Why Polyphenols Are Important and How They Feed Your Gut Bugs

andrea nakayama


It’s rare for me to meet practitioners who “Get it” – who have gone as deep as I have in the rabbit holes of food, gut health and overall body health.

It’s even more rare for these people to be educators…

Which is why I’m really excited to introduce you to a friend of mine, Andrea Nakayama. We’ve grown closer over the last year and it’s time for you to learn from her wisdom.

This post is for patients and practitioners alike and speaks to a problem that I’m seeing very frequently these days.

[Enter Andrea]

If, as you likely know by now, you are 90% bacteria and 10% human, just who (or what) are you feeding when you sit down to your morning meal?

Honestly, it’s not a trick question.

And if you think about it with that data in mind (shall I say it again? 90% bacteria and 10% human), I believe you know the answer. Your breakfast is mostly feeding your bacteria. And that goes for your lunch, dinner and snacks too.

Yet bacteria aren’t just good or bad. As Michael Pollan stated in a 2013 NY Times Magazine article called ‘Some of My Best Friends are Germs’:

These bacteria, which number around 100 trillion, are living (and dying) right now on the surface of my skin, on my tongue and deep in the coils of my intestines, where the largest contingent of them will be found, a pound or two of microbes together forming a vast, largely uncharted interior wilderness that scientists are just beginning to map.

And while, yes, we are still learning more each day (mapping what’s going on with those microbes and how they influence our states of health and illness, from gut to brain and immunity to pain), it’s not too early to chart new territory on the dietary front, to look at what we can do in the face of so many unknowns.

It’s critical that you keep your bacteria happy

Without healthy bacteria, your body is 90% unhappy. This can look like irritable bowel symptoms, joint pain, mood and memory issues, immune challenges, or all of the above!

I learned this first hand, as both a clinician and a patient. We are after all patients at one time or another in our lives, and my personal health journey started in earnest when I realized I had autoimmune hypothyroidism, or Hashimoto’s, and where there was a deep connection between my unhappy gut, my sluggish thyroid, and my hyperactive immune system.

Foods I thought were healthy were creating downstream symptoms for me. And not just the classic offenders, like quinoa or millet, but foods like eggs and pecans, cranberries and honey. The trouble was, my system wasn’t healthy enough to process certain foods that were nourishing to others — even when they fell into the realm of a healing protocol. I was reacting at a deep level to seemingly disparate foods — foods that defied any therapeutic categorization — and I didn’t even know it!

I see this all the time

As a functional nutritionist and educator, our clients show up with adverse reactions to healthy foods, so much so that they’ve limited their dietary diversity to the point where they’re triggering additional nutrient deficiencies. They understand quite clearly that food is medicine, and are baffled as to why so much of what they eat feels anything but medicinal!

Part of the problem is that we all need to shift our focus from food or diet as magic-bullet medicine to food as one of the many interrelated components that work together to create wellness. In my trainings to thousands of practitioners, I call this the “key and lock” approach — where food is a key, but what specifically are we trying to unlock in the body?

Another part of the problem is that we’re missing many foods that can heal the most pivotal system in the body, the system that is literally at the root of all our health woes — the digestive system. As you well know, without digestive health, your body simply cannot reap the benefits of all the good food you eat and it becomes a challenge to do some of the deeper explorations that we all want to do to feel our best (hormone and neurohormone balancing; immune management, and addressing genetic variants, to name just a few!).

The most important thing we can do…

You guessed it, it’s time to start eating for gut health — your unique gut health! — by feeding your microbiome with polyphenol-rich foods.

As a clinician, one of the biggest areas of focus for me falls into the realm of repairing a damaged ecosystem from its many potential insults (antibiotic use, C-section births, bottle feeding, stress or other environmental factors that serve to disrupt or cause alterations to our ecosystem). If you’re a practitioner, you likely encounter this in your practice as well, and if you’re not, you may be nodding your head with awareness of these offenses anyway.

Eliminating potentially troubling foods and repairing the barrier systems of gut integrity are often the first steps. The tricky part is when that’s not enough. And the truth is, it’s often not enough. Complex health challenges are now the norm.

In order to rebuild a healthier ecosystem, we need to consider the role, the make-up and the diversity of the microbiota. And we need to expand our protocols and take our work back to the table, using good old-fashioned foods to encourage the proliferation of beneficial bugs.

Many of these provocative foods are ones that are classically considered healthful anyway (like apples!). Yet it’s easy for us to overlook or dismiss their importance in our daily regime, and focus instead on the next pill (pharmaceutical or nutraceutical), dietary protocol or recommended practitioner that will help to shift the terrain.

Truth be told, for many of us with chronic conditions and leaky gut, it often takes an army of helpers. We need to support the practitioners and the pills with what we put on the table each day. This is where you become the hero of your own health journey. And to support your heroic and gutsy endeavors in functional self-care, there’s one class of microbiome-fueling foods that I don’t want you to forget:

What Are Polyphenols?

Polyphenol may be a crazy sounding word, but don’t neglect its sobering significance. Some of your good bugs’ best friends may be polyphenols!

This class of micronutrients acts as both an antioxidant and selectively encourages the growth of beneficial bacteria. Polyphenols are naturally occurring chemical compounds found in many of your favorite foods (like blueberries and red wine) and they act like a fertilizer for your microbiome.

Recent studies have documented that dietary polyphenols contribute to the upkeep of intestinal health, by maintaining the gut microbial balance through the stimulation of the production of beneficial bacteria and the inhibition of pathogenic bacteria. With a healthy microbiome, your body can actually better break down the nutrients you’re eating, which is your first step on the road to wellness. These polyphenols really do pack quite a punch!

Where Can I Find Polyphenols?

Polyphenol-rich foods are easy to include in your diet, and your belly (and your immune system) will love them.

SCD-friendly Polyphenol-rich foods include:
• apples (whole, including skins)
• blueberries
• plums
• cherries
• black elderberry
• hazelnuts
• chestnuts (but not chestnut flour)
• red wine (if you can tolerate it)
• resveratrol
• pomegranate
• weak black tea
• peppermint tea
• curcumin and other spices
• and my favorite, green tea!

Of course there are more, but this is a great start.

How do these polyphenols feed my bacteria (and help me feel better)?

The portion of these foods that is beneficial to your inner ecology is the part that your body doesn’t digest at all. Remember, we’re feeding the germs to help feed you.

The undigested parts of the polyphenol-rich foods that make it to the colon are broken down by your gut bacteria into metabolites that increase the good guys and decrease the bad guys, helping create a healthy microbiome.

The beneficial effects of dietary polyphenols are due to metabolites formed in the gastrointestinal tract. This is where it really is about where the food meets the physiology — where the list of polyphenol rich foods interacts with your existing inner ecology and helps to fortify it.

And with a healthy inner ecology comes less pain, more energy, better moods, a happier belly and more balanced immunity. Ultimately, it allows for more dietary variation and tolerance as well! Sweet relief.

Several of these polyphenol-rich foods, including green tea (admittedly my favorite), also have anti-microbial and anti-biofilm activity, supporting the inhibition of yeast overgrowth like Candida albicans and the formation of bacteria like E. coli, from disrupting the balanced microbiota population. In addition, phenolic compounds can act as metal chelators during times of heavy metal stress.

Now I’m not about killing any birds with any stones, but I am in favor of allowing food to multi-task for me and these polyphenol-rich foods do just that

So let’s get cooking! Here’s an easy, gut-friendly snack recipe for feeding your bacteria:


Gut Feeding Recipe

lemon-infused green tea gummies
2 cups water
4 bags green tea
3 Tbsp. grass-fed gelatin
1 tsp. lemon zest
2 Tbsp. lemon juice
2 Tbsp. raw honey
1/8 to 1/4 tsp. minced fresh ginger (depending on how much you like ginger!)

In a small saucepan, heat water until boiling. Add green tea bags and steep tea for at least 5 minutes. Once the tea is ready, slowly sprinkle gelatin over the tea and allow it to “bloom” or dissolve. (The key is to add it slowly so it doesn’t get clumpy. Stir out any clumps with a whisk or fork or whirl the mixture for a few seconds in the blender. It will get frothy but it will work.) Add remaining ingredients to gelatin mixture in pan and stir until well combined. Pour mixture into a glass dish or individual ramekins. Chill for at least 45 minutes or until gelatin is set.

8-10 servings

Putting it to practice

Over the years, I’ve built my functional nutrition practice around eight core pillars that create what I call The Art of Counseling. I’ve learned that my clients get better faster when I employ all eight because the how and the what of our eating is only one piece of the equation that delivers therapeutic results.

We don’t have the space here to dive deeply into all eight of the components that I attribute to my success as a clinician or that I teach in my school for practitioners, but let’s highlight the one pillar that’s most important for our discussion about polyphenols — instead of “food,” “diet,” or “nutrition,” it’s what I call “Where Food Meets Physiology.” It’s the intersection between the two; what’s consumed, and the biochemical response that actually matters. So many clinicians bypass this important understanding and intersection — focusing on either one or the other.

It’s a big mistake I see all the time

The question I always ask is what’s going on in there?

We have the textbooks that tell us what’s supposed to be going on in there, and the studies that tell us what’s likely going on in there based on a set of symptoms or diagnoses. But what I’ve come to know in my years of working with clients and teaching practitioners is this: in order to truly help the clients that need us, we must find out what’s actually going on in there. And it’s going to be different for every one of us, and for every person you see.

What’s going on in the person who’s sitting in front of me? What’s going on deep inside their physiology? What’s happening in the all-important synaptic cleft, where the food meets the physiology?

It’s not a single answer. There’s no “magic-bullet’ or quick-fix. This is where The Art of Counseling comes into play. It’s where you begin to practice functional nutrition, where you can begin to peel back the layers and start identifying the roots. It’s where the rubber meets the road — where it’s not just about what you eat, but how your body responds to what you eat.

Food is absolutely part of the stimulus, but how that stimulus responds inside each person’s body is something we need to learn and understand if we’re going to make the real differences in that person’s health. This is where the precept of bio-individuality is critical. For instance, the relationship we’ve been exploring between the polyphenol-rich foods and the gut microbiota isn’t a given; it’s a two-way street. The bio-availability of those dietary polyphenols is highly dependent upon and largely influenced by their degree of polymerization, a chemical reaction which itself is dependent upon the microbial population and composition.

There’s a real beauty to this reciprocity

Each sign, symptom or response to what we put into our mouths tells us more about that inner terrain. For us, specifically, or for our clients.

Ultimately, as a health practitioner, understanding the inner ecology and what’s going on in there allows you to be more effective in your ability to help people. It allows you to be a more transformative leader in the field. It enables you to provide the best guidance and support for the person, not the precept (of a diet or a diagnosis) alone. It allows you to be the ‘last best stop’ for people who have tried everything, just as I have been.

Does that bio-individuality end with the digestive tract and the make-up of the microbiome? Of course not! We need to take all of this a step further; there’s an art to how we work with the biome and with the host. (That host is you!)

If you’re a healthcare practitioner and you want to take that step into The Art of Counseling with me, come join me for a free Client 911 Power Jam. I’m going to be reviewing cases from my students’ most difficult patients. We’ll explore the intersection between food, physiology, and the critical skill set that will enable you to see the biggest results in your most challenging cases, just as I have.

Join me and we’ll start the conversation together:

Client 911 Power Jam: The Art of a Successful Nutrition Counseling Practice (for practitioners only)

I’m doing this at 3 separate times, because, as a practitioner, I know you are busy… so I’m trying my best to help you when you are free.

I look forward to seeing you there!

-Andrea Nakayama

Functional nutritionist and educator Andrea Nakayama is leading thousands of clients, students, and practitioners around the world in a health revolution focused on reclaiming ownership over one’s own health. Through Replenish PDX, she helps chronically ill people chart their path to recovery, and in her school for practitioners, Holistic Nutrition Lab, she teaches clinicians the science and art of a functional nutrition practice.

Andrea’s a co-producer of the Hashimoto’s Institute, has been featured in O Magazine and Martha Stewart’s Whole Living, and is the recipient of the 2015 Impact Award from the National Association of Nutrition Professionals.

Her passion for food as personalized medicine was born from the loss of her young husband to a brain tumor in 2002, and Andrea is now regularly consulted as the nutrition expert on medical teams for the toughest clinical cases in the practices of world-renowned doctors.


Up-regulating the Human Intestinal Microbiome Using Whole Plant Foods, Polyphenols, and/or Fiber Kieran M. Tuohy, Lorenza Conterno, Mattia Gasperotti, and Roberto Viola Journal of Agricultural and Food Chemistry 2012 60 (36), 8776-8782

Metabolomics View on Gut Microbiome Modulation by Polyphenol-rich Foods Sofia Moco, François-Pierre J. Martin, and Serge Rezzi. Journal of Proteome Research 2012 11 (10), 4781-4790

Antifungal Activity of Black Tea Polyphenols (Catechins and Theaflavins) against Candida Species. Sitheeque M.A.M, Panagoda G.J, Yau J, Amarakoon A.M.T., Udagama U.R.N, Samaranayake L.P. Chemotherapy 2009;55:189–196

The effects of tea polyphenols on Candida albicans: inhibition of biofilm formation and proteasome inactivation. Nikki A. Evensen, Phyllis C. Braun. Canadian Journal of Microbiology, 2009, 55:1033-1039

Effect of apple intake on fecal microbiota and metabolites in humans. Kenji Shinohara, Yuji Ohashi, Koh Kawasumi, Atsushi Terada, Tomohiko Fujisawa. Anaerobe. Volume 16, Issue 5, October 2010, Pages 510–515

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