurological conditions and how they are related/effected by the state of our microbiome. Dr Perlmutter mentioned how the lower class children on mediaid (or whatever it is called in the States) are more likely to be prescribed Addorrell and Ritalin as opposed to children in the middle and upper class. I thought about this sad reality and why that is. If the solution to problems such ADHD, anxiety and depression in children could be as simple as changes in diet; adding probiotics and nutritional supplements and factoring in exercise everyday -why isn’t that path taken as opposed to drugging these children up? I think it all comes down to money. Pharmaceutical companies are making billions off these drugs every year and im sure physicians get their share of the pie and some may not be driven by money and greed but just don’t have the natural alternative knowledge and are so stressed by the number of patients they have to see they cant sit and take the time to do a comprehensive medical history and get to the underlying cause of the problem so they instead just put pen to paper and write up that prescription and for lower class families this is the simple easy and most cost effective solution because there is coverage for medication and anything outside of that prescription wouldn’t be covered and I hear a lot of people on budgets say that healthy food is expensive and this can be true especially when buying organic but the alternative is treating their bodies like a waste can and putting garbage in it at the cost of their health and happiness and that of their families. It is a sad reality for many American families even the ones who can afford to eat very clean and healthy. I wish probiotics/prebiotics and other nutritional supplements were partially covered I feel its a whole other budget every month to purchase these at the health food store and for a single gal on a budget it can be tough but to me its worth it and I wish a lot more people would think so as well but if you cant afford it, you cant afford it and your stuck with your doctors prescription which often does more damage long term as all medications have side effects. Anyways im done my rant now! I felt compelled to write this but its long past bedtime and I realize how important sleep is now! Tomorrow ill be checking out Dr. Perlmutter.com to see before and after pictures of his patients and hopefully getting to the next chapter in the book!

  • Dr Mark Burhenne DDS

    Dr. Perlmutter, again as usual, you’re always on topic. Thanks for including the mouth in the discussion of overall health. As you’ve pointed out, it not only has a historical perspective, but also modern consequences. Our oral biome is under attack with pesticides on our toothpaste, antibiotics, and other chemicals in toothpastes and mouthwash, and even some dental procedures. For example, I believe that whitening of teeth may have a temporary or long term effect on the oral biome. The oral biome needs to be defined and discussed in detail because it, due to the oral systemic connection, has an effect on overall health. As a dentist, I have my own ideas about this and unfortunately, there is very little in the literature about this. One day, I predict that hygienists will scrape off calculus and send them to the lab to help people optimize their oral biome. This is long overdue.

    • Sally

      Thank you very much for your post and expertise. What would you suggest for a commercial toothpaste replacement? I’ve replaced shampoo and conditioner with baking soda and vinegar (sounds awful, but it works well), and use real soap to bathe. If you can suggest a safe, natural replacement for toothpaste, I would be most appreciative. Thank you.

      • XRF

        I make my own using a combination of 1/2 cup baking soda, 5 tbsp xylitol, 1/4 cup coconut oil & 2 tsp peppermint extract. Works great!

        • Sally

          Thank you! I’ll give it a try.

          • Sally, I make my own toothpaste, you can get the recipe here: askthedentist.com/homemade-toothpaste

  • Christina Limas

    I’m reading brain maker after having read a copy of grain brain and am amazed with the whole information. Thank you!

  • Oscar farias

    Hola me interesa un ejemplar de Cerebro Hacedor……pero lo puedo conseguir en español…?

    • David Perlmutter

      Hola, Brain Maker aún no está disponible en español. Estamos mirando adelante a la traducción pronto.

  • Josi

    Thank you all for your input ~ it’s interesting to see the different impressions/opinions/assessments of the material being presented. It varies as widely as the reader’s personalities. But I think it benefits no one for you to engage in your petty pissing matches. Leave religion out it ~ we’re discussing nutrition and bodily health here, and yes I know about about the mind, body, spirit connection. But if you want want to espouse spiritually, go to the many websites that having a running discourse on that subject. We don’t read Dr. Pearlmutter to get a Bible lesson. I read my own Bible every night, so don’t accuse me of being a non-Christian. I’m just sad over all the vicious, petty, and hateful blogs going on all over the Internet. If there’s a negative to be found, a negative person will find it or make one up if he has to just to fling that negatively out to all. Do us all a favor and take a walk, or meditate, or read your Bible, and empty your sophomoric rants that way. Please.

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