J.D. Moyer

sci-fi writer, beat maker, self-experimenter

All Your Guts Are Belong To Us (What's Your Enterotype?)

Your intestines circa 1900.

A recent study published in Nature and noted in the New York Times has discovered the intestinal ecosystems of human beings fall into distinct types.  While we all host many different varieties of bacteria, our guts are apparently dominated by one particular type, or family, of microbes, while other varieties are less abundant.

For example, what the study calls Enterotype 1 consists primarily of Bacteroides, while Enterotype 2 hosts high levels of bacteria from the genus Prevotella.

Different bacteria “do” different things in the intestines.  For example, the Type 2 bacteria synthesize enzymes that produce vitamin B1 (thiamine).  Type 1 synthesizes enzymes that produce vitamin B7 (biotin).  I would speculate that other vitamins that are synthesized in the gut, such as vitamin K2, are also produced at differing rates by different enterotypes.

The study included 400 individuals from Japan, Europe, and the United States.  Three distinct enterotypes where discovered.  Interestingly, each subject’s enterotype was not associated with age, gender, weight, health, or nationality.

So what determines the makeup of your biotic community?  And why does it matter?

Vitamin Factory

For those people with Type 2 biotic communities, are blood levels of vitamin B1 consistently higher?  What kinds of physiological effects would this have?  One study found thiamine supplementation increased self-reported mood, energy, and alertness, and improved measured reaction times.  A “built-in” supply of thiamine might prevent a wide range of diseases in Enterotype 2 individuals.  They might get fewer cataracts.  They might be less vulnerable to kidney disease.  They might experience fewer deleterious effects from consuming alcohol (alcohol destroys thiamine).  They might be less likely to be effected by Alzheimer’s and other forms dementia.

This is pure speculation on my part — I have no idea if thiamine blood levels are significantly higher in Enterotype 2 individuals (and if they are higher, if they are high enough to have any kind of therapeutic effect).  Still, it’s in intriguing possibility.

Enterotype 1 individuals might experience benefits from higher blood levels of biotin, including better insulin sensitivity (less risk of Type 2 diabetes), strong fingernails, and glossy hair.

Having a biotic community capable of producing abundant amounts of vitamin K2 could have significant positive effects on health, protecting against heart disease, tooth decay, and osteoporosis.

Diet, or Random Colonization?

The researchers speculate that as infants, our guts are colonized more-or-less randomly by one particular group of bacteria.  Those that get an early foothold then stick around for the host’s entire lifetime.  Perhaps we inherit the biotic community of our parents and other caretakers, just as we inherit language and culture.

Lactobacillus -- they even look friendly.

Another possibility is diet.  This study found diet-related differences in biotic composition between African-Americans and native Africans.  African-Amercians in the study consumed more animal products than the native Africans, and were found to have higher levels of 7-α dehydroxylating bacteria (which produce hydrogen) and lower levels of Lactobacillus plantarum (which produce methane, and are generally protective against other disease-causing bacteria in the gut).  The researchers hypothesize that the higher levels of hydrogen-producing bacteria in the gut are responsible for the higher rates of colorectal cancer in African-Americans (as compared to native Africans).

Does this mean that eating meat increases “bad” bacteria, and thus increases the risk of colorectal cancer?  Maybe.  However, the Inuit, after switching from a native diet (very high protein, low carbohydrate, very low fruit/veg) to a standard Western diet (lots of refined flour and sugar, refined vegetable oils) experienced skyrocketing rates of colorectal and other cancers.  So protein isn’t the problem.

So wrong, for so many reasons.

This animal study points to refined vegetable oil as being the culprit.  Animals fed a diet supplemented with corn oil showed increased levels of a number of risk factors for colon cancer (including higher levels of 7-α dehydroxylating bacteria).  High levels of fish oil supplementation had no negative effect.  Once again, high omega-6 fatty acid consumption is shown to have a deleterious effect on health.

In other words, it’s probably not the meat that increases levels of the “bad” bacteria, and thus increases cancer risk.  It’s probably the french fries cooked in refined vegetable oil.  This explains the increased cancer risk for both African-Amercians and Inuits eating the standard American diet.

Still, none of this is evidence that diet is linked to enterotype.  The “luck of the draw”/infant colonization hypothesis is just as likely.  Still, diet does have an effect on our biotic community, regardless of our enterotype.

What To Do?

I looking forward to learning more about enterotypes.  Should we be consuming different types of probiotic (and prebiotic) foods in order to support our own particular gut ecosystem?  Are people of different enterotypes more or less vulnerable to certain diseases?

Until more is learned, I’ll keep doing the following to keep my gut bugs happy:

  • don’t eat refined vegetable oils (corn, sunflower, canola, etc.)
  • limit omega-6 from other sources (grain-fed meat & dairy, nuts and seeds)
  • eat soluble fiber and other prebiotic foods (artichokes, asparagus)
  • eat fermented foods with live cultures (homemade sauerkraut)
  • limit gluten consumption (bread, pasta) and lectins (beans, nightshade vegetables) — both of which can disrupt the intestinal lining
  • don’t take antibiotics unless absolutely necessary

We Are Many

Human beings are giant walking colonies of human cells living symbiotically with bacteria.  Parts of the body once thought to be sterile, like the lungs, are now found to be colonized by microbes, just as our skin, nose, mouths and bowels are.  The makeup of our biotic communities have a profound impact on our immune systems, our ability to digest food, and our ability to synthesize certain vitamins.  Not all “germs” are our enemies — many varieties help us thrive.

It’s a little weird to think of yourself as a territory to be colonized, but that’s the way it is.  It’s a microbial world — we just live in it.


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  1. Elizabeth

    Wondering, what oil do you use when you cook?

  2. I use a lot of butter (Kerrygold). Also coconut oil (refined — the unrefined stuff is good too but makes everything taste like coconut). EV olive oil for quick vegetable sauté (but not for higher temps).

    I don’t use palm oil — nothing wrong with it but palm forest destruction kills orangutans.

    I save bacon fat in a jar in the fridge and sometimes cook with that (esp. eggs).

    Saturated fat is generally more stable for cooking. Effects from saturated fat on cardio health are neutral — refined vegetable oils and sugar are more dangerous. For more on that subject see http://high-fat-nutrition.blogspot.com/ or http://www.archevore.com/

    • Mr.Lasse

      just replying on the palm oil thing.

      There exist two distinc versions of palm oils. One is pressed from the palm tree fruits. and the other is pressed from the core of the palm tree. The first is healthy and vividly coloured red and the second version is unhealthy and destroys the trees.

      It is true that palm plantation is a serious threat to our environment, replacing jungle with monocultured and lifeless plantations as just one of the problems. If you buy and use the palm fruit oils, buy them cold pressed and organic, they are usually from environmentally protective farms and not from the big industrial wastelands.

      Anyway I dont use much palm oil, aas I dislike the flavor and I never eat refined oils, as I am too concerned with my health to do that. wanted to share my knowledge anyway. bye bye … 🙂

    • Mr.Lasse

      Ooops…I missed my comment on the butter thing!

      If you like to fry stuff in butter, why not try out Ghee? Its just an indian word for clarified butter. You can by it premade or make it yourself from ordinary (organic) butter. Its highly stable to frying temperatures and it does not brown as ordinary butter, as the residues and salts are filtered out in the production process. I use it a lot, and its great! 😀

  3. Nathan Koch

    You mention that there are three distinct enterotypes, but only discuss two of them. What’s the third, and why have you neglected it? How new is this field of research, and how much study has been done? What conclusions have others come to? Interesting topic.

  4. Nathan — I was going off of information in the nytimes article, which didn’t discuss Type 3, but it’s called Ruminococcus. An article in Wired discusses the same research, and includes some cool charts:


  5. To answer your other question — it’s a very new field, with more questions than answers. Here’s an interesting blurb from the Wired article re: nutrient processing differences among the enterotypes:

    Beyond identifying the enterotypes, “anything we say now will be a hypothesis,” said Arumugam. In terms of function, each of the enterotype-defining genera has been linked to nutrient-processing preferences — Bacteroides to carbohydrates, Prevotella to proteins called mucins, or Ruminococcus to mucins and sugars — but far more may be going on.

  6. Andrea Cayea

    Might enjoy this blog also on the same information. Dr. D’Adamo has been looking at diet and individuality for many years, and actually wrote about these differences in his books. Enjoy, and thanks for the great blog!


  7. Thank you for your post on the Enterotypes story. The enterotypes discovery is the result of a fruitful scientific collaboration called MetaHIT (metagenomics of the human intestinal tract), funded by the European Commission. It takes many researchers, labs, fields of expertise to come up with such a major finding and we simply want to thank and acknowledge all those who contributed to these exciting results!

  8. JD,

    Really nice article. It looks like gut bacteria and health is going to be a major part of understanding why different people respond to various environmental influences. I think we are just starting to get a glimpse of how much gut bacteria effects our health.

    You do a really great job of making complex topics seem simple and straight forward. I think you would have been a good teacher or something. If you have any thoughts on how to do this, I’d be interested.


  9. Thanks Tyler. It’s such an interesting time to be following biology and physiology. So much still to be learned about inflammation, bacteria and immune function, epigenetic expression, etc.

    I enjoy writing about these topics. Since I’m not a scientist — just a curious layperson — that may make my writing more accessible. Glad you’re enjoying the blog.

  10. emilie123

    Excellent article and comments.
    Thank you all…

  11. So Dr. Hazen has linked serum TMAO, which may be linked to heart disease, to a dominance of the prevotella gut bacteria, which apparently can thrive on supplemental free-form carnitine, and possibly carnitine in food (like meat), and also possible lecithin (found in egg yolks and other foods).


    But prevotella also thrives under different dietary conditions, such as a non-diverse diet high in whole grain, as discussed in this post:


    According to the same post, vegetarians and vegans tended to have low prevotella levels (which supports Hazen’s hypothesis), but a few paleo eaters who were tested had extremely low prevotella levels.

    Too soon to draw any conclusions …

    • Bob

      Bob73 JD Great article However Dr. Hazen”s study is intensely flawed.He feeds his subjects antibiotics(will kill nearly all gut bacteria) and then has them eat 2 hard boiled eggs, Then tests for TMAO in bloodstream. The Mythology of the Advanced Degreed Mental MIdget
      Choline does not hurt anyone other than causing diarrhea. Some causes of heart attacks, high levels MSG (hidden in foods) calcium deposits in arteries that have left your bones low levels of K3 Check the dairy industry

  12. This study (free to view full paper if you register) finds that the prevotella enterotype is associated with carbohydrate consumption, including fructose and sucrose, while the bacteroide enterotype is associated with eating more saturated fat and protein.


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