Polyphenols: The Link Between The Microbes in The Soil and Our Gut Microbiome


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“…our gut doesn’t have the machinery to break them down into smaller absorbable fragments.”

Polyphenols are large molecules made up of multiple components called phenolic compounds. You may have heard about these molecules in the media as the health-promoting components of red wine (resveratrol), pomegranate juice (ellagitannins), olive oil (oleocanthal), chia seeds (flavonoids) and cacao (flavonoids). When these compounds are synthesized by plants, a process for which plants require the assistance of the microbes living in the soil, these molecules are not only too big to be absorbed intact in our gut, but our gut doesn’t have the machinery to break them down into smaller absorbable fragments. So how can we benefit from these unwieldy, unabsorbable compounds?

“…based on studies on isolated cells or after injection into lab animals, without taking into consideration of the role of the gut and its microbiome.”

When these molecules were first promoted as health-promoting supplements, they were marketed as antioxidants and were even featured on a prominent, no-longer existent FDA website. Unfortunately, the antioxidant claim for many of these compounds was based on studies looking at isolated cells or after injection into lab animals, without taking into consideration of the role of the gut and its microbiome. However, when it became apparent that less than 5% of the ingested molecules showed up in the blood, scientists pointed out their low bioavailability and their use fell out of favor and they could no longer be marketed as potent antioxidants.

Here is where microbiome science fundamentally changed our view of these main representatives of the plants’ pharmacy! As polyphenols can’t be absorbed in our proximal small intestine, they travel down to the parts of our gut that is inhabited by trillions of microbes. There, microbes are able to break them down into hundreds of smaller absorbable molecules which get into our bloodstream and exert their health-promoting effects throughout our bodies, including the heart, the brain and our metabolism. In addition to their effects on our health, polyphenols also function as an important part of the microbes’ diet (prebiotics) and to suppress the growth of unhealthy microbes.

“These microbes then stimulate the rhizome to produce polyphenol molecules…”

And to add to this fascinating story, the plants use these same molecules to protect themselves against pests, diseases, droughts and UV light! When exposed to these environmental stressors, the plant sends signals down into its root system, the rhizome, where cells start to secrete sugar-like molecules (carbohydrates) which attract microbes living in the soil to colonize the root system. These microbes then stimulate the rhizome to produce polyphenol molecules which travel up the plant and are enriched in leaves, fruits and seeds of the plant, the most valuable assets of the plant.

Unfortunately, these fundamental changes in these phytochemicals are not easily distinguishable to the human eye, and fruits and vegetables grown with chemical fertilizers will grow faster and often look more attractive than those grown with true organic practices.

“Just like us humans, plants are dependent on the help of the microbes.”

However, plants grown without their own protective mechanisms are prone to diseases and pests, and it takes increasing amounts of pesticides and fungicides to keep them alive. Just like us humans, plants are dependent on the help of the microbes (this time in the soil) to produce them to resist stress and disease. Thus the diversity and richness of microbes in the soil is as important for the production of polyphenols by the plants, as a healthy gut microbiome is important for our own health. Plants grown in chemically fertilized soil and in the presence of other chemicals, or under hydroponic conditions are depleted in these health-promoting molecules, and regardless of how healthy and appealing they look, they will not provide the same health benefits of plants grown in regenerative organic conditions.

“…important to nurture your microbial ecosystem…”

It is important to note that not everybody has the right combination, diversity and richness of gut microbes to metabolize some polyphenols. It is therefore important to nurture your microbial ecosystem with a varied plant-based diet, full of different types of fiber molecules.

There is much more to the fascinating story about the health benefits of polyphenols, including the question if you can take them in the form of supplement pills, and how you can learn more about the polyphenol content of the food you eat. The polyphenol content of plant-based foods is not only dependent on the environmental conditions and the soil they are grown in, but also on the processing method (cooking) and the exposure to UV light.

In The Mind-Gut-Immune Connection, and in my gut-friendly cookbook Interconnected Plates, I not only address these questions, discuss the science, but offer clear-cut strategies including a model for nutrition to support the microbiome as well as a list of gut-friendly recipes. These recipes are based on two simple, but crucial principles:

  1. Follow a diet that is optimal for your gut microbes (full of polyphenols and fiber), and it will automatically be good for your own health as well.
  2. When you select your food, pay attention not only to what you eat, but also when you eat it and how it is produced.

Emeran Mayer, MD is a Distinguished Research Professor in the Departments of Medicine, Physiology and Psychiatry at the David Geffen School of Medicine at UCLA, the Executive Director of the G. Oppenheimer Center for Neurobiology of Stress and Resilience and the Founding Director of the Goodman-Luskin Microbiome Center at UCLA.

This article was reviewed and approved by Emeran Mayer, MD