The Gut Microbes of African Hunter-Gatherers | Hacker News Reader

The Gut Microbes of African Hunter-Gatherers

wired.com

103 pointsrosser38 comments

Excerpt:

In westerners, Bifidumbacterium is a microbe that many nutrition scientists thought was essential to good gut health, but it is almost completely absent in the foragers. Likewise, high counts of the bacteria Treponema have been linked to maladies like Crohn’s disease and irritable bowel syndrome. Neither of these diseases exist among the Hadza, but their guts contain abundant Treponema.

As someone who has consciously and intentionally altered my gut so it would work closer to normal, to me, this suggests a lot of questions that I do not see being asked.

1) Perhaps modern diets are the problem and the biochemistry they foster rather than microbes per se. How can that be tested?

2) What actually causes "disease"? This implies to me that germs per se are not really the explanation.

3) I would be interested in seeing some data on biochemistry and cell structure of this group as compared to people with modern/Western diets.

4) I would be interested in seeing information related to genetics and how that impacts how their bodies deal with gut flora, etc.

I'll upvote your set of questions and reply here rather than make my own top-level comment in this interesting thread.

1) The way to test a causal hypothesis is always, at bottom, to do a controlled experiment.[1] So we will tease out the effects of diet on different people by finding experimental volunteers, after institutional review boards approve the experiments, and subjecting the volunteers to controlled diets. This is very difficult to do, as almost all human beings eat when they feel like eating WHAT they feel like eating. Earlier human experiments on effects of diet have actually required the experiment subjects to live in the laboratory long-term, and to have every gram of everything they ate during the experiment measured exactly. Even at that, those experiments came up with few clear conclusions, perhaps because the experiments weren't lengthy enough or didn't include enough subjects for strong inferences.

2) Lots of different things cause lots of different diseases. Both poor diets and infections by microbes can cause some kinds of disease, each independently of the other. It is a fallacy of human thinking to think that there is only one true cause of disease.[2]

3) Yes, it would indeed be interesting to gather more data about biomarkers and tissues of people from more human groups, and especially so after experimental interventions as mentioned in my reply to your first question. It will take very detailed data-gathering to figure out what is going on at the causal level that makes the gut biomes different, and what the different gut biomes do.

4) Your "gut reaction" is correct that this study does not have what human geneticist Robert Plomin would call a "genetically sensitive design," such as what a study of twins[3] would have. The human behavior geneticists with whom I participate in a journal club during the school year have made me very sensitive to how much information is missed if studies of human subjects don't take into account genetic similarity and dissimilarity of the study subjects. Much more work needs to be done on this.

My comment to a friend on Facebook after I posted this same story and friends started talking about it was "One tricky thing for you and me doing 'research' on this is distinguishing short-term effects from long-term effects. My life expectancy here in the United States is already a lot longer than that of most people in the world." It may be that you and I, with the health problems we have today in the United States, are still much better off sticking with our current diets rather than emulating the diets of hunter-gatherers in Africa.

[1] http://escholarship.org/uc/item/6hb3k0nz

[2] http://www.sciencebasedmedicine.org/the-one-true-cause-of-al...

[3] http://www.hup.harvard.edu/catalog.php?isbn=9780674055469

Thank you.

You said: Lots of different things cause lots of different diseases.

Due to my genetic disorder, I am supposed to be overrun with disease and simply accept dying from it. I have been steadily getting well for the last thirteen years, which is very frequently met with incredibly dismissive feedback. (My favorite being: Thirteen years of steady forward progress is not evidence I know anything, it is mere wild coincidence. Stranger things have happened.)

My genetic disorder is known to cause the tissues to be too acid. There are multiple books about how the typical American diet is too acid. If you get certain kinds of sudden acidosis (this comes to mind: http://en.wikipedia.org/wiki/Diabetic_Ketoacidosis), they will promptly hospitalize you because it can be deadly within 72 hours. Yet, it is not standard practice to treat or even test for acidosis with my condition. Ant-acids are only prescribed for gut issues like GERD and acid reflux which can occur with my condition. Anecdotally, other people with CF report that they have fewer lung issues when on acid blockers and similar for their gut issues.

Altering my diet to make my body less acid has been one of the cornerstones of getting myself well. I have seen articles linking anti-biotic resistance and biofilms to high acidity and seen research that biofilms can be broken up and anti-biotic resistance reversed if acidity is addressed. Yet, again, this remains not a standard treatment for my condition, which kills you by fostering infections and, ultimately, antibiotic resistance in those infections.

My life expectancy is not supposed to be that high for a modern Westerner. It is supposed to be roughly mid-thirties (granted, my form of CF has an undetermined life expectancy, yet I did nearly die in my mid thirties).

Anyway, I just know of lots of different bits of information linking inflammation, acidity, infection and many of the issues typical of my disorder. So a) I would really like to see more biochemical data (like ph balance of sample tissues) in studies of this sort and b) I am ...flummoxed as to why people seem to think we do not have enough data to say, yea, verily, acidity is a primary issue we should treat for to control symptoms of various conditions. (Because there are a lot of conditions associated with my genetic disorder but not unique to it, such as early onset osteoporosis, diabetes, arthritis and on and on.)

I'm curious, what tests do you use to check how acidic your tissues are? How have you changed your diet, and what impact did it have on your body's acidity?

I kind of hate answering questions like this because a) No, I don't have a one paragraph answer (I had a website at one time to try to catalog what I have done and I moved it twice, because of the very ugly attacks on me -- it still exists but not much of it is published online) and b) the answers generally just fuel more ugly attacks.

For your first one: I didn't "test" anything. I followed progress symptomatically.

For your second one: I read up on alkaline foods and skewed my diet somewhat towards those (lettuce, white corn, and watermelon were a big part of my diet for a long time). I also took a lot of supplements ($300/month for years), some of which were alkaline minerals that people like me are typically deficient in (such as calcium and magnesium). I also found that excluding pro-inflammatory oils and certain other pro-inflammatory foods (like peanuts) made a big, big difference.

That's it in a nutshell, but, again, this is 13 years of work I am trying to summarize for you. So a nutshell doesn't really do it justice.

Edit: Sorry, I missed your third question: How it impacted my acidity. I no longer have acid reflux and similar. That's the best I can say about that specific question without being dismissed as a whack job. (I also have a lot less of other issues, but those issues are not things I can "prove" are related to reduced acidity.)

2) A "disease" really means just that: "dis"/not (at) "ease". It's a generic catch-all for something that makes you not at ease. It can have many causes, from microbial or viral sources (eg common cold), to inorganic toxins (eg lead poisoning), to genetic abnormalities (eg psoriasis), malnutrution and bad nutrition (eg fatty arteries), even social problems are sometimes considered a disease (eg gambling addiction). While there are some things that don't fall into the catch-all term, such as damage done by physical trauma, 'disease' has a great variety of causes and does not have to be communicable.

You seem to be intentionally looking for confirmation bias, trying to find a way to place blame on 'modern'.

No, I am not looking for confirmation bias. I am wondering about something complex that we don't seem to have good language for -- or perhaps that I don't personally have good language for.

I have spent a lot of years reversing symptoms of my genetic disorder as well as reversing issues in my special needs sons. Altering my diet is a very big part of that. Humans have been around a long time. Some of the issues my sons and I have are relatively "new." I spend a lot of time wondering how much that is a product of "new" environments rather than "new" biological issues within humans themselves, if that makes any sense.

My dad was old enough to be my grandfather. He grew up on a farm, without the constant noise of modern life. When I lived with my parents during my divorce, I realized my oldest son had many things in common with my father. I had never before realized. The sensitivity to noise that is viewed as pathological and worthy of labeling as ASD or as having sensory issues is something both my parents had. They were just old, grew up in a different era, and expected the house to be kept quiet. No on acted like their preferences were a "special need" requiring a label...etc.

Sorry if that is not very clear. I wonder a lot at how much our modern "ills" are really a product of our modern lives -- of environments that did not exist until recently but which we view as something "normal" that "everyone" should be capable of coping with. It isn't looking for confirmation bias. It is wondering how much bias exists in some of the assumptions we make in how we frame certain kinds of problems.

I wonder a lot at how much our modern "ills" are really a product of our modern lives

This is why I caution you against confirmation bias. The modern life also allows plenty of people who weren't previously viable to achieve adulthood. I'm not talking about Spartan exposure of sick infants (which is an outlier), but that people with sensitive constitutions were more easily taken young by disease in the first place. The high infant mortality of the past is a significant example.

I am quite well aware of that, in part because I and my oldest son are both individuals who could have easily died quite young without ...quite a lot of things modern peoples take for granted. I don't see how that rebuts any of my questions. Wondering about -- call it "side effects" of modern life -- in no way dismisses the benefits we do have.

I don't think it's fair to say that "modern diets are the problem". The availability of modern diets is, after all, largely responsible for modern civilization (which was enabled by agriculture).

But I think it's fair to say that the many benefits of modern diets are accompanied by some serious negative side effects, and that the human microbiome has not yet had enough time to evolve into an optimal state for coping with them. (It probably doesn't help that the "modern diet" isn't at all a stable target to optimize for, either.) Perhaps in another 20,000 years, evolution would naturally shape our microbiome to eliminate things like Crohn's disease and tooth decay.

"I don't think it's fair to say that "modern diets are the problem"."

Yeah, see, I didn't say that. You edited that to mean something completely different from what I said/meant. My sentence started with "perhaps", had no italics and I went on to ask how that could be tested. So I think this is a not great comment. It feels almost slanderous to me.

That's part of my assumption. But, also, it seems to me that the modern diet has chemical impacts that are pretty well-established as promoting disease. Not that we have to eat crap, but a lot of us do, in fact, live on rather crappy food -- microwave meals, food "products", etc. I think it's complicated and that the impact of food chemistry is not well studied or taken all that seriously. People who think relatively small changes may have big impacts tend to dismissed as quacks.

First and foremost: I apologize for making a comment that came across as hostile.

Perhaps my intent would have been clearer if I had said, "I don't think it WOULD BE fair to say...". I did not mean to suggest that you personally believed this to be true. That said, you were clearly suggesting that it is a possibility should be taken seriously, perhaps more seriously than biomedical experts have done to date.

And my addition of italics was entirely to emphasize which part of that suggestion I was responding to. In retrospect, a more careful post of mine ought to have said "[emphasis added]", though that still feels a bit like overkill to me. I think in the context of a threaded discussion I unthinkingly assumed that readers would have your original words and context freshly in mind when they saw my response.

It's disappointing to me that, given our evident agreement on much of the more substantive part of my comment, you took my initial words to be a hostile and deceptive attack.

Thank you for your response.

I have been quite open about the fact that both on HN and elsewhere, I have had the shit kicked out of me for talking about my medical issues and what I have done to get healthier. What with being human, it's a little hard for me to not be "overly sensitive" about the topic. I do try to be as even-handed as possible but repeated vicious attacks do take their toll, no matter how much the victim wants to rise above it.

Have a great day.

2) What actually causes "disease"? This implies to me that germs per se are not really the explanation.

IBS (and Crohn's, which is really just a type of IBD), is an immune disorder characterized by chronic, uncontrolled inflammation. All the disease's symptoms stem from this state, so the specific germs involved may or may not be all that important, the body's reaction to them is. When you get down to it, many disease states are just a consequence of regulation of inflammation failing at a critical location.

That's essentially the defining characteristic of a "syndrome". It is predicated on the condition or symptoms and not on the underlying cause, which isn't always known. As knowledge grows, more specific diseases can be removed from the classification.

This is not surprising to me at all. Pathogenic bacteria linked to diseases such as Crohn's and IBS are only pathogenic if we get them later in life. When we get these bacteria in childhood, before the age of 7, they grow symbiotically with us and help ward off disease. Check out the book An Epidemic of Absence by Moises Valesquez-Manoff [1] if you guys want to learn more about this stuff. It's a fascinating account of a man who experiments with altering his gut biome to overcome Alopecia areata (total hair loss). The book is loaded with science and references a lot of other studies dealing with the gut biome.

[1] http://www.amazon.com/Epidemic-Absence-Understanding-Allergi...

I would ask my friends here on Hacker News to be cautious about taking the statements in that book at face value without a lot of careful follow-up.[1] And I write that, with chagrin, as a participant here who previously submitted an opinion piece by the author to Hacker News, where it reached the front page and sparked a lot of discussion. The claims in the book are very far from settled science, and many of the anecdotes have not been independently verified or replicated.

[1] http://www.emilywillinghamphd.com/2012/08/autism-immunity-in...

There's a small public biotech company Coronado Biosciences that just announced a trial to study their drug (pig whipworms) in autism http://ir.coronadobiosciences.com/Cache/1001185864.PDF.

They have other studies in a couple different autoimmune diseases in various stages http://www.coronadobiosciences.com/research-development/pipe...

So we'll have some more data regarding this soon.

I found the book straightforward about how unproven the science is, and thought it did a good job of being clear about how speculative the theories are. Were there areas where you thought the book's claims were stronger than what is warranted?

I am now curious to see what happens when you switch some of the Hazda group to an Italian diet, and some of the Italians to a Hazdan diet.

That would be interesting - but, as the article says, the environment where you're living is also important.

That's what they say, but I'm sceptical this is really the case. What do bacteria behind strong barriers (stomach acid, small intestine) care about external factors?

Bacteria does not form spontaneously from nothing. You have to get them from your evironment. In fact there is a constant inflow.

And they enter the intestine at both ends.

Basically everything you swallow comes out the other end. Not all bacteria are destroyed by stomach acid or other digestive juices. Bacteria are on most food - pretty much everything you eat is bringing new bacteria into your body. Some of them are benign, some can't handle digestion, some have to be dealt with by your body's immune system.

I will add that heat, humidity, sea level, air pressure and on and on likely impact your internal biology more than you think.

Anecdotally, I moved back to Southern California as soon as I was able because my health is better in this climate than in other places I have lived. Also anecdotally: People who get stationed in Antartica have really bizarre, unexplained things happen to them sometimes, like their fingernails get a lot thicker and weird stuff like that. As I understand it, it is not just the cold. It is also anomalous in terms of height above sea level and other qualities. I don't know the details. It was just a snippet that stayed with me from an interview of a medical professional who had been stationed there and remarked on how this weird stuff happens and they don't even really have studies or any idea where to start hypothesizing.

> strong barriers (stomach acid, small intestine)

Just read this fun little page, and you'll re-think your stance on "strong barriers":

http://en.wikipedia.org/wiki/Dysentery

That would make a great new reality TV show: Baby Swap!

I'm sure if you had to survive in a different environment your gut flora and fauna would adapt to the new conditions given enough time. But unless you were forced to adapt with your survival at stake you'd just revert to eating whatever didn't cause you to become ill.

This does remind me of an Anthony Bourdain No Reservations episode where they ate with the bushmen, and they gave Tony the "best" part of the hog - the anus - unwashed, uncooked. If nothing else then eating those parts of animals with all their attached microbes would introduce them to you over time. Tony did get violently ill for a few days after filming the segment.

And that reminds me of a This American Life, where the show's producers were unable to actually uncover conclusive evidence that fried hog bung was being used as imitation calamari rings, but they did find in a blind taste test that you probably wouldn't notice if it were. So I wouldn't say it's the best part of a hog, but it certainly wouldn't be as awful as you might think. When prepared appropriately, of course. Nobody wants to eat raw swine manure as a condiment.

Really you'd want to send a few Hazda to live in Rome for a couple of months and send a few Italians the other way. It would be a good experiment - I'd watch the reality TV show.

A somewhat related and fascinating read is Dr Daniel Lieberman's "The Story of the Human Body: Evolution, Health, and Disease". He develops the concept of mismatch diseases and goes into a lot of details about evolution and diets across different eras and cultures (there's a part in the book dedicated to hunter-gatherers IIRC).

Somewhat related: presence or absence of diseases in an area may influence social and political systems, according to one theory (http://www.psmag.com/navigation/health-and-behavior/bugs-lik...)

Here's how to make a startup out of it: you could sell exclusive trips to Hollywood types to Africa to get a hunter-gatherer biome "transfusion", proclaiming the various health benefits - "slimming! rejuvinating! all natural!".

I think I'm joking, but who knows :-)

Stranger schemes have worked. Travelling to those sorts of places and eating with the locals often leads to effective and rapid weight loss thorough slightly unpleasant mechanisms. On a more serious note my sister had IBS for a couple of years and it went away completely and permanently after visiting Indonesia - presumably some gut flora transfer thing.

Gut flora-related disease could have also exerted pressure on an insulated population leading to tolerance for elevated levels of bacteria which are observed as being related to unwanted symptoms in other populations.

It takes more than a load of crap to tell the whole story.

I might show this to my mother. She is of the opinion that no disease is sufficiently severe that it cannot be cured through large quantities of probiotic yoghurt.

I wonder if there is any kind of feedback loop between long term gut flora makeup and taste preferences?

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