<img src="https://certify.alexametrics.com/atrk.gif?account=Kp9Uh1aon800iJ" style="display:none" height="1" width="1" alt="">

Dr. Sears' Blog

Breaking down the latest research on Anti-Inflammatory Nutrition
Written By: Dr. Barry Sears, Ph. D | Creator of the Zone Diet

Written by Dr. Barry Sears
on March 07, 2016

At 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.New call-to-action


  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).

Let Us Know What You Thought about this Post.

Put your Comment Below.

You may also like:

Polyphenols MaquiRx Delphinidins

Polyphenols, Maqui and Delphinidins: What You Need To Know

Polyphenols are the chemicals that give vegetables and fruits their colors. They also represent the plant’s primary defe...


Burn Fat Faster

Now that the Covid-19 epidemic seems to be slowing down, we must contend with the other epidemic that shows no signs of ...


Cocoa Benefits Q and A

Dr. Sears answers some of the top questions we receive about our new Cocoa Polyphenols.