Image Credit: Leonardo Aguiar / Flickr. This image has been modified.

We Are Human-Microbe Superorganisms

The microbiome revolution in medicine is beginning to uncover the underappreciated role our healthy gut bacteria play in nutrition and health.

Recently, it has become apparent that our DNA “does not tell the whole story of our individuality and other factors, environmental factors, play an important role in human health and disease,” researchers concluded. We can thank two revolutions in biology for this revelation. First, there was epigenetics, where diet and lifestyle changes have been shown to turn genes on and off. Second was our unfolding understanding of our microbiome—that is, how changes in our gut flora “appear to impact greatly on human biology.”

“Until relatively recently, the colon was viewed as a retention tank for waste,” and water absorption was its big biological function. The problem was it was hard to get in there, and we weren’t able to grow most of the bugs in a lab. As many as 99% of all microbes fail to grow under standard laboratory conditions. How do you study something you can’t study? Well, now we have fancy genetic techniques.

It took 13 years to sequence the DNA of the first bacteria ever. These days, the same feat might only take two hours. What we’ve learned is that we can each be thought of as a super-organism, a kind of “human-

microbe hybrid,” as one researcher called it. We have trillions of bacteria living inside us. One commentator went as far as to say, “We are all bacteria,” which is a provocative way of acknowledging there are more bacterial cells and genes in our own body than there are human cells and genes, and most of those bacteria live in our gut.

All animals and plants appear to establish symbiotic relationships with microorganisms and, in us, our gut flora can be considered like a “forgotten organ.” Studies indicate that the health-promoting effects of our good bacteria include boosting our immune system, improving digestion and absorption, making vitamins, inhibiting the growth of potential pathogens, and keeping us from feeling bloated. But, should bad bacteria take roost, they can release carcinogens, putrefy protein in our gut, produce toxins, mess up our bowel function, and cause infections.

Researchers are still in the process of figuring out which bacteria are which. There are more than a thousand different types of bacteria that take up residence in the human colon. In my video, Microbiome: The Inside Story, I include a diagram from a typical study of gut flora that gives a sense of the complexity. It comes from what happens to be the largest such study done on the elderly and shows that the frailest tend to harbor similar bugs. The study goes on to suggest that it may be the lousy diet in nursing homes that’s causing this shift, which may play a role in ill health as we grow older.

Based on studying what comes out of fraternal versus identical twins, those who eat different habitual diets, and stools from around the world, “[i]t has become evident that diet has a dominant role on the [bacteria in our colon] and that diet-driven changes in it occur within days to weeks,” the research found. Change your diet, change your gut flora.

“The hope of impacting health through diet may be one of the oldest concepts in medicine; however, only in recent years has our understanding of human physiology grown to the point where we can begin to understand how individual dietary components affect specific illnesses,” researchers explain, through our gut bacteria. Milk fat on that piece of pizza, for example, may feed the bacteria that produces the rotten egg gas hydrogen sulfide, and has experimentally been associated with colitis (inflammatory bowel disease). Fiber, on the other hand, feeds our good bacteria and decreases inflammation in the colon. Both choline, which is found in eggs, seafood, and poultry, and carnitine, which is found in red meat, can be turned into trimethylamine oxide and contribute to heart disease and perhaps fatty liver disease. Excess iron may also muck with our good bacteria and contribute to inflammation, as well.

The good news, researchers found, is that “[s]pecific dietary interventions offer exciting potential for nontoxic, physiologic ways to alter [gut microbiology] and metabolism to benefit the natural history of many intestinal and systemic disorders.”

 If you’re interested in more information about friendly flora, I suggest watching the following:

In health,

Michael Greger, M.D.

PS: If you haven’t yet, you can subscribe to my free videos here and watch my live, year-in-review presentations:


Michael Greger M.D., FACLM

Michael Greger, M.D. FACLM, is a physician, New York Times bestselling author, and internationally recognized professional speaker on a number of important public health issues. Dr. Greger has lectured at the Conference on World Affairs, the National Institutes of Health, and the International Bird Flu Summit, testified before Congress, appeared on The Dr. Oz Show and The Colbert Report, and was invited as an expert witness in defense of Oprah Winfrey at the infamous "meat defamation" trial.

34 responses to “We Are Human-Microbe Superorganisms

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  1. Are we skipping the 2017 year-in-review? It’s fine either way, I’m just curious.

    I’d like to suggest that nutritionfacts adopt adding a slight indent to comment replies. You can find a great example of this on Reddit. It gives a much cleaner and more organized look. Plus it would make it much easier to follow conversations.

      1. Thanks Steven! It’s a bummer about the year end review but the TED talk he just blogged about is a very exciting replacement.

        Huh. I guess I don’t see the indents because I’m viewing the mobile format on an Android phone. Good to know that it is formatted nicely on bigger screens though.

  2. I’ve just received the Cookbook. Let me say that it is wonderful! It has given me many ideas to make my WFPB foods more flavorful. The Caesar Dressing is worth the price. I’ve made several batches and use it on salads & quinoa. The Spice Mix is in a shaker in my purse for eating out. One very interesting finding is the use of miso paste. I’ve previously avoided it due to very high salt content. His explanation of it has given me the freedom to use (in much smaller amounts) it again. Do yourself a favor and look through the recipes and try them. They are so close to my current way of eating except for the miso. Eye-opener. I’m so thankful for the book, ideas and new things. Be well friends. Pat.

  3. ” . . . we can each be thought of as a super-organism, a kind of “human-microbe hybrid,” as one researcher called it.”

    Animals are not half human, half microbe hybrids. Rather we are a chimera; a combination of the two. All plants are as well.

    1. “hybrid” is, “1.of mixed character; composed of mixed parts.”
      “Chimera : a monster from Greek mythology that breathes fire and has a lion’s head, a goat’s body, and a snake’s tail. : something that exists only in the imagination and is not possible in reality.”

  4. Animals do not carry the bacteria lineage in the DNA. They are separate but benefit from the interaction when the interaction is good. One thing you may want to look is fulvic acid. It is made by bacteria in the dirt but does wonders in the gut (the root of your body). Another one is humic acid. They benefit the operation inside or outside all the body cells. So the potential effect of bacteria is not exclusive to the gut alone.

  5. Thank you for including all the links there.

    I feel like that series is truly one of the ones I had zero concept of a few months ago and it now is so important to me.

    I keep copying and pasting several of those and pasting them in emails to friends and this makes it so much easier having the links grouped like that.

    I work odd hours and never do get to see the various “doctor” shows and also never had a doctor who ever said any educational sentence, and when I compare this site to several of the doctor sites I have gone to on-line, those seem so focused on selling products and pushing a diet or miracle product and this site gives me the education.

    Dr. Greger, I have posted hard comments during this last series, but I genuinely appreciate all that you are doing and I can’t even tell you how much I have learned and I cannot say that about the television doctors or sites, which are selling products. They point to the studies differently. More in the abstract, without a sense of whether the studies are strong or weak or how the logic builds or even if the substances are toxic or dangerous. Often, I find out after months of taking Spirulina or other product, then, feel tricked.

    I don’t feel tricked here. I feel the complexity of the science is presented before me and that I can analyze the data for myself and that important information isn’t being held back.

    I read a review where someone accused you of cherry picking by doing things like skipping the benefits of fish for something, but I “get” that once you have already toppled the logic of eating fish, you don’t have to keep going back to whether to look at the benefit.

    I understand that if we were picking our own cherries at a store, we would pick the ones which looked good and I am not worried about you building on the arguments you already are building. They didn’t point to you hiding bad studies, like they are. My internal logic process says that once the choline in eggs is being used by the bad bacteria in that way, I won’t blame you at all for not doing videos of the “benefit” of eggs or milk or whatever.

  6. After looking at the research on kefir, I have begun to believe we are all just a firm of bacteria and yeast..It explains reincarnation..

  7. Discussed on the 2018 Holistic Holiday at Sea cruise was the believed impact of GMO foods on our, and it would appear all other living organisms’ microbiomes due to the fact that it is engineered to kill bacteria, without discriminating the good from the bad. Unless, our food we buy and consume is organic there may be a high likelihood that significant damage is being done. Another issue is that the (revolving door) FDA simply accepts the word of GMO suppliers that we are not damaged by their products without verifications by independent researchers.

      1. ?The evidence is that the allium family (Greger did a video on this recently) and especially garlic, do NOT kill the good bacteria or attack healthy tissue- unlike various drugs. I recommend raw garlic for all infections especially of the GI.

      2. Where are the links to that research? I am interested in hearing Dr. GREGER’S findings on this.

        I just realized something–Dr. GREGER’s research findings are THE only such I never questions their veracity. For me, WDGS (What Does GREGER Say) is the new definitive in speaking the truth in the matter. Move over Wiki!

    1. Where do you find that GMOs are designed to indiscriminately kill all bacteria. That sounds like a huge over-generalization and simplification of a very complex subject. Genetically Modified Organisms are modified for specific purposes and not all perform equally in any function.

    1. Generally it appears of no value. What we eat plays a much more important role in determining what form of bacteria flourishes in our gut..
      If you want good bacteria that helps rather than harms whole food plant based is the key.

      1. To add I can think of one probable. If one is on strong antibiotics which are continually killing good bacteria in our guts it may make sense to supplement while on those, discontinuing after.

        1. Okay, I have a question about this.

          I was talking with my sister-in-law yesterday and she told me that the only fruits or vegetables that she ever ate was corn and potatoes, but they have gone keto, so she isn’t eating either of those anymore. (Yes, I didn’t know that she was zero fruits or vegetables and has been for years.)

          I think her diet is 90% chicken right now, because she doesn’t like red meat either.

          I pondered whether probiotics or vitamins would do anything at all or is it why bother?

          1. Those on all meat diets will develop scurvy. Doubt that occurs as most drink orange juice or some other but it has been known to occur. One of the true life shows out of Alaska one of the people a young male admitted he was on a only meat diet by taste preference and he did develop that…

            Vit C is the most overt deficiency. Others will present over time which I suspect a supplement will help but not remove. Meat chicken is simply not a complete food nutritionally.

            1. Fiber which has a recommended daily intake requirement is probably the second most overt deficiency which is little served by a vitamin supplement.

    2. Why bother. Eat the right food and you get all the benefits without disrupting delicate balances.

      It is possible to add psyllium husk power to a mixture of seeds and grains to make something resembling bread, popular with those who won’t eat wheat- and that is the closest you need get to a probiotic. But I wouldn’t even go there. Psyllium swells in the gut.

  8. I would love to know what I can possibly do to get rid of the small (6-7cm) area of inflammation in my colon that I have had for at least 10 years (3 colonoscopies) and continues to get larger with each one. I have zero symptoms, am vegan, and eat a really well balanced diet with lots and lots of fiber. I was so disappointed when it was still there after really getting more strict with my diet over the last 10 years. The gastroenterologist is not worried since my health is so good otherwise and I have no symptoms of colitis or Crohn’s and is a bit perplexed as well. Anyone have any suggestions?

    1. Hi I’m a RN and health support volunteer with Great job on the healthy diet and lifestyle. I wonder if that is why you are not having any symptoms at all with how well you take care of yourself. I think you already doing everything we would recommend if you are eating a healthy, whole food, plant based diet.
      Have you seen any of Dr. Greger’s videos on Crohn’s and inflammatory bowel disease?

      You could also look into adding foods which are specifically found to be anti-inflammatory.

      You might also like some of the info Dr. Greger has done on autoimmune disease.

      Great job on the healthy plant based diet. All the best to you.

  9. I just realized something–Dr. GREGER’s research findings are THE only such I never, never questions their veracity. For me, WDGS (What Does GREGER Say) is the new definitive in speaking the truth in the matter. Move ove Wiki-. When is WDGS going to be an app???

  10. Related a bit and some may find it interesting. IN Tibetan Buddhist theory one may not kill oneself in part as one is not only killing perhaps a nonexistent thing a self but also as one is killing many other things as well. In traditional terms these were described as spirits who reside in the body.

    But are not these things entire worlds of their own really….entire places with their own things that make them grow or die equal to spirits in that sense? Seems so to me, being just a change in word useage.

  11. I just wondering Dr. Gregger have you read the work of 19 century scientist “The Blood and its Third Anatomical Element” by Antoine Bechamp 1912; and the “BÉCHAMP OR PASTEUR? A LOST CHAPTER IN THE HISTORY OF BIOLOGY by ETHEL DOUGLAS HUME, prefaced by Pasteur: Plagiarist, Impostor-The Germ Theory Exploded; R.B. PEARSON.
    Sadly saying, 21 century scientific work revealing how advanced understanding of Bechamp were about complexity and significance of microbiotic content of human body. Your article and pioneer work of Bechamp, for me as Naturopath, just confirming the solid ground I have in understanding of different health issues related to imbalance of intestinal microflora.

  12. Getting fed up now with all these fancy words: ‘biomes’, ‘epigenetics’. Just keep active, eat healthy (no flesh) have great sex and your life will be just so. My granddad was a coalminer from the age of 15, smoked 20 a day for 60 years, died aged 78. Please stop all this BS – it’s not clever and it’s not funny!

    1. Or you might still die young.  The point is you will have lived well, as well as you reasonably could. At least, you will if you have got out and lived your life rather than got stuck on first base anguishing about how to take the next step, constantly testing the ground, measuring your pulse… etc etc.

  13. Homologous Lag

    Hair follicles do not know
    That the man is dead,
    And continue to grow his beard
    For a few more days.
    Thus, citizens would not know
    That the country is dead
    And would continue to toil
    For a few more months.

    Boghos L. Artinian MD

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