gut

09/06/2011 - 18:52

 I usually don't like to watch people speak about stuff. Maybe that's why I almost never went to lectures in college. I prefer to read things. As Data from Star Trek might say, I find it to be the most efficient form of assimilating information. So you can watch my talk on Vimeo thanks to AHS, but if you read much faster (or you are hearing impaired), you can read the transcript below, which was donated by Averbach Transcription, which is run by a paleo enthusiast and you should consider hiring him if you need a transcript:

 

"Clues from the colon: How this organ illuminates our digestive evolution and microniche" by Melissa McEwen from Ancestry on Vimeo.

Dynamic Evolution and The Gut

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  [applause] So, hi everyone. I was at Mat Lalonde's talk this morning, and I was thinking, "How am I going to introduce myself, what are my credentials?" And I don’t really have any. I have a degree in agriculture and I study anthropology currently at Columbia University, but I'm not in the Ph.D. program.
But I have had the pleasure to study with Professor Ralph Holloway, who's a really excellent physical anthropologist, and he inspired a lot of this presentation. And I have a website, it's called huntgatherlove.com, and you can visit it, and I have also a lot of the stuff from this presentation is there, and a lot of the references to the papers, if you want to read the original ones.

And yeah, I'm not a core scientist, but my boyfriend Chris is, and I try to study, you know, remind myself that chemistry and biology are really important even in anthropology, and I think a good physical anthropologist tries to really incorporate that into their studies.

What is so special about the human gut? Why do we care about it? Why don't we just eat like this nice ape in this picture on the left and just eat some healthy, high-fiber diet, which is low in fat? Just eat like a salad, because everyone knows that salad is really really healthy.

Well, the problem is we are not like gorillas; we're great apes, we have a shared history with gorillas, but we have our own unique niche. And I think when I'm reading a lot of the literature on evolutionary health, I'm seeing these different viewpoints. One I'm going to call statics, and it has an emphasis on what has been conserved from our evolutionary past from some time period, often which is defined somewhat arbitrarily.

And it also focuses on primate relatives such as gorillas. You know, we're great apes, they're great apes, we should eat like them maybe. And I think of course they have very interesting lessons, but I'm going to emphasize more the dynamic view of evolution, the emphasis on unique adaptations that humans have to their own niche, and our continuing evolution even now.

We're evolving as we speak.

So the static viewpoint is that the ancient human diet of some timespan, you know, Precambrian, Upper Paleolithic, was the optimal human diet. And there was a great deal of emphasis on the fossil record. Professor Holloway always likes to say, "When you look at the fossil record, sample size equals two, because there's not that many fossils from certain periods."

You know, we have part of a cranium and that's it of some periods. So it's pretty hard to abstract from the fossil record. And also emphasize related species that we share a common ancestor with. And a lot of times some of this research comes to the conclusion that a high-fiber diet consisting primarily of plants is optimal, and that everybody, every human being should be able to eat this way and be healthy.

There's a lot of Paleolithic Diet papers, but why not the Cambrian Diet? I mean that was a really long timespan, it was 52 million years versus like two and a half, and these creatures look perfectly healthy to me, and they seem way healthier than I am.

Here's a quote from Stephen Jay Gould that, I was a fan of Stephen Jay Gould for a long time, and I still admire him, but I don't agree with this quote, that, "There's been no biological change in humans for the past 40,000 or 50,000 years. Everything we call culture or civilization we built with the same body and brain."
And I thought Stephen Jay Gould was just this nice guy who talked about dinosaurs, but actually Professor Holloway told me that he has some questionable stuff in his research, and that idea that humans haven't changed for a long time is one of those. Another one is that he denies modern human variation quite strongly.
He has this idea that we're mostly the same, which in some ways is true; in some ways it's not true. And I think it denies the fact that we can gain a lot from looking at continuing evolution. And the dynamic view, which I'm going to talk more about, is humans are unique among the great apes, and recent human evolution has led to important changes, especially in digestion.

And besides our own genetics, we have the bacterial microbiome, and our evolution in that has been even more rapid, because bacteria have many more generations, they reproduce faster than we do. And there's high variation among modern humans, particularly with a growing population and introduction into new environments.

So there's probably high variability in [their optimal diet]. And a book that's been a big influence to me is "10,000-Year Explosion" by Gregory Cochrane and Henry Harpending, and it's, "How Civilization Accelerated Human Evolution." And it has pretty convincing evidence that human evolution not only didn't stop 10,000 years ago at the end of the Paleolithic; it's continued to accelerate greater and greater because of all this new environments and greater populations, and also the changes in culture and technology that have happened since then, which have been very rapid.

And in dynamism we have these four keystones I like to think about. One of them is our unique anatomy. Another one is our unique cultural behaviors. Another is our unique bacterial microbiome, which isn't shared with any other primate, and each person has a unique one. But also just in general a very high variability among humans.

And a lot of this is relatively unexplored because it's very controversial. It's hard to get funding. I've met people who do studies on human variability who can't publish them because they're so controversial.

And especially very important in unique cultural behaviors is a shift towards exogenous food processing. So in humans, in our evolutionary past, we processed food inside of ourselves, but in modern humans and in our evolution towards modern humans we have a shift towards processing food outside the body with cooking and grinding and soaking and all these other processes.

So when we're thinking about human evolution, we have to think of—this is an estimate of cells in the human body, and that there's maybe 10 trillion human cells and 100 trillion bacterial cells. And these bacteria are evolving faster than we are. And they're very very important.

They process nutrients, they produce nutrients, they fight off infections, are an important part of our immune system. They have a role in nearly every disease, even diseases you might not even expect, such as heart disease. There's a new paper that shows that metabolites produced by certain gut bacteria that some people have and some people don't have, in response to certain foods, can produce things that are implicated in heart disease.

And also, behavior. I mean, we can't do many of these studies in humans because they're unethical, but in fruit flies if you change the gut bacteria, you can change their sexual orientation. And you can understand why we can't do that experiment with humans; that wouldn't be good.

So there's several factors with these bacteria, and we have to think about interspecific competition—competition between different species, which is driving a lot of this evolution, intra-specific competition—so within even one species, you have tons of strains that are very different, and they're competing with each other, often in one person.

You can have several strains of one bacteria within you at one time. The host function, our own unique anatomy and genetics; our host fitness, which is quite important nowadays, now that a lot of people aren't as healthy as they once were. Particularly in the gut, there's a lot of people with dysfunctional gut permeability, which really affects the bacterial population.

You have food ingested by the host, and you have the metabolites themselves in microbiota, which is tons of different chemicals and fatty acids. And quite important for humans but not unique to humans is culture and technology. These can affect the gut microbiota too.

And there's a bunch of papers that are quite interesting that have more of a static view, and static's this view that we're going to look at other great apes and see what we should eat today. And I think a lot of this research is very admirable, but I think sometimes they come to conclusions that don't make sense in the light of our own unique anatomy.

One of them is Nutritional characteristics of wild primate foods: do the diets of our closest living relatives have lessons for us by talented primatologist Katharine Milton. Then you have this paper, "The Western Lowland Gorilla Diet, are there implications for health of humans. "

And here's a sample sentence from a paper like this, this paper is called "Case Closed: Diverculitis, Epidemiology and Fiber." It says, "The western lowland gorilla, whose diet may approximate a Paleolithic human diet, has an estimated intake of nearly 60% of its calories through the colon," and the second part of this sentence really puts a question mark on the first part:

You can see that this is quite interesting about gorillas. You know, they eat a diet very high in fiber, and it's all plants, pretty much, and they're getting a lot of carbohydrates in the diet, ingesting in their mouth. But then their colon, the bacteria in the colon is this giant bio-reactor. It's turning this carbohydrate, this fiber, this otherwise indigestible fiber into something called short-chain fatty acids.

And short-chain fatty acids are providing over 60% of calories for the gorilla. So the gorilla is eating a high-fat diet, actually; it's just not eating the fat directly. It's turning the carbohydrates that it's eating into fat, fatty acids.

And humans are quite different from other great apes. Here's a famous paper called "The Expensive-Tissue Hypothesis" by Aiello and Wheeler. You can see they did some linear regressions that looked at, based on other primates that we have data for, what should human organ weights look like?

And here's the expected human organ weights, and here's the observed. And what is different? Look how big our brain is and how small our gut is. But even within our gut, there's reorganization, and the reorganization, the driver of this is this food quality. And when I talk about food quality, I'm not talking about [Hardee's] versus Whole Foods; I'm talking about caloric density.

And with this high caloric density, there's less need for this processing equipment that's internal, these internal organs. And so energy is freed up for other organs, such as the brain, in this expensive-tissue hypothesis.

In this gut-brain tradeoff, you have higher diet quality, increased energy availability, and so larger brain. The small gut with the higher diet quality also frees up energy; larger brain. And more complex foraging behaviors, which keep enable… It's driving like a feedback cycle. You know, the more energy we're getting for our brain, the better—the bigger our brain is and the smaller our gut can get.

And you can see that the organization of the gut too, versus other primates—you have all these great apes here, and you have humans here, and look at the human small intestine; look how much bigger that is compared to the other great apes. And the colon is so much smaller. And you can see this in this chart from the Beyond Veg site, which is a great site.

You can see the chimpanzee has a quite long, well-developed colon. The orangutan does as well. But look at the human colon—it's very under-developed and small compared to these other apes. And we're not sure when this change happened in our evolutionary history. It's not like you can find frozen Paleolithic apes very easily.
But we do have this gut—in the post-cranial anatomy you have some indicators that might correspond to a smaller gut or a larger gut. And here is a chimpanzee here, a modern human here, and Australopithecus afarensis, living around maybe 2-3 million years ago, perhaps one of our ancestors.

And you can see this funnel shape in the ribcage, and a large pelvis, which could accommodate a bigger gut. And humans have this defined waist, which we also find very attractive in humans, and a smaller pelvis. And here's some of these apes stripped down, where you can see this giant gut in the gorilla, and the chimpanzee has a pretty bit gut, and an orangutan does.

Humans and gibbons do not. Gibbons are frugivores, so they eat a higher-quality diet than even the more leafy, kind of sticks and stuff that these other apes eat. And here's a human waist—very small compared to the other great apes, except for the gibbon.

And so in humans, how much do we get from short-chain fatty acids? How much do we get from the colon? The colon's smaller. And the human current maximum estimate is maybe nine percent from short-chain fatty acids. So if we go and eat a gorilla diet, we're not going to get as much out of it as the gorilla does.

We'll probably die if we just eat leaves because we can't turn it into short-chain fatty acids with the efficiency that a gorilla does. We don't have the equipment. But I must add a caveat to that. Most of these studies have been done in Westerners, and there's this new hypothesis floating around in papers, this idea that Westerners are the weirdest people in the world—and we are.

Our culture is totally different from most other cultures, and very unique in the history of the world. And so when we're taking data from Westerners, we have to be cautious, and we need more data from other cultures. Because as I say, humans have high variability. Maybe there are people who can get more short-chain fatty acids from fiber than the average Westerner.

And there's very few papers on this, but I found one from South Africa, and they look at autopsies of humans, and they found that some humans have different-shaped colons than other humans, and divided them up into three different kind of morphological types. Here is a short pelvic sigmoid colon, the so-called "classic type", and the long, narrow type.

And different people had different colons. And certain people, like Africans were more likely to have this colon type, and Indians and whites were more likely to have this smaller colon type. And whether or not this has implications for digestion, I don't know. And I think we really need to explore this, because if this colon is so much bigger, what kind of implications does this have?

Can this person get more energy from short-chain fatty acids? Is this person better adapted to a high-fiber diet? And you can see why this sort of research is controversial, because it also has data about different races. But it's very interesting to me. A lot of papers on this subject are not published in English journals at all; you have to read like Czech or something, so it's hard to track down. But it is out there.

What about the evidence that we see in some papers on the Paleolithic Diet, that Paleolithic humans ate 150 grams of fiber a day? I don't know anyone who eats that much fiber, and there's no known modern human culture that eats that much fiber. And most of those estimates are based on [coprolites], and the method for estimating that is quite questionable to me.

We also have to consider the cultural context. There are some good coprolites from hunter-gatherers in the Pecos Basin. But when you look at those coprolites
and the skulls they're associated with, not all Paleolithic or Stone Age or foraging humans are healthy. The Pecos Basin hunter-gatherers have high amounts of tooth decay.

And some anthropologists who study these skeletons say that these are caused by [tooth wear], but this Ota tribesman, he has extensive tooth wear, which is purposeful in this culture. They wear the teeth down to make them look like that, because it's considered beautiful, and they don't have high rates of tooth decay.

If you look at the Pecos Basin skulls, you'll find that they have really high rates of tooth decay. We need to look at whether or not there's impairment of calcium and vitamin D metabolism, and there's a lot of studies that show that really high-fiber diets can impair these. And unfortunately, some of these studies have come about because in places where the macrobiotic diet is popular—the macrobiotic diet, it idolizes high-fiber, particularly brown rice—and in England, in some communities that eat this macrobiotic diet, they're seeing a return of a disease that is associated with developing countries, which is rickets.

And it's infants on macrobiotic diets that have this. And I think there's an upper limit to fiber consumption that's way below some of these so-called Paleolithic accidents. But there's data you can see in some older papers, in particular data from modern hunter-gatherers, foraging people, like this bushman or the Hanza, and they see that these people eat a very high-fiber diet.

But if you look at the later papers, you really have to look at those because they realized that their method for measuring fiber was incorrect. And you can see, this is a very interesting thing. Here's from one of the papers where they're regretting that it was incorrect. And this is inedible material recovered after these Hanza tribe members were eating wild tubers.

They were sending, when they were doing the original fiber assay, they just sent the wild tubers to the lab and they were like, "Estimate the fiber of this," but as you can see here, these people don't eat all the fiber; they're chewing these tubers and spitting out this part of it. So just like you don't eat the tops of your bell peppers, I hope, or the peels of your bananas—although I did meet a raw vegan who was eating banana peels, [laughs]

So cultural evolution is important, and culture isn't even uniquely human. You can see this primate here, this chimpanzee, it's hard to see, but he's taking a leaf and chewing it, and then putting it in this tree that has a hole filled with water and then pulling it out and chewing on it again, and he's doing that to get water.
Humans have even more elaborate techniques. And one of these, of course, is cooking. And we don't know how old cooking is. I mean, you can ask every different anthropologist and they'll give you a different answer. But here we have sago palm starch processing—sego palm is, you know, they're eating a tree. It's not very edible.

Once you cook it, you pound it, and it's quite delicious. I mean it's bland, but it's good to eat; it provides starch for these people, which is very valuable to them. But we also should think about how is food being changed by cooking? It's increasing the food quality, it's increasing the amount of calories you can get from each amount of food.

But it's also really changing some of the nature, the chemical nature of the fibers. Different types of fiber feed different bacteria different ways. So that's very important. And you can look at markers for this. Here's a different kind of culture that a lot of people don’t think about—literal culture, cultured foods.
Fermented foods are universal in nearly every culture. And fermentation increases the bioavailability of protein and several micronutrients. It preserves food. It is a source of short-chain fatty acids. Perhaps it provides us with essential bacteria. Sadly, some fermented foods are in danger of dying out.

And here's an interesting chart—it's comparing the colonic fermentation, this inner fermentation, with exogenous fermentation in fermented foods. And fermented foods can play many of the same roles as colonic fermentation. And perhaps in our evolution as we're shifting towards eating more fermented foods, this was replacing, this exogenous processing was replacing some of the role of colonic fermentation and cooking provides all kinds of different micro-substrates, short chain fatty acids, bacteria, all kinds of metabolites, which also colonic bacteria provide…

They both modulate the system, actually, and there are studies that show fermented food has all kinds of strange effects that you wouldn't expect if it didn't have all these different weird bacteria in it and stuff—to help people lose weight and the way that non-cultured milk would, yogurt is very interesting.

And in terms of metabolites, here's a really interesting one: Butyric acid. It is produced by fiber. Research has focused on just the bulking properties of the fiber. So a lot of early people who wrote about fiber, they were going to Africa and seeing that a lot of different people who ate a very high-fiber diet didn't have the digestive diseases that Americans have.

And they were saying, "No, because it's because fiber is a bulking agent and it increases transit time, keeps toxins from spending a lot of time in the body." But after they were studying more, they found that there were people in Africa who didn't have these digestive disorders who weren't eating a lot of fiber. But what they were eating were other fermentable carbohydrates.

And so now research has shifted away from just fiber as bulking agent, and into seeing fiber more as food for bacteria, whether bad or good. Unfortunately, a lot of research in this area has focused more on fiber being a universal good, when actually it can also feed pathogenic bacteria.

And butyric acid is an interesting byproduct of some of these bacteria. People with colitis, Crohn's Disease, have low amounts of this butyric acid, and butyric acid is very important for modulating inflammation and all kinds of other processes too. They fed these mice the same diet, and the ones that had butyrate didn't gain weight, and the ones that did, that were fed butyrate gained weight. So, pretty interesting.

But you know, when you're thinking of fiber, often your doctors tell you eat more fiber, but different fiber has different effects. And now that we're thinking of fiber more as food for bacteria, you don't need to just think about fiber. And scientists are looking at more of these like resistant starch, for example, and other different complex polysaccharides and carbohydrates. You can see some types of resistant starch are produced by cooking.

Like if you cook potatoes and you leave them in the fridge, then that's resistant starch, and it's very good at producing butyrate. Some of these other fibers aren't so good at making butyrate. A lot of these fibers, a lot of doctors recommend, for example, wheat bran, and that's not even very good at increasing butyrate.
And I'm very sad that there's not a lot of research that is using a lot of these fibers that traditional foraging or horticultural societies eating. A lot of research uses synthetic fibers that's never been eaten before. And they're interesting, but I'd like to see more research on natural fibers.

But also, as humans have developed culture, we have exogenous butyric acid. A lot of people don't know this, but butyric is in the dairy fats and some of the fat under the skin of some animals, particularly cows, goats, sheep. There's a little in elephants too. And there's some in some fermented foods.

Like this is Ogi, it's a pretty delicious fermented food, although it's an acquired taste a bit. But it has some butyric acid. Most Western fermented foods don't have butyric acid because Westerners don't like the taste. If you have tasted skunked beer, you know the taste and you know why we don't like it.

So, it's incrappy traditional foods, you know, foods we don't really like from around the world. But there is one food that you will eat that has butyric acid, and that is butter. The butter is delicious and it has butyric acid. But we don't know whether or not this butyric acid has the same effect as butyric acid produced by colonic fermentation, there's not a lot of research on it.

This presentation's more about hunting hypotheses than presenting research. I'd love to see research on this; maybe I'll do it when I enroll in a program.
But also, not only do humans have all these differences from primates in terms of anatomy and our culture; we have different microbiomes in the gut. And this is a really great study because it looked at the gut biota of wild primates. Most of the other studies have been primates in labs. And you can see, even among these chimpanzees here, these chimpanzees are, some of them are quite geographically isolated from each other.

They have very different branches in the microbiota. They have different gut bacteria. Humans are here. But you can see, we need more data, especially since a lot of these unique cultures are dying out. We should try to collect gut bacteria from them before that, because, so we can get a real accurate reflection of human biodiversity.

And if you think about gut bacteria, it's very complicated because gut bacteria interact with each other, they interact with the metabolites of each other. You have all kinds of diversity among people. Like some people are methane excreters, and some people are not methane excreters. And scientists aren't sure why that is—if that's something that people acquire at a very young age, or if it's something that can be changed.

Methane excreters are quite unfortunate because when they have this bacteria, when it excretes methane, it smells quite bad. So if you're a smelly person, it's probably because you're a methane excreter. But there's just so many questions about why some people are like this and why some people aren't.

And there's so many different sources of gut variation: Cooking and food prep techniques, microbes in food, types of fiber in food, total fiber consumption. Most of us get most of our gut bacteria actually from our mothers, and when we're born, going through the birth canal, we're colonized.

But a lot of us didn't go through the birth canal. I was born by C-section, and C-section babies have different gut microbiota than non-C-section babies, and what is the impact of this? There's some preliminary evidence that C-section babies are more susceptible to certain digestive disorders.

Antibiotic use:antibiotics, if you take them, they can affect your gut microbiota for years. And there's some interactions with genes too. The real question is how plastic is our gut? How much can we change? As adults right now, if we eat differently now, can we really change our gut? Big question.

Here's a really interesting study. This is children in Burkina Faso; this is children in the EU. You can see, you have all these different species, and they differ between these two populations, in different amounts and different species. There are species here that you don't see here. It's interesting because they followed these children when they were breastfeeding, and they had kind of the same gut bacteria when they were breastfeeding.

But when they started eating solid food, their gut bacteria really differentiated. When does this plasticity end? Is it when a child eats its first food? Is that going to really affect the future of that microbiota? Can an adult do this? We suspect they're already there, but in smaller amounts when the infant was breastfeeding.
And then when the solid food was eaten, did it really differentiate based on the food or because of the population seeds planted at birth? We really need to do these studies while different cultures exist because all our multinational corporations are expanding into the developing world, and soon everybody's going to eat the same crappy diet, pretty much, and we won't have this diversity.

And here's the traditional diet of Burkina Faso, a lot of really high-fiber fermented grains. And the environment is very dry. Also, an interesting thing about gut bacteria: Genetic engineering's very controversial, but bacteria have been genetically engineering stuff for ages; it's called horizontal transfer.
A very interesting study looked at Japanese gut bacteria, and they found that some Japanese gut bacteria had species, they had some genes that the gut bacteria had taken from bacteria that live on seaweed, and these bacteria used to digest carbohydrates in seaweed. So these gut bacteria were able to steal these genes and digest these seaweed carbohydrates.

And only Japanese individuals have them, and even breastfed infants have them. So they've probably been in this population for a while. But it really brings it to highlight that our co-evolution with plants, how long have we been doing this? How many genes do we have that are from plant bacteria, for example?
What about the future? Now that we're genetically engineering plants, are we going to acquire some of that bacteria?

And we can use gut bacteria to track human migraation such as h. pylori. H. pylori's considered a pest in the United States because it's associated with some cancers, but actually in Africa, the African strain is not as pathogenic, it's not associated with these things. So these strains are diverse, and you can use their DNA, changes in the DNA to track h. pylori and human colonization of the world.

H. pylori's been with us for 100,000 years, they think. And right now, and most of us don't have it anymore because we tried to eradicate it. What is that doing to us? Did it have positive effects on us that now we've gotten rid of it? There's a lot of variation with it. And also h. pylori has—there's a lot of epigenetic switches that it turns on and off in response to diet.

And a lot of Westerners who do have h. pylori have two strains: They have the non-pathogenic strain and the pathogenic strain. And it's possible that diet can effect an overgrowth in this pathogenic strain. And perhaps the Western diet is taking this h. pylori and turning it into a monster.
But you know, when I'm looking at these different studies, what I said before about Westerners being weird, you really have to question what is normal. There's a hypothesis in anthropology that humans got their first meat and their first high-quality food from scavenging carcasses. It's controversial, though, because most of us don't have the equipment to process rotten meat, although I have met people in the Paleolithic community that are eating rotten meat, and they say they feel fine.

So, you know, that really begs the question if it's normal. And stomach acid, they is genetic variation in stomach acid, but also it's affected by h. pylori—different kinds of h. pylori can affect stomach acid in different ways. Your diet can affect stomach acid. Inflammation. Actually, we associate gastric cancers with the developed world, but actually there are certain types of cancer that are more common in developing nations, such as squamous cell carcinoma, and this is very common in Africa communities that just adopted corn as a staple crop.

And the theory is that, you know, this corn, this omega-6 excess in the diet increases prostaglandin E-2 and it increases inflammation, and that decreases the acidity of the stomach, and leads to heartburn, which is not treated in these developing nations, and then that leads to cancer. There's also an issue I realized studying carrion scavenging, that humans have high transit time variation.

You can feed two people the exact same diet and it'll go through their stomach in different times. And transit time, if you eat carrion, you want a high transit time, and that just varies between humans. An interesting [disease] that I found out about is called [pig bel], and it's people who are in Papua, New Guinea, many who are cultural foraging people, and they eat mainly a very low-protein diet.

They eat primarily tubers, like sweet potatoes and yams. And occasionally they get a pig, and they're very excited about this pig. So they eat it all really quickly. And they get this thing called clostridial necrotizing enteritis. And if I ate this meat, I wouldn't get this, but because they don't eat meat very much, they have low amounts of protease in their gut, so they can't destroy the toxins made by this and can't digest this meat properly.

And it kills some children in these cultures. So, you know, what you eat can affect the different enzymes in your gut too.
And also, the also case of this in a Western individual was a vegetarian who was living in Samoa, and they ate some fish because they were training for a marathon, and they got this disease.

So the point of my talk is that humans are truly unique, and we're not really sure how we got this way, so I'm hunting hypotheses. And within our population diversity is waiting to be discovered. And I'm really worried about loss of biodiversity in cultural adaptations, and what the implications for this are when we're trying to study and trying to flesh out our human history.

When we don't have very much biodiversity to work with, it'll be harder, I think.

And you know, I think the key is balance. I very much admire some of these models that are looking towards the past, and looking at our primate relatives. But also I'm really excited about plant adaptations, new technology and new mutations in human and microbiota DNA.

I think we have to look at both of these things when we're looking at, you know, looking for the best diet for humans. But it also, you know, we often wonder—I have an uncle who's been a vegan for a long time and he's very healthy, and he says, "I've been a vegan for 30 years," and I was a vegan for only a short time and I felt awful.

And we're related to each other, but there's probably some difference in our microbiota or our genes that make him better adapted to this diet than I was. So it gives a new viewpoint on why do some people do better on one diet or another?

So I'd like to thank Ralph Holloway, Chris Masterjohn, Stephan Guyenet and John Speth. They've really helped out. So thank you.
[applause]
Male Voice: So you would say that your main point is that the diversity of humans is under-appreciated and the difference between people is under-appreciated? Is that fair?
Melissa: Yeah. That people are very different from each other, and will thrive on different diets.

Male Voice: I was struck by a thing you said about most of the gut bacteria comes from your mother when you're born. I was wondering what the implications are for celiac, whether that can spread celiac disease.
Melissa: Yeah. I think a lot of celiac research has focused maybe too much on our own genome, what we share, that there's genes that make us susceptible to celiac. But there's also probably gut bacteria that make us susceptible to celiac, and genes within our gut bacteria. So I think that'll be a future avenue of research in the future.
Male Voice: I was wondering about [unintelligible] research on doctor [unintelligible] work? He looked at the microbiota and found that people have different communities, three communities of microbiota.
Melissa: Oh yeah, I saw that. But they're not sure what the implications of that are. They couldn't connect it with anything, like obesity or any diseases yet. But it's very interesting. They found that some people have very specific—that they divide Westerners, at least, into three specific groups of dominant bacterias. And it was fascinating, but I'm really excited to see what that doctor comes up with.
[applause]
 

05/21/2011 - 10:39

The following presents data that gasp...people might be different and those differences might correspond to ethnic groups/"races." I would note that research in this area is scant because funding is hard to come by since it's so controversial. I know American researchers who have gotten funded for this research though and then have been pressured to suppress their results. Either way, it's important to identify the specific causes (genes, diet, environment, etc.) of such variation when applying it to health since often such characteristics aren't exclusive to one group, but merely of a different frequency

Some humans may be better at fermenting than others. Recent studies of human gut variation have revealed possible genetic variations as well as those caused by environment and lifestyle. There have been a few studies of human gut anatomical variation, but more are needed. One of the most interesting comes from South Africa, where researchers examined the colons in 590 cadavers (Madiba & Haffajee, 2011a). They found significant variation in colon morphology and made the decision to classify colons into three types based on anatomical differences. Classic was the normal shape in typical anatomy book. The long-narrow was longer and had a redundant long sigmoid flexure between the descending colon and rectum with narrow mesocolon root. The long-broad type also had a redundant long sigmoid flexture, but the mesentery was broader and the limbs of the loop for further apart.

 

The study found that Africans were more likely to have the long-narrow type and the least likely to have the classic type. Indians and whites were more likely to have the classic type and less likely to have the long-narrow type.

Are these differences a result of genes or environment? It is hard to tease out in the moment. There are a few animal studies showing gut size can be affected by diet, but none in humans. (Topping et al., 1997). The authors of the autopsy study noted that the difference was also found in children and that unlike in other animals, including the other great apes, human colons are not known to enlarge with age. (Madiba & Haffajee, 2011b). A limit to this particular study was that “African” represents the most genetically diverse population on Earth. Some preliminary work in Uganda showed that colon size varies between different African tribes, with the Baganda having larger colons than the other tribes studied (Katsarski & Singh, 1977). There is a strong possibility that colonic variation is connected with adaptations to diet and ongoing evolution of the digestive tract. The digestive implications of these anatomical differences remains to be studied, but there is a strong possibility the colon has continued to decrease in size in populations less and less reliant on colonic fermentation for nutrients and more and more able to acquire high-quality food.

It is also possible that gut size calculations based on a broader population would alter the equations Aiello and Wheeler used in the Expensive Tissue Hypothesis, either reducing the trade-off between brain and gut or finding that the tradeoff is present and variable between human populations. More study is needed on the matter, but it underscores the major importance of the colon in human evolution. The colon’s microbiome and anatomy hold much promise in illuminating our evolutionary past and teaching us about the importance of a healthy colon for overall health. Current data suggests the colon may be more variable in our species than previously thought, calling into question whether the representative colon used in medical and scientific textbooks and anatomy studies represents recent adaptations. Clues point to the adaptations being related to both the type and amount of fiber, as well as dietary constituents like butyrate.

Katsarski, M., & Singh, U. (1977). [Anatomical characteristics of the sigmoid intestine and their relationship to sigmoid volvulus among the population of Uganda and the city of Plovdiv, Bulgaria]. Khirurgiia, 30(2), 159-63. Retrieved May 10, 2011, from http://www.ncbi.nlm.nih.gov/pubmed/916568.


Madiba, T. E., & Haffajee, M. R. (2011b). Sigmoid colon morphology in the population groups of Durban, South Africa, with special reference to sigmoid volvulus. Clinical anatomy (New York, N.Y.), 24(4), 441-53. doi: 10.1002/ca.21100.


Topping, D. L., Gooden, J. M., Brown, I. L., Biebrick, D. A., McGrath, L., Trimble, R. P., et al. (1997). A High Amylose (Amylomaize) Starch Raises Proximal Large Bowel Starch and Increases Colon Length in Pigs. J. Nutr., 127(4), 615-622. Retrieved May 9, 2011, from http://jn.nutrition.org/cgi/content/abstract/127/4/615.

 

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05/20/2011 - 14:55

 Another hypothesis is that lack of SCFAs is behind such diseases of civilization. A SCFA called butyrate provides some insight into this. Butyrate is the preferred fuel of the colonic epithelial cells and also plays a major role in the regulation of cell proliferation and differentiation (Wong, de Souza, Kendall, Emam, & D. J. a Jenkins, 2006). Lower than normal levels have been found in patients with several diseases, notably types of colitis and inflammatory bowel disorder. Studies show such diseases can be treated through application of butyrate in the colon. That and the fact that some studies show complete remission through bacteriotherapy transplants point to these diseases being caused by disturbed populations of gut bacteria. Interestingly, these diseases are common in captive populations of apes and unheard of in wild apes (McKenna et al., 2008).

Bacteria affect butyrate production, but so do dietary inputs. Certain fibers produce more butyrate than others in humans, whether or not this differs between primates would be an interesting avenue of research (Smith, Yokoyama, & German, 1998).

Figure 1: Butyrate production in response to fiber

Interestingly, one of the top producers is something known as “resistant starch.” Resistant starch represents the growing nuance in understanding of fiber, since it is a starch that acts like a fiber in terms of acting as a bacterial substrate. It first showed up on the scientific radar when scientists found that low rates of colon cancer were not just found in populations with high-fiber diets, but those with high-starch diets (O'Keefe, Kidd, Espitalier-Noel, & Owira, 1999)1. Researchers found that a particular starch resisted digestion and ended up being fermented by colonic flora. They called this resistant starch and it is found mostly in cooked starches, some raw starches like green bananas, and some rough unprocessed grains and seeds. The former is termed type III and is a major part of the diets of many foraging populations who consume pounded and cooked starches like cassava, taro, true yam, and sago palm.

Whether or not humans are better adapted to certain types of resistant starch remains unexplored, but could account from some inconsistent results in studies that used type I resistant starch, mostly found in grains and seeds that would have probably been relatively uncommon in our ancestral diet. These studies have shown poor results and others with promising results are marred by high drop out rates due to unpleasant gastrointestinal side effects (Rinne et al., 2005; de Vrese & Marteau, 2007; Vuksan et al., 2007). Whether some populations would do better on this type of starch versus others would be an interesting investigation, but very few cultures consume large amounts of unmilled seeds and grains.

What type of starch we are best adapted to is interesting because the role of starch in human evolution is so controversial. Richard Wrangham has suggested that utilization of cooked starches was one of the dietary quality innovations that fed our rapidly expanding expensive brain tissue as it evolved towards hominid size (Wrangham, 2003). Recent analysis throws a wrench in that theory because it suggests habitual use of fire came after encephalization, about 300,000 years ago (Roebroeks & Villa, 2011). However, this does not mean that such cooked starches did not change humans, even if it reduces their significance in human evolution.

The burgeoning field of archeological starch grain analysis has transformed our view of hominids once thought to be mostly carnivorous. Microfossils on Neanderthal teeth from around 44,000 years ago show evidence of the consumption of many roots and tubers, some of which show evidence of cooking (Henry, Brooks, & Piperno, 2010). The full impact of the adoption of cooked starches on the human body has not been fully elucidated. One promising adaptation is the starch-digesting salivary amalyse gene, AMY 1 (Perry et al., 2007). Chimpanzees and bonobos have only two copies of this gene, humans have as many as 10 copies, though it varies quite heavily by population from 2 to 10 correlated with the importance of starch in the diet. Molecular genetic evidence places the origin of divergence on this gene at about 200,000 years, about the time when habitual fire use became common. Further genetic analysis shows that adaptations to root and tuber starch as a major source of calories may account for variation in human folic acid metabolism, since folic acid is usually low in starchy vegetables (Hancock et al., 2010).

Another relatively unexplored avenue of research would be whether butyrate in the diet itself has led to decreased reliance on butyrate for colonic fermentation in some cultures that consume large amounts of dietary butyrate. The major source of butyrate in food is from the milk fats of grazing animals (Smith et al., 1998).

It is most common in the modern diet in butter at 3%. It is possible that pastoral cultures consume substantial amounts of exogenous butyrate. Currently there have been few studies on oral consumption of butyrate in humans. Animal studies have been inconclusive, with some showing positive effects and some showing negative effects, which is complicated by the fact that if ingested orally it is also present in the small intestine, where it may play different roles (Sengupta, Muir, & Gibson, 2006; Wächtershäuser & Stein, 2000). A small study found orally-administered butyrate had a positive effect on symptoms of Crohn’s disease, but the method of administration was through pills rather than food (Di Sabatino et al., 2005).

Another potential source of butyrate is fermented foods. Some fermented foods like ogi, a pounded fermented starch, contain measurable levels (Hesseltine, 1979). Fermented foods are worth examining evolutionarily because they represent another human dietary innovation in improving food quality. Fermentation increases the bioavailability of nutrients, breaks down starches, and reduces levels of anti-nutritional factors and toxins (Mugula, 2003). It is unknown how long humans have been purposefully fermenting food. Fermentation naturally occurs in the wild and many wild animals are known to indulge in such foods to the point of drunkenness (Dudley, 2002). Spontaneous fermentation and consumption of such foods by wild primates is unfortunately not well studied. However, fermentation is practiced by almost every known culture to some extent, with the largest diversity in fermented foods among African farmers (Dirar, 1993) It is estimated that fermented foods make up 1/3 of the diet of humans worldwide (van Hylckama Vlieg, Veiga, Zhang, Derrien, & Zhao, 2011). Exogenous fermentation may substitute for the reduced fermentative ability of the human gut.
 

1. The researchers concluded that colon cancer risk was increased with meat consumption. I will remain skeptical until they do studies on other cultures that eat relatively low-fiber and high-meat diets like the Masai and Siberian cultures for example.


Di Sabatino, A., Morera, R., Ciccocioppo, R., Cazzola, P., Gotti, S., Tinozzi, F. P., et al. (2005). Oral butyrate for mildly to moderately active Crohnʼs disease. Alimentary pharmacology & therapeutics, 22(9), 789-94. doi: 10.1111/j.1365-2036.2005.02639.x.


Dirar, H. A. (1993). The indigenous fermented foods of the Sudan: a study in African food and ... (p. 552). CAB International. Retrieved May 9, 2011, from http://books.google.com/books?id=J-ogAQAAIAAJ&pgis=1.


Dudley, R. (2002). Fermenting fruit and the historical ecology of ethanol ingestion: is alcoholism in modern humans an evolutionary hangover? Addiction (Abingdon, England), 97(4), 381-8. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11964055.


Hancock, A. M., Witonsky, D. B., Ehler, E., Alkorta-Aranburu, G., Beall, C., Gebremedhin, A., et al. (2010). In Light of Evolution IV: The Human Conditions Sackler Colloquium: Human adaptations to diet, subsistence, and ecoregion are due to subtle shifts in allele frequency. Proceedings of the National Academy of Sciences of the United States of America, 107(Supplement_2), 8924-8930. doi: 10.1073/pnas.0914625107.


Henry, A. G., Brooks, A. S., & Piperno, D. R. (2010). Microfossils in calculus demonstrate consumption of plants and cooked foods in Neanderthal diets (Shanidar III, Iraq; Spy I and II, Belgium). Proceedings of the National Academy of Sciences of the United States of America, 1-6. doi: 10.1073/pnas.1016868108.
Hesseltine, C. W. (1979). Some important fermented foods of Mid-Asia, the Middle East, and Africa. Journal of the American Oil Chemists’ Society, 56(3), 367-374. Springer Berlin / Heidelberg. doi: 10.1007/BF02671501.


Hylckama Vlieg, J. E. van, Veiga, P., Zhang, C., Derrien, M., & Zhao, L. (2011). Impact of microbial transformation of food on health-from fermented foods to fermentation in the gastro-intestinal tract. Current opinion in biotechnology, 22(2), 219-211. doi: 10.1016/j.copbio.2010.12.004.


McKenna, P., Hoffmann, C., Minkah, N., Aye, P. P., Lackner, A., Liu, Z., et al. (2008). The macaque gut microbiome in health, lentiviral infection, and chronic enterocolitis. PLoS pathogens, 4(2), e20. doi: 10.1371/journal.ppat.0040020.


Mugula, J. (2003). Microbiological and fermentation characteristics of togwa, a Tanzanian fermented food. International Journal of Food Microbiology, 80(3), 187-199. doi: 10.1016/S0168-1605(02)00141-1.


OʼKeefe, S. J., Kidd, M., Espitalier-Noel, G., & Owira, P. (1999). Rarity of colon cancer in Africans is associated with low animal product consumption, not fiber. The American journal of gastroenterology, 94(5), 1373-80. doi: 10.1111/j.1572-0241.1999.01089.x.


Perry, G. H., Dominy, N. J., Claw, K. G., Lee, A. S., Fiegler, H., Redon, R., et al. (2007). Diet and the evolution of human amylase gene copy number variation. Nature genetics, 39(10), 1256-60. doi: 10.1038/ng2123.


Rinne, M. M., Gueimonde, M., Kalliomäki, M., Hoppu, U., Salminen, S. J., & Isolauri, E. (2005). Similar bifidogenic effects of prebiotic-supplemented partially hydrolyzed infant formula and breastfeeding on infant gut microbiota. FEMS immunology and medical microbiology, 43(1), 59-65. doi: 10.1016/j.femsim.2004.07.005.


Roebroeks, W., & Villa, P. (2011). On the earliest evidence for habitual use of fire in Europe. Proceedings of the National Academy of Sciences of the United States of America, 1018116108-. doi: 10.1073/pnas.1018116108.


Sengupta, S., Muir, J. G., & Gibson, P. R. (2006). Does butyrate protect from colorectal cancer? Journal of gastroenterology and hepatology, 21(1 Pt 2), 209-18. doi: 10.1111/j.1440-1746.2006.04213.x.


Smith, J., Yokoyama, W., & German, J. B. (1998). Butyric Acid from the Diet: Actions at the Level of Gene Expression. Critical Reviews in Food Science and Nutrition, 38(4), 259-297. doi: 10.1080/10408699891274200.


Vrese, M. de, & Marteau, P. R. (2007). Probiotics and Prebiotics: Effects on Diarrhea. J. Nutr., 137(3), 803S-811. Retrieved May 9, 2011, from http://jn.nutrition.org/cgi/content/abstract/137/3/803S.


Vuksan, V., Whitham, D., Sievenpiper, J. L., Jenkins, A. L., Rogovik, A. L., Bazinet, R. P., et al. (2007). Supplementation of conventional therapy with the novel grain Salba (Salvia hispanica L.) improves major and emerging cardiovascular risk factors in type 2 diabetes: results of a randomized controlled trial. Diabetes care, 30(11), 2804-10. doi: 10.2337/dc07-1144.


Wong, J. M. W., Souza, R. de, Kendall, C. W. C., Emam, A., & Jenkins, D. J. a. (2006). Colonic health: fermentation and short chain fatty acids. Journal of clinical gastroenterology, 40(3), 235-43. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/16633129.


Wrangham, R. (2003). “Cooking as a biological trait.” Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, 136(1), 35-46. doi: 10.1016/S1095-6433(03)00020-5.


Wächtershäuser, a, & Stein, J. (2000). Rationale for the luminal provision of butyrate in intestinal diseases. European journal of nutrition, 39(4), 164-71. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/11079736.

 

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05/17/2011 - 20:39

 This will be one of the few series posts I'll actually finish since it's already written :) I'd like to thank Stephan Guyenet, Chris Masterjohn, and Professor Holloway for their tips, critiques, and inspiration! I welcome more such educated thoughts in the comments. Full disclosure: yes, I did write this for a class, but I thought some people might enjoy it and then I could also kill two birds with one stone. Haha. 

In 1995, anthropologists Leslie C. Aiello and Peter Wheeler published a paper on a theory they termed The Expensive Tissue Hypothesis (ETH). Expensive refers to our brain tissue, which is uniquely metabolically demanding compared to other primate brains (Aiello & Wheeler, 1995). However, our total metabolic rate is close to what would be predicted for a primate our size, so according to the ETH, humans compensated for the increased metabolic costs of the brain by evolving less metabolically expensive splanchnic organs, which include the gut and liver. Humans were able to fuel their large brains using only a relatively small gut because increased dietary quality reduced the need for gut mass. The hypothesis was that the main driver of this increased dietary quality was the increased use of animal products.

Aiello and Wheeler

This hypothesis rests on assuming that reduced gut size coincided with the major jump in encephalization experienced by hominids millions of years ago. In their calculations, Aiello and Wheeler used the modern human gut to demonstrate its uniquely small size. Unfortunately, using the modern human gut as a hallmark has some problems, as there is some evidence that it has been reduced in size due to dietary innovations that may have taken place long after encephalization and since these innovations it has possibly continued to evolve. The trend in human innovation has been towards a diet of increased quality and this innovation continues even today. In response to these dietary changes, the human population shows variation in dietary adaptations. The reorganization and variation of the human colon provides important clues about this process.

Exactly how unusual is the modern human gut? Based on a reduced major axis equation computed for higher primates, the human gut should be about 781 grams larger (Aiello & Wheeler, 1995).

It is hard to know when this change started, as guts do not fossilize nor do they leave their impressions as brains do in endocasts. However, it is possible to infer some information from post-cranial anatomy. Living apes with big guts have protuberant abdomens to accommodate them.

Skeletally, they have a rounded abdomen continuous with the lower portion of the rib cage, giving it a funnel shape, as well as a wide pelvis with flared upper margins. In the fossil record we can see that Australopithecus afarensis had skeleton anatomy that would indicate a large gut if this pattern holds.

Figure 3: Chimpanzee, human, and Australopithecus afarensis, from Aiello and Wheeler

In contrast, the human pelvis size is reduced and the abdomen has a defined waist region. Hominids start exhibiting this in the fossil record starting with Homo erectus, about 1.5 million years ago. However, there is some evidence that this anatomical change may not have to do with gut size. For one, it is not entirely a consistent pattern among hominids. Reconstructions of a post-cranial Neanderthal skeleton based on the 70,000 year old La Ferrassie 1 and 60,000 year old Kebara 2 specimens shows a wider trunk showing up again (Sawyer & Maley, 2005).

It is possible that the trunk and pelvis size represented adaptations to cold, a type of hunting, or some other lifestyle variable (Bramble & Lieberman, 2004). Until more data is collected and analyzed tying post-cranial anatomy to gut mass, it is hard to tell if the inference is valid.

In response to the ETH paper in 1995, Katherine Milton questioned whether the data presented was really representative of our species. She stated that our guts may have played a larger role before the relatively recent invention of agriculture when fiber consumption was much greater and our guts might have been larger then because of “gut plasticity.” She mentioned that what really sets us apart from our primate relatives is the reorganization of the gut morphologically rather than the size.

In humans compared to primates, the gut is reorganized. The size of the colon is much reduced and the size of the small intestine is increased. The human colon takes up 17-23% of the digestive tract. In chimpanzees, orangutans, and gorillas it occupies 52-54%. Instead of a large colon, humans have a small intestine that represents 56-67% of the gut (Milton, 1989).

from Milton

These are important to note because of their role in digesting food. The small intestine is where primate enzymes digest and absorb nutrients immediately available in food. In contrast, the colon can be thought of as a bioreactor, where bacteria digest otherwise useless dietary constituents into important nutrients and other chemical byproducts. These include short-chain fatty acids (SCFA), organic fatty acids with 1-6 carbon atoms created by the fermentation of polysaccharides, oligosaccharides, protein, peptides, and glycoprotein precursors in the colon. The major source of these in primates is through the fermentation of fiber and some types of starch. The major difference in this matter between humans and the other great apes is that apes such as the gorilla are able to use their larger colons to obtain as much as 60% of their caloric intake from SCFA alone (Popovich et al., 1997). Upper estimates for human caloric use of SCFA range from seven to nine percent. (McNeil, 1984).

Figure 6: The contribution of SCFA to metabolism in gorillas from Popovich, et al.

Aiello, L. C., & Wheeler, P. (1995). The Expensive-Tissue Hypothesis: The Brain and the Digestive System in Human and Primate Evolution. Current Anthropology, 36(2), 199. doi: 10.1086/204350.

Bramble, D. M., & Lieberman, D. E. (2004). Endurance running and the evolution of Homo. Nature, 432(7015), 345-52. Nature Publishing Group. doi: 10.1038/nature03052.

McNeil, N. (1984). The contribution of the large intestine to energy supplies in man. Am J Clin Nutr, 39(2), 338-342. Retrieved May 2, 2011, from http://www.ajcn.org/cgi/content/abstract/39/2/338.

Milton, K. (1989). Primate diets and gut morphology: implications for hominid evolution. In M. Harris & E. B. Ross (Eds.), Food and Evolution: Toward a Theory of Human Food Habits (p. 93). Temple University Press. Retrieved May 8, 2011, from http://books.google.com/books?hl=en&lr=&id=xHYxSHr86T8C&pgis=1.

Popovich, D. G., Jenkins, D. J. A., Kendall, C. W. C., Dierenfeld, E. S., Carroll, R. W., Tariq, N., et al. (1997). The Western Lowland Gorilla Diet Has Implications for the Health of Humans and Other Hominoids. J. Nutr., 127(10), 2000-2005. Retrieved April 28, 2011, from http://jn.nutrition.org/cgi/content/abstract/127/10/2000.

Sawyer, G. J., & Maley, B. (2005). Neanderthal reconstructed. Anatomical record. Part B, New anatomist, 283(1), 23-31. doi: 10.1002/ar.b.20057.
 

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03/20/2011 - 18:42

 Mark Sisson posted a link to a sad essay called IBS Is Why I'm Still Single. Every day I'm able to eat and live normally, I am so grateful. You see, most of my life I had painful stomach problems. When I was four I remember crying in the bathroom. I remember at sleep away camp being too embarrassed to use the communal bathrooms and sneaking out in the middle of the night to the isolated outhouse. It wasn't until I was 15 or so that I was diagnosed with IBS. When I was a freshman in college it became so disruptive to my life that I was finally given Librax. At that point I was also on quite a bit of asthma medication. Then I started having serious heartburn. I went on proton pump inhibitors. At my low point I was on Allergra, Advair, Singulair, Albuterol, Librax, Nexium (Prilosec stopped working at some point), and continuously on and off antibiotics for various ailments ranging from yeast to sinus infections. I was miserable. I missed most of my classes. 

The single part of that essay hit home because I remember my first Valentine's day with my first boyfriend. We had a delicious meal, but soon after I was bent double with incredible pain and spent most of the night in the bathroom. I didn't think I'd be able to do anything. 

I honestly thought that my condition was caused by eating fat, tomatoes, and peppers. The handouts my doctor gave me insinuated as much. I really didn't like all the side effects of the medications I was on, but when I complained to one of my doctors he said I'd on them for the rest of my life. I tried all kinds of high-fiber low-fat veg*n diets to no avail. 

I didn't want to live like this. But all the sudden my condition took a turn for the worst. I felt like my whole body was falling apart. One day I collapsed in the hallway of the dorm. I was diagnosed at the hospital with chronic salmonella. That's not something a 19 year old should have. Afterwards I had trouble with constant burping.

I vowed to do more research and found a small study on GERD and low carbohydrate diets. I also discovered Evolutionary Nutrition on Art De Vany's site through the blog Marginal Revolution. I learned about the Specific Carbohydrate Diet and wondered if my symptoms were caused by bacterial overgrowth. My first attempts to get off my medicines didn't work. I tried to eat low-carb in the dining hall, but I guess the foods had too much crap on them. Luckily, I took summer school and lived dining-hall free in graduate student housing, though my "kitchen" had only a microwave. Looking back, my diet wasn't all that great. I didn't know that much about cooking and nothing about meat. The first meat I bought was some sausage, which I tried to cook in the microwave only to get a massive bowl of exploding grease. Gross. I had to eat out a lot, but stayed mostly paleo and very low carb. I tried lots of remedies like probiotics and drinking apple cider vinegar after each meal. I started drinking kombucha. I read everything I could get my hands on about traditional nutrition. It seemed clear my illness was a modern disease. 

I had a goal in mind: as a freshman I had tried spicy food for the first time and learned to love it, but I had thought it was causing all my problems. When it was clear that this was a secondary problem to the inflammation and dysbiosis, I decided to make eating it without pain a goal. I didn't reach that goal until six months into the regimen, but I've been eating delicious curries without incident ever since. 

I've also been able to travel extensively without incident, something I thought I'd never do. 

Unfortunately I still had some residual IBS issues. I realized a year ago that I was going to have to let go of beer and gluten-containing cheat meals. The IBS has been gone ever since, but I really do miss some of those foods. 

So basically the principals I went on were that bacteria was at the root of most of my problems. Being born by C-section, a low-nutrient diet, and constant antibiotic use had put my gut ecology into an imbalanced state. Probably some of my medications made it worse, like Prilosec/Nexium, which is known to allow bacterial overgrowth. My principles were to first starve out the bad bacteria, which was inspired a bit by Hyperlipid, and then gradually try to balance the gut through gentle traditional probiotic and nutrient-rich foods. I suspect I had both hypochlorhydria and small-bacterial overgrowth, which was why I was so excited by the paper I just blogged about

I'm still quite fiber-intolerant. I can't really do brown rice, quinoa, or many other fiber-rich grains. But I am able to eat a fair amount of carbs, which I'm happy with. As an aside, even some in the alternative health community are very wrong about IBS. Giving up simple sugar will do nothing, as they are digested in the small intestine, which is a point made by the SCD diet. It's the complex sugars that cause the problems in the lower intestine. 

As for romance, duh it's easier when you aren't a miserable gas-filled bloated cramped up woman who alternates between diarrhea and constipation (with hemorrhoids) every two days... 

So when people say paleo or traditional foods are trivial, I'm just happy I can live a relatively normal life thanks to them. So I thank these things for my good health

  • High fat
  • Low carb
  • Probiotics
  • Acidic foods like pickles, kombucha, and apple cider vinegar that helped make up for my low stomach acid
  • Traditional foods
  • Grass-fed meat
  • Gluten-free

03/11/2011 - 21:38

 When I was a child I was obsessed with several things, but two of them were Motown Oldies and aliens. I also had a bad habit of hearing things rather strangely. A good example would be the song "It's in his kiss" by Betty Everett. For quite some time I thought it was actually "It's in his skin." Since I was also into aliens I kept thinking about would would be in his skin besides baby aliens? I must have seen that scene from Alien when my mother wasn't looking...

Today I found a paper that is about how your skin isn't just a reflection of whether or not aliens are gestating within you, but whether you have a healthy gut. This paper has almost all of the real food/paleo blogospheres interests: probiotics, cod liver oil, leaky gut, acne, stomach flora, depression, and aliens. Just kidding about the aliens. Unless you consider our gut flora aliens...who knows?

Acne vulgaris, probiotics and the gut-brain-skin axis - back to the future?

Either way, the authors have put together many interesting puzzle pieces to lend support to the idea that the bacteria in your gut are connected to the condition of your skin and your mood. 

So first there is the association. I bet you are thinking that "of course people with acne aren't happy because acne sucks." But there are a lot of other medical conditions that probably suck more like epilepsy and diabetes. Mental health impairment scores, a measurement of distress, are higher for acne sufferers than from people with these conditions and many other unpleasant illnesses. The gut connection has also been documented, for example in a student of 13,000 adolescents that found that people with acne were more likely to experience stomach problems, in particular abdominal bloating. These and other studies are shining a light on this connection, but it has been theorized for a very long time. The authors of this paper particularly pay homage to a 1930 paper by dermatologists John H. Stokes and Donald M. Pillsbury that contained this hypothesis. 

I would like to get ahold of this paper and have requested it at school. One of the main reasons is it apparently contains evidence that many people with acne have low stomach acid AKA hypochlorhydria. The idea that many people have a sub-clinical form of condition is popular in alternative health circles and I've looked for evidence for some time and it seems to be poorly studied. 

Also, 80 years ago these dermatologists were thinking about stress altering gut bacteria and this leading to leaky gut (abnormal intestinal permeability)!! Whoa. These doctors were ahead of their time.

The lack of research into stomach acid in otherwise "healthy" people is unfortunate, but the growth of heartburn in America has given us some research that we can make some inferences with. For example, half of people on proton pump inhibitors, a heartburn medicine that gives you low stomach acid on purpose, have small intestinal bacterial overgrowth. Wow, I'm so glad I got off those...SIBO is connected with leaky gut pretty well in the medical literature.

 SIBO has also been connected with depression. Most research needs to be done on specifically connecting acne to SIBO, but it's clearly something to investigate. 

Studies found that people with acne have circulating endotoxins from gut bacteria in their blood, which healthy controls did not have. These endotoxins belong in the gut, not in the blood and it's likely they got there through abnormal intestinal permeability. Eventually the body develops reactions to these toxins, which have been connected to depression and anxiety. 

 There is also evidence that decreased digestive transit time can be caused by stress and this increased time can lead to bacterial overgrowth as well. Constipation has been connected to acne in several studies. Other studies showed that people suffering from constipation have low levels of good bacteria. 

So what did they do about this issue in 1930? Their prescription was for fermented milk and cod liver oil...sounds kind of Weston A. Price-ish huh? But wait! Doesn't dairy CAUSE acne? Well Cordain and other paleo authors who have made that connection have rightfully said that dairy contains IGF-1, which IS connected to acne. BUT fermentation reduces this 4-fold. And studies on dairy and acne show the connection doesn't hold for fermented dairy. Dairy also contains the anti-inflammatory protein lactoferrin, which has shown to decrease acne. 

A Russian study showed that drinking milk fermented with lactobactillus reduced acne and an Italian study showed that a probiotic with freeze-dried L. acidophilus and B. bifidum did the same. Saccharomyces cerevisiae has been found to improve both acne and constipation, as well as to improve the integrity of the gut lining. Surely more studies need to be done, but it sounds promising. 

Interestingly probiotics might also help with depression. One study found that depression patients had low levels of lactobactillus. Some other studies have shown depression can respond positively to probiotic treatment. Why? They have been found to increase tryptophan levels, alter serotonin and dopamine turnover (those are the neurotransmitters that antidepressants alter), decrease negative response to stress, increase omega-3 tissue levels, decrease internal lipid oxidation and other good stuff. Unfortunately some of these studies were on mice, so we need more human studies. But there have been a few studies in humans and they have shown positive effects. 

The authors of the paper make a valuable point which is that in many folk health theories there is a focus on things rotting in the gut which causes constipation which causes all manner of problems. Usually the thing they blame is meat. This has led to way too much focus on what ends up being a symptom which is ironically caused by things not rotting in your gut. But rotting is kind of a mean term for the valuable services that gut bacteria perform. They will rot your body, but that happens AFTER you die...

This research is especially important because common treatments for acne include some seriously harsh drugs with terrible side effects, as well as antibiotics, which might end up making other problems worse since they decrease all bacteria instead of improving the gut ecology. 

Isn't it crazy that little tiny weird bacteria can affect your appearance and mood so much? Maybe I was right about the aliens...

 

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