Microbial Diversity – Comparing The Richness Of Gut Microbiota

What a humbling notion it is to consider the fact that 99% of the DNA contained within the human body is actually DNA that is associated with the bacteria that live within us. When we consider how the human genome has been so aggressively studied as representing the “holy grail” in terms of its role in determining our health destiny, to get our arms around the notion that in fact almost all of the DNA in the human body is actually bacterial certainly changes our perception of who we are and what we are.

And even more compelling is new research that indicates that even that 1% of the DNA in our bodies that we consider our own is itself actually and powerfully influenced by the gut bacteria, our microbiome.

In a new study, published in December 2014, researchers attempted to unravel the finding that changes in the various groups of bacteria contained within the human microbiome have an effect on metabolism. It is known that the ratio of two very large groups of bacterial organisms, the Bacteroidetes group and the Firmicutes group strongly relates to risk of things like obesity, metabolism, insulin sensitivity, and even inflammation. Those individuals with higher levels of Firmicutes organisms, in comparison to the Bacteroidetes group, are more prone to problems in these areas. Moreover, the ratio of Firmicutes to Bacteroidetes is strongly influenced by diet.

What these researchers looked at was the effect of the ratios of these two groups of bacteria in terms of how they influenced human DNA. What they found was really quite remarkable. Higher levels of Firmicute activated human DNA pathways that are associated with detrimental changes in fat metabolism, increased production of fat, and heightened levels of inflammation.

So the end result of this research reveals that not only is most of the DNA in the human body represented by bacteria, but that those bacteria themselves are actually regulating our own DNA! Not only is this humbling information, but it should be looked upon as opening the door to powerful new therapeutic techniques based upon interventions that will alter the ratios of gut bacteria, and therefore change our gene expression in a favorable way. And it’s these concepts that I explore in Brain Maker: The Power of Gut Microbes to Heal and Protect Your Brain–for Life.

  • David Gwynne

    So eating animal fats is… bad now? Sorry – confused.

    • Lynn Dell

      I try to keep in mind the whole picture while noting the study is just looking at one aspect of these people’s lives. Nobody who has been watching the news wants to relocate to that section of the world. Many rural people near this part of the world whose gut bacteria are in all likelihood just as healthy have been wiped out by Ebola, which was probably carried by an infected bat. The point is about probiotics and gut health of reasonably healthy children there, and that is all. Not about the fact that they consume carbs, make bread, etc.. The question it raises for me is how do we keep the bad stuff out while letting the good stuff in.

    • Lynn Dell

      David, I just re-heard the presentation, and I missed your point a couple weeks back. I have the same question about their hypothesis about animal fat. I am wondering if there is some research that says it is not good for the gut microbiome which would make them say that. I have never hear this, but there’s a lot I’ve never heard about it and would be interested in knowing why they said that.

    • lynette mayo

      Try to listen to Dr.Mercola & Dr.Perlmutter on interview on youtube, listen daily, listen when doing chores, learn it, its so powerful !!

    • it goes beyond food…dont try to simply things more than necessary…optimal is also about reducing EMF radiation, fixing your circadian clock, reducing artificial light exposure, appropriate exercising, etc….+ each microbiome is different…if we both eat the same food, we most likely will react differently to it…

    • Aristotle

      Since reading Grain Brain last May I have been on a ketogenic diet based on 50 – grams of carbs, 100 – grams of protein and tons of fat (including animal fat). After watching this video I am left with the impression that the animal fat was a mistake. Has anyone here reduced their animal fat intake after watching this?
      Thank you,

  • Al C

    So , does that mean what we eat is making us sick?

  • Susan Haynes

    It means that what we DON’T eat is making us sick. We need to eat more dirt, honest to goodness. Sounds crazy but we do. Some of the best probiotics available now are Soil Based Organisms (SBO), dirt bugs! And, interestingly, all the tubers and gourds that rural populations eat also provide a very important type of food for those bugs, called resistant starch, something that only the bacteria in our guts can digest and utilize, and it makes them thrive. And don’t even get me started on the benefits of fermenting foods – there is no refrigerator in that African village so all the food sits around and ferments and grows fabulously beneficial bacteria.

    • Marlee

      Yes, and we need to grow our own vegetables without pesticides and artificial fertilizer so that we can eat them as unwashed as possible. I just started new batches of mild kimchi and komucha today. I use unwashed kale from my garden as my “wild starter” for the kimchi. As a nod to modern hygiene, it’s a raised bed garden with a fence around it to keep cats and dogs out.

      • David Perlmutter

        Yes, as much as we can do to keep organic with our produce, we should. Those fermented foods are important too!

      • Lynn Dell

        I’m getting a starter for kombucha today or tomorrow, and am looking forward to trying it!

    • CommonSense

      Fermented foods in moderation though, they take a toll on your teeth because of the high acid content. And contrary to conventional wisdom, don’t brush your teeth right after eating, especially fruit and fermented foods.


      • Lynn Dell

        Yes, CommonSense. I’ve started my own kombucha from a friend, and it appears the people who write this site know what they are talking about. I want to take kombucha as a supplement, not as a substitute for drinking water: http://www.orawellness.com/blog/how-to-drink-kombucha-and-not-destroy-your-teeth/

        • lynette mayo

          This may be the smart thing to do. I met someone who knows the owner of KyVita, l may not have it exactly right, but you cannot miss the Vita? he said she use’s a gmo derived Probiotic? l think that is so disgusting, someone needs to expose her !!

    • lynette mayo

      Try to find the article by Dr.Leach, he is testing the stools of the last of the hunter gatherer natives, its fascinating, they eat tTubors, they get 100grams of fiber a day. Closest to that, Sun chokes, Leeks. I still need help in deciding to do Leach’s gut test or the uBiome test, both the same price, let me know if you find out? ($100.00)

  • Alfonso Enriquez

    In other words, lets look for retirement paradise in rural towns or third wolrd counties

    • Lynn Dell

      Yesterday I was looking up info on sustainable retirement communities.

  • maria

    My son was sick when we adopted him at 3 months of age. He was allergic to just about everything and had diarrhea. When we visited my mother and he was exposed to dirt in her garden his stomach issues resolved. (My mother’s garden was organic – done the old fashioned way.) When we returned home, my son’s stomach issues returned, but I always believed there was some value in that rich composted organic soil. The regular dirt from the playground didn’t seem to have the same benefits. (It took years to sort my son’s problems out, though they did eventually resolve. I wish I knew then what I know now.)

  • CommonSense

    It’s been know for a while that a too clean environment can lead to allergies and other issues in children. Go play outside and dig in the dirt is one of the best things to say to a kid.

  • Kat Milacek

    Always love getting your weekly e-mails and listening and watching your short, yet very informative videos Dr. Perlmutter.

    • David Perlmutter

      Thanks Kat. Always good to know that content is well-received!

      • Ri

        me too its the first thing i read/watch in the morning thank you for this life changing empowering information that you present to us ! knowledge is power.fascinating stuff

        • David Perlmutter

          Thanks to you as well RI.

  • plants with pesco

    The diet of the African (Burkina Faso) children in this study is rich in starch, fiber and plant polysaccharides, predominantly vegetarian. It is low in animal protein and fat, overall fat and refined sugars. If you have never tried millet which is the staple of their diet- it’s delicious. It tastes like cous cous without the wheat. An easy copycat to B. Faso meal would millet topped with black-eyed peas, herbs and mixed vegetables with a bit of flax (has similar fatty acids to termites-also part of diet). The only other meat besides termites were small amounts of non-factory farmed (assuming organic) chicken. If you want your kids to be more exposed to germs, just take them to an indoor jungle gym! Change your diet; change your gut; change your life!

  • Joanie

    You know what scares me as a 61 year old is the crap they serve in Nursing Homes! There needs to be a movement to change this!

  • Plants with peso

    Combining the insights of the study Dr. Perlmutter shares here with the current knowledge that our gut biome changes rapidly with dietary change,

    (Link: http://www.nature.com/nature/journal/v505/n7484/full/nature12820.html)

    Americans can, within just a few weeks, completely change their gut biome and one of the best changes may be lack of TMAO production (see links below).

    Americans can increase their fiber intake, by replacing non-fiber foods (soda, sugar, dairy, meat, eggs) with fiber rich prebiotic and probiotic foods like artichokes, blueberries, cooked and cooled starches (beans, millet, sweet potatoes..), sauerkraut, kimchi, miso, tempeh, cortido… Currently, 97% of Americans do not meet the RDA of fiber, but 99% exceed (many as 2x as much) the RDA of protein. We need to eat more high fiber plant foods and not obsess about protein!! If you want more fiber and protein put these in your cart: tempeh, peas, broccoli, spinach, black beans, millet, black and brown rice and lentils.

    links/sources on TMAO:

    1 N Engl J Med 2013; 368:1575-1584 April 25, 2013 DOI: 10.1056/NEJMoa1109400
    2 Nat Med. 2013 May;19(5):576-85. doi: 10.1038/nm.3145. Epub 2013 Apr 7

    3 Am J Clin Nutr. 2012 Oct;96(4):855-63. Epub 2012 Sep 5
    4 Nature 505, 559–563 (23 January 2014) doi:10.1038/nature12820

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