How the Paleo Lifestyle Optimizes the Microbiome: Part Two

How the Paleo Lifestyle Optimizes the MicrobiomeIn Part 1 of this 2-part series, we defined the microbiome and outlined its many functions. In Part 2, we’ll compare the microbiomes of contemporary populations with those of our ancestors, we’ll see how the Paleo lifestyle benefits the microbiome, and we’ll examine the claims of a prominent Paleo critic who believes the exclusion of grains detracts from microbiome health.

Learning from Hunter-Gatherers

In Part 1, we learned that bacterial species diversity is key to microbiome health. As diversity decreases, the microbiome becomes less robust and less capable of optimally performing its many duties. To assess the impact of diet and lifestyle, several studies have compared the microbiomes of modern city dwellers with those of traditional hunter-gatherers. Invariably, the microbiomes of hunter-gatherers are far more diverse. For example, a 2013 study published in Nature showed Hadza hunter-gatherers from Tanzania to “have higher levels of microbial richness and biodiversity than Italian urban controls.”1

In a 2015 study out of Alberta Canada, researchers analyzed microbiome samples from an Yanomami Amerindian village with no previous documented contact with Western people. This group exhibited the “highest diversity of bacteria and genetic functions ever reported in a human group.”2 One explanation for the Yanomami’s microbial diversity is the diversity of their diets. Food seasonality and foraging lifestyles, for example, “lead to oscillating microbial populations depending on resource availability.”3

Those of us following contemporary Paleo diets should take clues from the Yanomami. We’re creatures of habit, but monotony has its consequences. To harness the potential of the Paleo diet, we should eat seasonally, selecting a wide variety of foods from the Paleo template.

The Consequences of Low Microbiome Diversity

Modern lifestyles have resulted in decreased microbiome diversity, but what does this mean from a health perspective? Low microbiome diversity may cause or accelerate the following conditions:

  • Obesity4,5
  • Inflammatory bowel diseases6
  • Liver diseases, including nonalcoholic fatty liver disease, steatohepatitis, alcoholic liver disease, and cirrhosis7
  • Allergy diseases8

Additionally, there is growing interest in the microbiome’s role in neurological conditions, including anxiety, depression, autism, schizophrenia and neurodegenerative disorders. The US Office of Naval Research recently committed $14.5 million to study the gut’s role in cognitive function and stress responses. Meanwhile, the European Union has launched MyNewGut, a €9 million, five-year project investigating links between the gut, brain development, and brain disorders.9

Does Paleo improve or detract from the microbiome?

Paleo critics are frequently confused about the Paleo diet. Dr. Thomas Kellman, author of The Microbiome Diet, is no exception. Kellman has repeatedly criticized the Paleo diet (see here and here), which he mistakenly believes “revolves around burgers, sausage, bacon, meat snack bars, cured meats, jerky and meat sticks.” According to Kellman, “The Paleo people have it exactly backwards. It’s not that our genes have programmed us to eat only a certain diet. Rather, our diet ‘programs’ our microbiome—and its genes.10” In some ways, Kellman is right, but he’s missing the larger picture.

In Part 1, we discussed the Human Microbiome Project (HMP), which was preceded by the Human Genome Project (HGP). Originally, HGP researchers expected to discover around 100,000 human genes. When they only discovered around 20,000, roughly the same amount attributed to fruit flies, they were surprised and humbled.11 Gradually, geneticists embraced the idea that we have two genomes, (1) our human genome and (2) our microbial genome.

Kellman points out that the microbiome rapidly adapts to our food choices. These adaptations, however, don’t override our human genome. They don’t alter, for example, our unique requirements for essential amino acids and essential fatty acids, which are best satisfied through animal protein and animal fat. When grains and legumes enter the diet, as Kellman recommends, the microbiome adapts, benefiting from the fiber those foods contain, but what about their pernicious components, like lectins, wheat germ agglutinin (WGA), and gliadin, which can damage the gut?12,13, What about phytates, which bind to minerals, preventing proper absorption?

The microbiome adapts rapidly, making the best of whatever we eat, but this doesn’t mean that “whatever we eat” suddenly becomes our ideal diet. Kellman’s recommended diet “is one that focuses on strengthening the numbers and types of bacteria that confer good health on humans,” which is precisely what Paleo does. As discussed in Part 1, a high-fiber, low-sugar diet is best for microbiome health. Kellman, however, wrongly believes the Paleo diet derives “55 percent of daily calories” from meat. He doesn’t realize the Paleo diet is extremely high in fiber, as Dr. Cordain has repeatedly highlighted.

A true Paleo diet does strengthen the number and diversity of gut bacteria through:

  • A high fiber content of the diet through the inclusion of large amounts of fruits and vegetables and sparing amounts of nuts and seeds in the diet
  • Increased diversity of bacteria (like our hunter-gatherer ancestors) by eating a variety of seasonal fruits and vegetables.


Our hunter-gather ancestors had extremely diverse microbiomes, primarily due to the diversity and high-fiber contents of their diets. Grains and legumes contain fiber, but they also contain gut-harming molecules. Whereas microbiome health depends on fiber, the best sources are those yielding net-positive health benefits, primarily vegetables, fruit, nuts, and seeds, all of which, incidentally, are Paleo foods.


[1] Schnorr S, et al. (Apr 2014). Gut microbiome of the Hadza hunter-gatherers. Nature Communications, 5(3654). Retrieved from //

[2] Clemente JC, et al. (Apr 2015). The microbiome of uncontacted Amerindians. Science Advances, 1(3). Retrieved from //

[3] Clemente JC, et al. (Apr 2015). The microbiome of uncontacted Amerindians. Science Advances, 1(3). Retrieved from //

[4]Le Chatelier E, et al. (Aug 2013). Richness of human gut microbiome correlates with metabolic markers. Nature, 500(7464). Retrieved from //

[5] Cotillard A, et al. (Aug 2013). Dietary intervention impact on gut microbial gene richness. Nature, 500(7464). //

[6] Kostic AD, et al. (May 2014). The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead. Gastroenterology, 146(6). //

[7] Schnabl B, Brenner DA. (May 2014). Interactions Between the Intestinal Microbiome and Liver Diseases. Gastroenterology, 146(6). Retrieved from //

[8] Abrahamsson TR, et al. (2015). Gut microbiota and allergy: the importance of the pregnancy period. Pediatric Research, 77(1-2). Retrived from //

[9] Smith PA. (October 14, 2015). The tantalizing links between gut microbes and the brain. Nature, 526(7573). Retrieved from //

[10] Kellman, R. (Jan 14, 2015). The Microbiome Diet: Evolving Past Paleo. The Huffington Post. Retrieved from //

[11]Turnbaugh, PJ, et al. (Oct 2007). The human microbiome project: exploring the microbial part of ourselves in a changing world. Nature, 449(7164). Retrieved from //

[12] Ertl, B., et al., Lectin-mediated bioadhesion: preparation, stability and caco-2 binding of wheat germ agglutinin-functionalized Poly(D,L-lactic-co-glycolic acid)-microspheres. J Drug Target, 2000. 8(3): p. 173-84

[13] Dalla Pellegrina, C., et al., Effects of wheat germ agglutinin on human gastrointestinal epithelium: insights from an experimental model of immune/epithelial cell interaction. Toxicol Appl Pharmacol, 2009. 237(2): p. 146-53.

About Christopher James Clark, B.B.A.

Christopher James Clark, B.B.A.Christopher James Clark, B.B.A. is an award-winning writer, consultant, and chef with specialized knowledge in nutritional science and healing cuisine. He has a Business Administration degree from the University of Michigan and formerly worked as a revenue management analyst for a Fortune 100 company. For the past decade-plus, he has been designing menus, recipes, and food concepts for restaurants and spas, coaching private clients, teaching cooking workshops worldwide, and managing the kitchen for a renowned Greek yoga resort. Clark is the author of the critically acclaimed, award-winning book, Nutritional Grail.

*You can unsubscribe at anytime

Comments to this website are moderated by our editorial board. For approval, comments need to be relevant to the article and free of profanities and personal attacks. We encourage cordial debates for the betterment of understanding and discovery. Comments that advertise or promote a business will also not be approved, however, links to relevant blog posts that follow the aforementioned criteria will be allowed. Thank you.

“5” Comments

  1. Hi Bob M, if you want to improve your gut sympthoms you may better leave, at least for a while and diminish whenever possible thereafter, the potatoes & green bananas. Like many other food, what they give you is much less than what they take out of you and harm you. You may get similar & better benefits with other food.

  2. I think studies of the biome are in their infancy, and many times the people discussing these are saying things that go well beyond the science. For instance, I was listening to NPR, and they had someone discussing the biome. He implied he could ascertain the differences in biome by, say, eating more raw onions. I don’t think we’re anywhere near that level of data (or ever will be). I also think this denigration of meat based on biome has to stop. Even if a diet is 55% by calories of meat (and mine is probably well beyond that, as I try to average 70+ percent fat per day), there are no long term, randomized studies of the biome in this group, nor is there any reason to believe that this is somehow bad. The biome just changes to accommodate that diet.

    I do try to eat vegetables and the like, and even some fruits (primarily berries). I also will eat potatoes and other tubers periodically. I think the rotation of fruits and vegetables is potentially a very good idea, particularly seasonally. The problem is that in the American market, that rotation often doesn’t exist. There are some winter squashes, and more strawberries at times, but I can find fruit year round. I have to program myself to ignore what’s available and concentrate on eating what should be available if we were in the “wild”.

    Will there be a part 3 to this? I spent a few months increasing my resistant starch intake and increasing my probiotics (mainly fermented vegetables, but I also started on probiotic pills), and I couldn’t determine much of a difference. I did seem to dream more, but I had horrible gas, indigestion, etc. The detriments seemed to far outweigh the benefits. Also, I was taking potato starch and other prebiotics, but I also was adding “real food”, too, such as potatoes (cooked, cooled, reheated), plantains, green bananas, etc. I also started taking probiotics, some soil-derived. To me, it seems like I was on a “fake” diet that I could not maintain. I can eat a diet with real food and fermented vegetables, but when I start having to buy starches and prebiotics and pills (probiotics), that’s when I think it’s fake. So, I’ve stopped that. I would like to know, however, whether any of that is recommended.

    • Absolutely, the microbiome changes to accommodate the diet. It makes the best out of whatever inputs it receives. But certain inputs feed the microbiome and promote microbiome diversity better than others. In Part 1 of this series, we discussed MAC’s, or microbiota-accessible carbohydrates, the most relevant source of which is fiber. On a high-fat diet, you can still consume plenty of fiber, especially from non-starchy vegetables (which are very low in calories).

      While you’re right that much more research on the microbiome still needs to be done, it’s becoming increasingly clear that low-fiber diets detract from microbiome health. Also in Part 1, we referenced the Sonnenburg Nature study from January 2016, which demonstrated irreversible multi-generational microbiome damage in mice eating low-fiber diets. It’s true that human studies of this sort haven’t been done, but it’s clear that our ancestors were hunter gathers and that the “gathering” part was just as important as the “hunting” part.

      Probiotics may be a viable strategy for reintroducing lost strains of gut species. We’re not planning a Part 3 at this time, but resistant starch is indeed an interesting topic. Anecdotally, I experienced similar side effect that you did and came to similar conclusions after experimenting with resistant starch powders.

  3. Right, the exploitation of some alleged components on a certain food to claim that “it is good because it contains this..” is silly and misleading. Moreover grains mostly contain unsoluble fibers that is really hard on our gut, and its abuse may lead to tearing it. With the aforementioned claims we should say that hemlock is good because it has phytochemicals and minerals…would you like to have some?
    Besides, the concept of microbiome is being exploited in a misleading way to push miraculous probiotics. We co-evolved with our microbiome, and we are supposed to harbor certain species, others that interact badly with our DNA may be harmful, like the grain degrading ones. We should look at what kind of molecules their metabolism produces, like butyrate etc..even lysine degrading bacteria, recently discovered, produce antinflammatory butyrate, and what is the main source of lysine? Beef, my friends!

    • Insoluble fiber is also present at significant levels in leafy greens, cruciferous vegetables, onion-family vegetables and others. Insoluble fiber can cause problems for those with IBS or other serious gut issues, but shouldn’t be wholesale avoided otherwise. Insoluble and soluble fiber work in concert together to feed the microbiome while promoting healthy bowel movements. Other components of grains (WGA, gliaden, lectins) are more serious threats to gut inflammation.

      Certainly you are right that microbiome health is and will continue being exploited to sell products, but that doesn’t mean all such products are scams. Probiotics supplementation can be appropriate and beneficial in certain situations, but of course not all probiotic products are comprised equally.

Leave a Reply

Your email address will not be published. Required fields are marked *

Affiliates and Credentials