“The Microbiome Diet: Evolving Past Paleo”

I don’t usually like to blog one single article, but I sometimes make an exception because there are some keen insights here. And I especially like them because all of them have been in my book draft for some time. 🙂

This is an article by Dr. Raphael Kellman, author of The microbiome Diet and the founder of the Kellman Center for Integrative and Functional Medicine. I was actually sent the book back when it came out but have done nothing more than leaf through it and no nothing of the proposed diet. At any rate, this article is worth a read.

For the past several years, the biggest buzzword in diet has been paleo. This approach to food supposedly re-creates the way our ancestors ate during the Paleolithic period, before the invention of agriculture. Although there are many different incarnations of paleo, they all agree on one thing: Human genes evolved when our ancestors were still hunters and gatherers. Therefore, according to the paleo perspective, our genes have simply not had time to catch up to a diet of grains and legumes.

But our bodies are far more flexible than the paleo people would lead you to believe. That’s because Paleo leaves out a crucial factor in the equation: the microbiome.

Now, here’s key insight #1:

It’s Your Bacteria’s Genes That Matter

That’s right. While everyone has heard over and over that in terms of cell number, the bacteria in our guts outnumber our own cells by a factor of 10 (estimates vary, actually), it’s really the massive disparity in genome that’s the biggie.

Not only do our bacteria outnumber us, their genes outnumber our genes — by a factor of 150 to 1. In many ways, their genes have more of an influence over our day-to-day life than our own genes do.

When your microbiome is balanced, you have a terrific ally that keeps your body healthy, promoting good digestion, clear thinking, balanced mood, and glowing overall health. When your microbiome goes out of balance, however, you risk such symptoms as brain fog, depression, anxiety, bad skin and insomnia — and, down the road, obesity, diabetes, and cancer.

I personally have experienced a pretty profound gradual “chill factor” over many months that’s ongoing, actually. Sure, I still go off in rants and rages now & then, but I get over them quickly and I sure do pass up a lot more opportunities than I used to. Not perfect, but better

Key insight #2:

Now, what does this have to do with paleo? Well, the paleo view is that human genes evolve with glacial slowness, and that humans haven’t yet caught up to the dietary changes brought on by the invention of agriculture.

Maybe human genes do change that slowly (although they have changed more since the paleolithic era than Paleo orthodoxy would suggest). The population of the microbiome, however, changes extremely rapidly — often, within a single day.

After all, the average lifespan of a microbe is only 20 minutes. That’s long enough for your entire microbiome to change its composition.

And when your microbiome changes, its genes change too. You literally could wake up with one set of microbial genes on Monday and a whole other set of microbial genes on Tuesday.

Yes, and then integrate horizontal gene transfer and you’ve got a real whopper of a very complex picture on your hands.

Key insight #3:

You Are What Your Bacteria Eat

It’s arguably as important or even more important than the nutrients going toward your own cellular nourishment. The makeup of your microbiota can change very rapidly.

A breakthrough study from Harvard’s Peter J. Turnbaugh and Duke’s Lawrence David reveals some of the ways in which our diet shapes our microbiome — and thereby affects our ability to digest various types of food. In 2011, the researchers fed volunteers two very different diets. One group was given a high-protein diet consisting of bacon and eggs, spareribs, brisket, salami, cheese, and pork rinds. The other was fed a very high-fiber diet of fruits, vegetables, grains, and beans. Bacterial analysis of fecal samples collected before, during, and after the experiment showed that what each group ate had a huge — and almost immediate — effect on their gut bacteria. […]

The microbiome‘s dynamic ability to respond to our diet is why our bodies can adapt to so many different ways of eating — regardless of how long it might take for our genes themselves to change. Our genes aren’t what matter — our microbiome‘s genes are the key. We don’t have to move at the millennial pace of genetic evolution. We come equipped with a mechanism that is exquisitely responsive to a number of different types of foods, which is why humans all over the world can survive on a remarkably wide range of diets.

Key insight #4:

We Can Eat Almost Anything — But Should We?

The paleo diet varies depending on which expert you listen to, but they all agree on one thing: We humans can’t digest grain. They say that our genes just haven’t evolved enough to metabolize it properly, and that therefore grain is responsible for all sorts of serious disorders.

Not only is that bad genetics, it’s bad nutrition. […]

…Nor do you want to consume a typical Western diet — refined flour, sugar, unhealthy fats, additives, preservatives, and artificial sweeteners — because those ingredients also feed exactly the wrong kind of bacteria.

So, it’s a bit nuanced. Your microbiota can handle a lot of grains. Eliminating of greatly curtailing gluten may be important for some or a lot. But at the end of the day, grains (and legumes) are likely one whole lot less of a problem than is all the crap that comes in boxes and bags of highly processed modern industrially produced food.

I’ll close with a short section from Chapter 1 of my own book in draft (without formatting or references—just a quick copy/paste).


Bacteria are living creatures made up of exactly one cell. They’re amongst the simplest forms of life—probably one of the earliest forms of life on Earth. Our personal microbes are mainly either spherical (called cocci) or rod-shaped (bacilli). They all have cell walls that protect them from the surrounding environment. Bacteria require nourishment, but have no mouth. Its skin (cell wall) is rigid, but it can allow molecules to travel in and out. They have no nose, ears, eyes, arms, or legs; but they’re mobile, and they communicate. Many of the bacilli have tails, used to navigate the fluids in which they inhabit. As with the lizard, their tails are detachable. Some have special tubes, known as pili—used to transfer material to other microbes. But what could a single-celled organism have that it needs to share? Information! For instance, when an antibiotic (a poison to the organism) is detected, this information is shared with its fellows. Over many lifecycle generations, bacteria evolve to resist antibiotics and become what the medical profession calls superbugs—bacteria that can’t be eradicated by the antibiotics du jour.

Even though we know bacteria to be single cells, they’re anything but simple. Within the cellular membrane of each is contained mostly water. Within this water resides the material of DNA. DNA carries genetic information that’s literally billions of years old, and all cellular functions are controlled by it. That’s right: our microbiome is operating, in part, on basic instructions billions of years older than primate life itself! If that’s not impressive enough—recalling that our gut microbes possess a combined 3 million genes to the 24,000 for our human cells—also present in this watery interior are ribosomes. These free-floating structures attach themselves to DNA to carry out instructions to manufacture proteins, antibiotics, vitamins, hormones, poisons…a veritable complete line of synthesized chemicals. Our microbes, each of some 100 trillion, are only single cells that are, nonetheless, microscopic chemical plants, the likes of which ought to make Eleuthère Irénée du Pont, Herbert Henry Dow, and Friedrich Engelhorn all blush.

Microbes are astoundingly complex, versatile, and resilient, even though a single complete microbial life might be measured in mere minutes. Various strains have obtained the ability to live in a wider array of environments than any other life form. They can be equally at home in boiling water, and polar ice caps. They can live and thrive in oil spills, hot sulfur, salt water, the air, dirt, and everywhere in between. Some have evolved ballasts to control buoyancy in liquids. Some microbes are magnetic, navigating by means of the Earth’s magnetic field. In terms of our gut microbiota, they all have one thing in common: whatever it takes to get inside your gut, as that’s where its kind took up residence millions of years ago in the first primates.

Since they’re quite effective getting where they belong, in a protected environment with a constant supply of nourishment, our bodies are teeming with them. The vast majority are mutualistic. But a few can be deadly—meningitis, tetanus, cholera, pneumonia, and anthrax are all common bacteria that thrive in, on, or outside the human body, potentially infecting and killing millions. The lengths to which bacteria have evolved to do good or harm in all facets of life is staggering. …Corkscrew shaped microbes called spirochetes cause syphilis and Lyme disease. …Rickettsia is a pathogen that can only live inside of other living cells, causing typhus and Rocky Mountain spotted fever. Other bacteria, such as the much maligned e. coli, the culprit behind many food-poisoning outbreaks, are only harmful when found in large numbers or where they don’t belong, but when living happily in your gut are crucial to keeping other pathogens at bay. And conversely, there are gut bugs that appear to do nothing but good things for us…bifidobacteria is one type of microbe with no downside—their presence is linked with excellent immune function and vigorous health.

Hans Christian Gram was a Danish bacteriologist who, in 1884, invented a way to classify bacteria into two large categories. He found that he could stain bacteria with special dyes and if they turned purple, they were considered ‘positive’; but, if they turned red, ‘negative’. Later, these classifications became Gram positive and Gram negative. To this day, Gram staining is one of the most important tests done on bacteria.

Gram staining allows medical professionals and lab technicians to differentiate between two distinct bacterial groups—critical in a medical emergency where minutes count. Gram positive bacteria respond well to certain types of antibiotics, like penicillin, while Gram negative bacteria are very hard to kill and require harsher drugs. Without this knowledge, it would take much guesswork to treat patients, with lives lost to time wasted.

There are dozens of other ways in which bacteria have been classified over the past 50 years, with new methods being developed all the time. Later on, we’ll introduce classifications such as domain, kingdom, phylum, class, order, family, genus, and species.

Richard Nikoley

I'm Richard Nikoley. Free The Animal began in 2003 and as of 2021, contains 5,000 posts. I blog what I wish...from health, diet, and food to travel and lifestyle; to politics, social antagonism, expat-living location and time independent—while you sleep—income. I celebrate the audacity and hubris to live by your own exclusive authority and take your own chances. Read More


  1. martin on January 15, 2015 at 12:20

    The whole idea of “the gene” is questionable to begin with, as is well known in the philosophy of science. Only works for (simple-minded) reductionists, as far as I can tell. After all, we’re 50% banana on that view.

  2. Onlooker on January 15, 2015 at 11:05

    Fascinating stuff. And yet another example of why we should remain humble about what we think we know about the human physiology and guard against dogmatic and absolute stances.

  3. Billy Bob on January 15, 2015 at 11:58

    That passage at the end…that’s from Kellman’s book? Wow! What a fantastic description.

    • Richard Nikoley on January 15, 2015 at 12:16

      No from the draft of my book.

    • Trevor on January 20, 2015 at 12:36

      This is from a draft of a *NEW* book of yours, correct, not from this book?

    • Richard Nikoley on January 20, 2015 at 13:06

      Way new book. Lots of drama surrounding, blogged lots about. 🙂

    • Trevor on January 20, 2015 at 14:29

      Yea, I’ve been a sporadic reader, last I recall was a while back when you mentioned there was some disagreement between you and other contributors that led to them not contributing anymore.

  4. John on January 15, 2015 at 14:11

    Very cool.

    I’m about a week into my personal honey (and maple syrup) experiment. I’m probably eating about 1/4 cup/day combined, or like 2 tablespoons of each. Some days less some days more.

    One thing is for sure – and I’m not sure quite how to word this – no more sweet tooth. I’m never thinking after dinner that I need something sweet, when deliberately eating honey and syrup by the spoon full. In a way, duh; following dinner with several large spoon fulls of honey curbing a sweet tooth is kind of like saying I’ve curbed hunger by eating food.

    The reality is a little more nuanced, though. I don’t keep a lot of sweets on hand, and the go to’s are dark chocolate or ice cream. It takes a lot of dark chocolate to satisfy my sweet tooth (perhaps its relatively low in sugar for that purpose). A pint of ice cream is easy to finish too – Sometimes I’ll feel full after the first 2 bites of ice cream, then when the container is half gone, think its fascinating how I was able to eat so much after the first 2 bites and want the second half more than the first, then I finish the pint almost ready to open a second. Easy 1k calories.

    Honey is a whole different animal. The sweetness blows me away, one or two spoonfuls are amazing, but very quickly I feel like any more is off-putting. Also, I’ve noticed that I’m not craving my weekly large pizza, or if I do crave something like that, the honey leaves me either satisfied, or wanting lean protein.

    I haven’t counted anything, but I expect over the week my protein intake has remained about the same, fat down, carbs up, and sugar way up.

    My workout this morning was amazing. One of those “how did I add multiple reps to multiple sets this week” squat days. I did have the best nights sleep in a while last night, though.

    I’ve been between 162 and 172 at 5’10” for about 5 years. I’m not at my leanest, which invariably occurs when I’m eating less fat than usual. Too soon to tell, but I expect bf% to decrease if things progress similarly going forward with deliberate honey/maple intake.

    Final note – any time I’m low carb, unless I go crazy high in protein (like 250 grams a day), I feel weaker and look less defined, regardless of calorie intake. Lowering calories while low carb (and not supplementing 80+grams of liquid protein/day) translates to quick losses in the gym, and negligible effects on visible fat.

    • George on January 16, 2015 at 18:32

      I bought the book and according to that honey is a no-no like most sweeteners. Feeds the wrong bacteria.

    • Richard Nikoley on January 17, 2015 at 08:31


      That’s an overly simplistic view. As I’ll be posting in a couple of days, raw honey contains tons of bacteria, yeast and fungi. But in a balance, ie, it has been used as an antiseptic for wound healing for eons. The notion that one can identify and have only “good” bacteria, yeasts, fungi while identifying, eradicating and never feed the “bad” is a fool’s errand perfectly suitable to con artists like Grace and her hypochondriacs.

    • George on January 17, 2015 at 09:38

      Pretty sure are right about all your statements there

    • George on January 17, 2015 at 10:24

      So that brings me to believe that it is actually good to have “bad” bacteria too, right? Do we just need some type of balance in the gut too? Can you have too many of one of the good ones too just like you can have too many of the bad ones?

    • space on January 17, 2015 at 22:21

      George, I certainly wouldn’t know for sure, but maybe our gut is just like the natural kingdom. If everything is in a state of balance there can be no good guys and bad guys. The vultures have their role just the same as tigers and gophers do.
      But if the gophers over-populate and there are millions or billions of them, then there is trouble.
      Probably not surprising most people’s gut is as out of whack as what the world is.

    • space on January 17, 2015 at 23:11

      To add, I believe that having more of the good guys changes the ph of the gut and that creates tighter junctures so that it is possible for the environment itself to support a healthier state of balance.
      Maybe it’s a bit like sending in a good algae which suffocates out the bad algae, thereby allowing the water to be less stagnant and putrid so that all the fish thrive.

    • George on January 18, 2015 at 05:34

      Richard would be the expert on this and I think would not argue against it. We don’t know enough about the guts yet but it seems plausible that we should have both good oir bad ones, even though we should have more of the good ones. Maybe, just maybe, when we get out of balance we need/create more of the good ones that will fight the bad ones with our food? If most of our problems stem from what we eat and from our gut, then it seems like need to be aware what we put in out mouth most of the time. It seems like no “diet plan” ever though of the connection between the gut, loosing weight and that we get healthier not because of their diet but because of we change our gut flora every time we eat.

    • Tracy on January 22, 2015 at 10:27

      Am looking forward to raw honey post and have just discovered honeydew honey, isn’t this the best stuff?

  5. MMW on January 15, 2015 at 14:43

    Whoa. That will teach me to drop by the site as I’m on my way out of the office.

  6. Christina M on January 16, 2015 at 14:26

    Interestingly, many bacteria considered “pathogenic” only become so when infected by a bacterial virus. Maybe some non-pathogenic bacteria can become so when infected as well.

  7. George on January 16, 2015 at 18:40

    I bought the book today and it is very interesting so thanks for getting me into this area.the did not mention once about the resistant starches in the book., which I thought was interesting. It has a 7 week diet plans that I am sure I won’t follow. The food seems delicious but created by a chef so I am not sure what in the recipes are for your gut or just for taste. I like the idea that if you heal your gut, you heal yourself and since wheat belly worked for a while I am ready to go look somewhere else. I have dfonbe the RS for a month, I think, after reading about it here and I do the sdoil based probiotics as well as prebiotics which seems to help in getting over/under the plateau/stall.
    I will try to incorporate some of the recipes in the book to at least try.

    • Richard Nikoley on January 17, 2015 at 08:34


      There’s a one sentence blurb on page 191 (hardcover) I believe on RS. How one can do an entire book on the Microbiome and not have a chapter on resistant starches is beyond me.

    • George on January 17, 2015 at 09:35

      I totally agree and thought it was “surprising”. Interesting though, like you have said many times, is that he can sell you anything you need in his store! I guess his idea is that you eat stuff and get the prebiotics from that. I am still skimming through the book researching things. It’s interesting but since the research is kind of just in the beginning I am sure a lot of his thesis will be changed. You have said that diversity is the way to go and I believe that is true!

  8. Fred on January 17, 2015 at 08:31

    I’ve recently been told to take GI Microb-X ( )

    According to lab tests I have tons of Bacteroides and pretty low Firmicutes and Bifido. I have other random bacteria that are really high and others that are really low.

    I also have an overgrowth of Klebsiella oxytoca (likely the cause of my Reactive Arthritis) and Enterobacter cloacae.

    I can’t eat any starch or inulin without a joint flare-up and other issues. I’ve never heard of someone recovering from my disease and being able to eat starch again. Is it possible that this GI Microb-X + taking tons of different probiotics could really fix me? Is there a risk? It seems like a random blend of herbs.

  9. Craig on January 17, 2015 at 11:29

    Hi Richard,

    What do you think of the idea that we eat less fiber than our grandparents, coincidentally we produce less testosterone?

  10. JasonC on January 19, 2015 at 14:27

    Seen this?:

    Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory
    microbiota, and may be the primary dietary cause of leptin resistance and obesity

  11. JasonC on January 19, 2015 at 14:55

    Among the healthiest groups Weston Price identified, IIRC none of them ate wheat, and the only grains eaten (by one group(?)) were oats. And they had a lengthy preparation process…

  12. sl on January 25, 2015 at 08:44

    I saw this book on amazon when it first came out and decided to pass as I was pretty sure the information I was getting from FTA and VegPharm would be more update. But after I read the article you mentioned above, I thought I’d give the book a shot. While he does have useful information for people who are new to the concept of a microbiome and how the gut effects overall health, you and Tim have covered most of what he talks about. But there was one section on Proton Pump Inhibitors that was incredible. He talks about how bad they are for you and how persuasive and successful marketing companies have been at selling PPI’s to the public. And I suppose all those millions of Rx’s written by doctors before the drugs went otc had nothing to do with the drug’s success?

    • Richard Nikoley on January 25, 2015 at 08:56

      I went on PPIs in like 2000 or thereabouts. Could be coincidence, but that’s exactly when my weight began creeping up. Not like I was super lean, but always pretty well controlled, probably within 10-15 pounds of optimal. So, between that time and 2007 when I decided to do something about it, i’d put on like 60 pounds. As part of Paleo, I got off them and that’s when the weight began coming off.

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