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The Missing Piece in the Paleo Diet

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Many people consider the Paleo Diet to be the new Atkins Diet.

The agricultural revolution may not necessarily be at the root of disease—as the Paleo Diet asserts.

Some people may disagree.

They may argue that the Paleolithic Diet focuses on protein and fat quality—meaning that animal products are sourced from sustainable, organic, or even “wild” farms.

While this is often the case, Paleo foodies eat large quantities of meat. And sure—their meat is often topped with healthy fats like coconut oil and egg yolks from happy hens.

But plants are often used like condiments.

Paleo foodies claim that many plant foods are “difficult to digest.” But is this a good reason to minimize plant foods in the diet?

The reality is that plant foods ultimately enhance your digestion.

What Is the Paleo Diet?

Is the Paleo Diet really all it's cracked up to be? Supporting the inner ecosystem may be the missing link to reduce the risk of chronic disease.

The Paleo Diet is based on the principle that the human gene pool hasn’t changed much in the last 50,000 years.

Our Paleolithic ancestors foraged for their food, hunted, and moved on foot according to the season and their environment. They were nomads. Around 10,000 years ago, this all changed as groups of people began to settle and farm land. Also known as the Neolithic Era, this is when grain became a staple in the diet. (1)

According to the Paleo Diet, the introduction of cultivated plant foods—which includes grain—heralded an age of chronic disease. This includes disorders like obesity, high blood pressure, insulin resistance, heart disease, and autoimmune disorders. (2)

Those who support the Paleo Diet claim that human beings are not genetically adapted to fully digest domesticated plant foods or dairy. But is this true?

The Missing Link in the Paleo Concept: The Inner Ecosystem

The gut is an ecosystem. And in addition to all the cells that make up the intestinal wall, you will find living microorganisms like bacteria, yeast, and sometimes even parasites.

Studies have shown that these microorganisms are critical to your health and even your survival. They balance the immune system. They help control inflammation. They keep your moods buoyant. They support the liver and metabolize toxins, like heavy metals. And—of course—these microorganisms also help you to digest food and create metabolic energy. (3)(4)

Over the past several years, scientists have studied these bacteria. They have discovered that:

  • The human body contains 10 times more microbial cells than human cells.
  • There are 3.3 million unique genes in the human gut.
  • There are 150 times more microbial genes than human genes.

According to these numbers, you could say that we are far more microbial than we are human!

Furthermore, researchers have concluded that the inner ecosystem is shaped by diet, environment, and the health of the immune system. (5)

For example, Japanese people have genes that help them break down some of the complex carbohydrates that are found in seaweed. Most Americans do not. But these genes are not human—they are microbial. (6)

As it turns out, bacteria living in the gut of the Japanese picked up the genetic information on how to digest seaweed from bacteria living in the ocean.

It works like this: Bacteria do not rely solely on their ancestors for genetic information. Horizontal gene transfer allows bacteria to quickly exchange genetic information as easily as you hand over a dollar bill for change.

Thus, while Paleo supporters contend that the human genome has not adapted to digest domesticated grains, legumes, or dairy, they are missing the key fact that the microbial genome has evolved to do those very things.

What Are Cultures Without Chronic Digestive Issues Doing Differently?

The Paleo Diet removes domesticated food crops—like grains and legumes. Strict Paleo also does not allow dairy. But are these foods really the problem?

An interesting study published in 2010 compared the diet and inner ecosystem of two groups of children. (7) One group of children lived in a rural village in Africa that closely resembled the Neolithic farms of our ancestors. The other children were from Florence, Italy. Both sets of children were the same age.

The children living in rural Africa came from a community that did not have any chronic disease of the gut. This means no irritable bowel syndrome. No dysbiosis or small intestinal bacterial overgrowth. No gas, bloating, cramping pain, or heartburn.

The African diet in this small village was a traditional diet. It was rich in starch, fiber, and complex plant sugars. This included gluten-free grains like millet and sorghum, in addition to legumes, vegetables, and herbs. The intake of animal protein was low.

On the other hand, the children living in Italy enjoyed a typical Western diet that was high in animal protein, sugar, starch, and fat—and low in fiber.

This study shows that the agricultural revolution may not necessarily be at the root of disease—as the Paleo Diet asserts. Both groups of children were fed agricultural foods.

Researchers discovered that the group of children from the rural village had a more diverse inner ecology than the children living in Italy. The diet high in plant fiber increased the beneficial bacteria and the microbial genome—all of which enriches the inner ecosystem.

Likewise, generic and refined foods are often missing not only fiber, but they are also more “sterile.” Traditional food preparation techniques—like fermentation—preserved food, protected against infection, and supported the inner ecosystem.

Building Your Inner Ecosystem

Across the globe, diets that are rich in fat, protein, and refined sugar—but are missing dietary fiber—are associated with an increase in chronic gut disorders.

But it’s not just the ratios of protein, fat, and carbohydrates that matter. The missing link that many diets fail to address is how these foods affect the inner ecosystem of the human body. (8)

Whether you are vegan, Paleo, or somewhere in between—there are always success stories. The Paleo Diet has helped many people drop weight or resolve nagging inflammatory disorders. But we often hear that many of these health concerns return.

It is not the presence or the absence of grains, legumes, and dairy that shapes human health. It is the presence or absence of overly processed, generic foods.

Overly processed, generic foods are the cornerstone of the Western diet. And these foods starve the inner ecosystem. When combined with an overuse of antibiotics and oral contraceptives, you have the perfect storm for chronic disease, inflammation, obesity, hormonal imbalance, digestive disorders, and Candida fungal overgrowth.

Whatever dietary guidelines you may follow, working in partnership with your inner ecosystem is the best way to get to the root of chronic health disorders. It is crucial to improve both digestion AND absorption, cleanse toxins and infections, heal the gut lining, and repopulate thriving colonies of beneficial bacteria and yeast.

Donna designed the Core Programs to simultaneously work on all of these essential steps in order to rebalance the inner ecosystem.

What To Remember Most About This Article:

Today, the Paleo Diet is all the rage. Paleo followers eat large quantities of high-quality proteins and fats, while minimizing plant foods that are considered hard to digest. Paleo Diet principles are based on the fact that the human gene pool hasn't changed significantly over the past 50,000 years. Modern, cultivated plant foods are thought to trigger the development of chronic disease.

Yet the Paleo Diet is missing one important link… The inner ecosystem of the gut.

Your body contains 10 times more microbial cells than human cells. Your inner ecosystem can be influenced by environment, diet, and immune health. Horizontal gene transfer changes gut bacteria through the exchange of genetic information. As a result, the microbial genome in your body is equipped to digest domesticated grains, legumes, and dairy, which are often avoided on the Paleo Diet.

No matter what diet you choose, cutting out overly processed, generic foods can support the health of the inner ecosystem. In addition, it's critical to improve digestion and absorption, cleanse toxins, heal the gut lining, and repopulate the digestive tract with beneficial bacteria. You can find the support you need to rebuild your inner ecosystem with Body Ecology's Core Programs.

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  1. Cordain L, et al. (2005) Origins and evolution of the Western diet: Health implications for the 21st century. Am J Clin Nutr 81:341–354.
  2. Blaser MJ (2006) Who are we? Indigenous microbes and the ecology of human diseases. EMBO Rep 7:956–960.
  3. Ley RE, et al. (2008) Evolution of mammals and their gut microbes. Science 320: 1647–1651.
  4. O'Hara, A. M., & Shanahan, F. (2006). The gut flora as a forgotten organ. EMBO reports, 7(7), 688-693.
  5. Zhu, B., Wang, X., & Li, L. (2010). Human gut microbiome: the second genome of human body. Protein & cell, 1(8), 718-725.
  6. Hehemann, J., Correc, G., Barbeyron, T., Helbert, W., Czjzek, M., & Michel, G. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota Nature, 464 (7290), 908-912.
  7. De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J. B., Massart, S., ... & Lionetti, P. (2010). Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proceedings of the National Academy of Sciences, 107(33), 14691-14696.
  8. Thomas, F., Hehemann, J. H., Rebuffet, E., Czjzek, M., & Michel, G. (2011). Environmental and gut Bacteroidetes: the food connection. Frontiers in microbiology, 2.

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  • Jeanmarie

    I have to concur with the majority of commenters here. The insights in this article -- that our cells and genes are largely microbial, and that a healthy inner ecosystem and good digestion are keys to health -- are also well known in the Paleo/Primal/ancestral health world, thanks in large part, no doubt, to the influence of the Weston A. Price Foundation's teachings. I consider myself part of both camps. I also bought BED early on but didn't find many of the recipes very appealing. I do like the veggie starter culture, but man is it expensive!

    If people are breastfeed as children then raised on properly prepared, wholesome traditional foods, it is possible that many would be able to consume (raw and/or cultured) dairy and (soaked/sprouted/soured) grains, but many of us alive now did not get the best start in life and probably have to avoid grains, at least gluten grains, to feel our best. Some people seem to be able to heal their guts and go back to these foods, but many cannot or don't see the point in trying. Grains, after all, aren't that nutrient-dense. Personally, I eat far more vegetables now following a paleo lifestyle than when I was a vegetarian/macrobiotic. They go down a lot easier with pastured butter, pastured lard, bacon drippings, coconut oil, etc.

    And I don't think eating massive hunks of meat is really typical for Paleo adherents. That is an old but outdated stereotype. Not everyone eats low carb or high protein. We don't all eat high fat, either, though I certainly do! And I make and consume large amounts of lacto-fermented vegetables as well as kombucha. Works for me.

  • Tim

    I happen to be a doctor who focuses on nutrition. You missed this one.... I was just about to recommend your website to my two daughters (23 and 17) who are taking a greater interest in fermented foods, recipes and greater responsibility in their own health. I like differing opinions that lead to better understanding. I've always enjoyed your website, follow you on tweeter, and often have recommended or shared your website to my patients. Interesting, I choose not to share your website now to my own daughter because this article creates undue confusion, is misleading, and under researched with a wrong conclusion.

  • Karla

    I have to agree with Brian. Ive never found the Paleo diet to relegate plants in the diet as no more than condiments. Yes, there is an emphasis on good quality proteins and fats, but the diet also emphasizes a good balance of fruits and vegetables, including cultured vegetables.

  • Indy

    I agree with you about the necessity of a proper balance of internal flora. I disagree with the take on "Paleo" as you have it stated in your article. I know of no one promoting or practicing this diet who does not place as much emphasis on quality vegetables as they do on quality meats and fats. Fermented foods are included, as your other posters has commented thus far, and are by no means excluded by anyone promoting this diet. I see no conflict with Paleo with what you have to teach and share, but I am a bit surprised by the shallow depth of research into the Paleo diet as the vast majority of us know it. It is very unlike you.

  • Sherry

    The point of this article appears to be pushing a product. Of course they had to find fault with something (e.g., the Paleo diet) somewhere so at the end they could throw the ad in your face for some digestive remedy. Just eat the sauerkraut!

  • Debbie

    I have even following a paleo diet for years. It helped me loose 15 kgs, discover a gluten intolerance and feel better than I've felt in years. The main part of my diet is not meat but lots of fresh organic vegetables and fermented foods. Your article is not quite based on truth. I also eat a huge variety of different veggies, organic chicken, limit organic gluten free grains. Nuts. Seeds and
    Oils. Grains are very irritating to my very sensitive gut, so best avoided.

  • Megan

    the original premise of the paleo diet was that modern-day human beings are not genetically adapted to digest agricultural foods. as the article shows, gut bacteria outnumber our own cells and are a formidable genetic force. whether or not our paleo ancestors could digest certain foods--our gut bacteria can and they will adapt to their environment and our diet.

    diary and fermented foods are neolithic foods-- they were born out of the agricultural revolution.

    over the last several years, the paleo movement has adopted many of the traditional food principles from the weston a price foundation (which obvi is not paleo).

    properly prepared grains have not been "paleo-approved." and only some forms of dairy (like ghee) are "paleo-approved." this is because so many people have gut disorders. even if your everyday "modern" person were to eat properly prepared grains or drink raw dairy from a grass-fed cow-- many of them would still have a cross-reaction to the proteins in the grain or the dairy. this is why paleo seems to work-- but there is more to the story.

    (not to mention how so many people get caught up in carb counting which throws the thyroid out of balance.)

    like the article points out-- it's not grains that are the problem. it how most of us eat every day (or did, if we've gone paleo) and the effect this has had on our inner ecosystem.

  • Tiffany

    This is not true. I have a culinary job in the Paleo field and there are loads and loads of vegetables in our recipes for breakfast, lunch, and dinner, and an understanding of and emphasis on fermented foods. This article seems written by someone unfamiliar with what we in Paleo actually eat, and is based entirely on untrue speculation.

  • Diane

    This makes sense. However, I have tested sensitive to molds and have been told to avoid fermented foods and any foods that use aspergillis in processing. Are there any options for me? I am not sure where to find good info on dealing with this issue.

  • Anna Venizelos

    Cordain is one of the references listed even though his initial "vision" has been revised. The majority of people that are part of the modern day paleo movement eat tons of vegetables and fermented foods. In fact, most of the paleo best seller books include at least one recipe on how to prepare sauerkraut or some sort of cultured vegetable. It's only those of us with very sensitive guts that avoid vegetables that could cause irritation such as FODMAPS-temporarily- with the ultimate goal of healing the gut and reintroducing them somewhere down the line. Grains that are not soaked and sprouted (which most people don't do) are highly irritating to the gut- containing large amounts of phytic acid and saponins. They're also far less nutrient dense than vegetables and are very easy to over consume. I don't think anything is "missing" from the paleo diet. It's just how you choose to interpret it and most paleo followers are all about gut health and vegetables and cultured foods.

  • Bryan

    Not exactly true, Donna. If you read Robb Wolf, Dallas and Melissa Hartwig, Mark Sisson and others you'll see there's an emphasis on fermented foods and lots of non-starchy vegetables. There's no talk of vegetables being hard to digest...

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