An Alien World, Right in Your Gut

Dr. Sears and An Alien World in Your Gut blogAt the beginnings of modern medicine some 2,500 years ago, Hippocrates provided me inspiration when he said, “Let food be your medicine, and let medicine be your food.” For more than 20 years, I have been talking about the hormonal implications of that quote. So this day in March, in the midst of National Nutrition Month, let me turn to one of Hippocrates’ lesser-known inspirational quotes: “Bad digestion is root of all evil.”

The Atmosphere in Your Colon

Our knowledge of what goes on in the gut, and especially in the colon, is extremely primitive.

The medicine world tends to ignore things it doesn’t understand. Fortunately, new breakthroughs in analyzing bacterial DNA makes it possible to understand the profound impact that microbes residing in your colon have on physiology. The atmosphere that microbes need to survive in the colon is a very different world compared to that needed for our human cells to exist. Human cells require oxygen. Oxygen is toxic to the vast majority of bacteria that reside in the colon. When these worlds mix, there is the possibility for disaster.

The barrier that separates these two seemingly alien worlds is exceptionally fragile. It is the lining of the epithelial cells on the surface of the gut. When it is compromised by inflammation, these two alien worlds begin to collide. One aspect of this collision is often called leaky gut syndrome.

The Last Thing in the World You Need – A Leaky Gut

Development of a leaky gut means that microbes and usually microbe fragments from the bacteria can enter our bloodstream more easily to initiate inflammatory responses in every cell in the body. At high levels of bacterial invasion, this leads to sepsis and high rates of death. At lower levels, it creates metabolic endotoxemia and promotes obesity and diabetes. However, the door can swing both ways, as oxygen from our blood can begin to enter into the colon to potentially destroy beneficial microbes in the colon.

We think of ecosystems like the Amazon Rain Forest as being complex and diverse. In reality, the ecosystem of microbes in the colon is vastly more complex than the Amazon, and represents the highest density ecosystem on the planet. However, the diversity of an ecosystem provides resilience to environmental damage.

Two recent research articles shed new insights into the damage we are causing to our internal “microbial rain forest” and how those changes can echo through succeeding generations.

Effect on Microbes in the Colon Due to Fiber Removal from Diet

Researchers studied the effect on the microbes in the colon simply by removing the fiber from the diet. (See Stanford Medical School study from Nature.) For the bacteria in the colon, it is fiber (and really the fermentable fiber) that is their only source of food. Within weeks after the removal of fiber from the diet, the overall balance microbial composition rapidly changed along with more than half the bacteria experiencing more than a 75% reduction in their numbers along with many species of bacteria dropping to such low levels that they had become undetectable. Those diminished bacterial strains had literally starved to death.

After seven weeks on microbial starvation diet, fiber was reintroduced and the bacterial ecosystem was only partially restored as more than one-third of the bacteria never returning to their original density. It was as if a fiber-depleted diet was acting as a continual antibiotic.

More disturbing was when they continued the experiment not for seven weeks, but for four generations. Each generation on the low-fiber diet had increasingly lower levels of bacteria so that by the fourth generation of mice the levels of bacteria that could be detected had decreased by 75% compared to the starting generation.

Unlike the earlier study, when fiber was added back to the diet of these fourth generation mice more than 67% of the original bacteria had become extinct. This ranks as a mass extinction event. Without diversity, any complex ecosystem collapses. With such a collapse, the health of the organism will soon follow a downward path.

That’s the bad news. The good news comes in the second research article.

Polyphenols Dramatically Improve Colon’s Bacterial Composition

This second article demonstrated the ability of polyphenols to dramatically improve the bacterial composition of the colon. (See study from Diabetes Journal.)

Since the colon is virtually devoid of oxygen, any trace of oxygen coming from our human side of the gut barrier may destroy important bacterial strains for which oxygen is toxic. One of these is known as A. muciniphila.

This particular microbe appears to one of the “best of the best” microbes in the colon’s ecosystem as it not only heals a leaky gut, but also reverses weight gain as well as stimulating satiety.

One of the great mysteries of polyphenols is that while only very small amounts ever enter into the bloodstream, they somehow can generate profound health benefits. This study suggested an intriguing new possibility that polyphenols can change the microbe composition by acting as the ultimate anti-oxidant to remove any remaining traces of oxygen that may have leaked into the colon. As a result, high levels of supplemental polyphenols demonstrated a dramatic increase in the levels of A. muciniphila in the gut along with a corresponding decrease in inflammation, reduction in body fat, and regaining of blood sugar control in the body. By decreasing the oxygen content in the alien world of the colon, the oxygen-rich world of the body was dramatically improved.

What in the World Does All This Mean?

You may be wondering what this all means for you.

First, you need to eat adequate levels of fermentable fiber to keep the microbial ecological diversity in the colon, but without over-consuming carbohydrates that would stimulate insulin secretion. Second, you need a continual intake of polyphenols to strip out the last traces of oxygen in the colon to allow an increase in the beneficial microbes like A. muciniphila that make our human physiology more functional.

As Hippocrates first noted 2,500 years ago, health is complex and is intimately tied to our diet. That means not only managing the complex ecological system in the gut, but also constantly managing the changing hormonal balance in the blood and the brain.

Sound difficult? It’s not if you follow the Zone Anti-inflammatory program especially by adding extra polyphenols.


  1. Sonnenburg ED, Smits SA, Tikhonov M, Higginbottom SK, Wingreen NS, and Sonnenburg JL. “Diet-induced extinctions in the gut microbiota compound over generations.” Nature 529:212-215 (2016).
  2. Roochand DE, Carmody RN, Kuhn P Moskal K, Rojas-Silva P, Turnbaugh PJ, and Raskin I. “Dietary polyphenols promote growth of the gut bacterium Akkermansia muciniphila and attenuate high-fat diet-induced metabolic syndrome.” Diabetes 64: 2847-2856 (2015).

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About Dr. Barry Sears

Dr. Barry Sears is a leading authority on the impact of the diet on hormonal response, genetic expression, and inflammation. A former research scientist at the Boston University School of Medicine and the Massachusetts Institute of Technology, Dr. Sears has dedicated his research efforts over the past 45 years to the study of lipids. He has published 40 scientific articles and holds 14 U.S. patents in the areas of intravenous drug delivery systems and hormonal regulation for the treatment of cardiovascular disease. He has also written 14 books, including the New York Times #1 best-seller, The Zone, which have sold more than 6 million copies in the U.S. and have been translated into 22 different languages.


  1. Ray B.

    Dr Sears I am a very grateful customer of your omega 3 capsules. I have great friends with a young son suffering
    from Angelman Syndrome.
    Can you offer any advice on how your program may benefit him?

    Many thanks for your dedication to Our health. I am 70 years young and follow the Zone diet and take my Omega 3 every morning. Never hungry also!
    Feeling great, and an interesting benefit, this summer here in Sunny Queensland, Australia, I have not felt the heat at all, even though this is something that has always drained my energy and enthusiasm, Wow what a difference. From November i have taken 8 capsules a day, and will get blood tests and the blood spot test in a few weeks.

    Thank you for your time and your advice

    Kind regards


    • Dr. Sears

      Thank you for your long-term use of the Zone Diet. Relative to your friend’s son, Angleman’s syndrome is a genetic disorder for which there is no cure. However since a short attention span and hyperactivity is one of its symptoms, our work with high-dose omega-3 fatty acids int he management of ADHD may be germane. I would suggest titrating with omega-3 fatty acids until the AA/EPA ratio is between 1.5 and 3.

  2. Kathy

    I’m going to do your 30-day test. You say to take these supplement levels “until inflammation is reduced”. What do I look for to know inflammation is reduced?

    • Dr. Sears

      The most reliable marker of inflammation is the AA/EPA ratio. The goal is to get the AA/EPA ratio in the range between 1.5 and 3 as found in the Japanese population. The average AA/EPA ratio for Americans is 18.

  3. Kathy

    Your previous answers very helpful. Regarding your statement “without over-consuming carbohydrates that would stimulate insulin secretion” How does stimulating insulin secretion play into this? What damage does it do?

    • Dr. Sears

      Increased insulin secretion in the presence of higher levels of omega-6 fatty acids leads to the increased formation of arachidonic acid (AA). AA is the molecular building block for a wide variety of powerful pro-inflammatory hormones (prostaglandins, leukotrienes, etc) that generate increased inflammation in the brain, blood, and the gut.

  4. chris stephens

    is there an upper limit to polyphenol consumption where benefits taper? I ask because i have 2 big bowls of organic berries in addition to a ton (>10 servings) of vegetables every day. it’s taken me a while to reach that amount and have little to no grains/poor quality carbohydrates as a result. i feel extremely good these days. wondering if i could feel better with some additional polyphenol supplements? i also take 8 omega Rx capsules/day.

    • Dr. Sears

      There appears to be no upper limit to polyphenols in foods given their low concentrations (0.1 to 0.2% by weight). Highly refined polyphenol extracts can reach 50% by weight. The two that I recommend (cocoa polyphenols and maqui polyphenols are very safe up to 1-2 grams per day as supplements.

  5. Maria Garrido





    • Dr. Sears

      Polyphenol supplements are highly concentrated polyphenol-rich extracts from natural sources. A purified polyphenol extract should be 25 to 50 times more concentrated than the natural starting material. Zone Labs is one of the leaders in the world in the development and marketing of polyphenol extracts. You can get them here:

      • Julie Frost

        I take your omega supplements as well as probiotics every day. I was told I have leaky gut. Which of your polyphenols should I take and would it actually heal my leaky gut or does it just control symptoms? If it can heal it, how long would it take?

        • Dr. Sears

          The MaquiRx has been demonstrated to have a more powerful anti-inflammatory effect than the extract used in the study mentioned in the blog. Other studies have indicated that the omega-3 fatty acids also due an effective job in healing a leak gut by reducing inflammation. I would recommend 3 MaquiRx capsules and 8 OmegaRx capsules per day until the inflammation is reduced and then begin reducing their levels. You should see a significant effect within 30 days especially if you are also following an anti-inflammatory diet.

          The combination of polyphenols and prebiotics (to feed the microbes so that they don’t start digesting the mucus layer that protects the gut lining) will have a greater effect than probiotics. However, both the polyphenols and prebiotics have to be present in therapeutic concentrations. In addition, high-dose omega-3 fatty acids will reduce reduce the inflammation and speed up the resolution of the existing damage to the gut lining. Combining all of these with a strict anti-inflammatory diet like the Zone Diet should demonstrate significant benefits within 30 days.

      • Joe

        Could I substitute Sea Vegetables for MaquiRX?

        Also, I am a strict vegetarian. I will NOT do fish oil. Substitute?

        Thank you. I have been following a modified soy zone diet for years. Zone protein powder is the best. Dr. Sears, Thank you for all that you do.

        • Dr. Sears

          There are new algae mutants that contain both EPA and DHA. Although lower in concentration and much higher in price than OmegaRx, they would be suitable for a vegan.

  6. sally

    Dr Sears,

    Can you tell me this in a few easy sentences?

    I would be so grateful!

    Sally LaRhette


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