IRA FLATOW: This is Science Friday. I’m Ira Flatow.

We’ve all heard the phrase, you are what you eat. And when it comes to the human gut microbiome, all those microorganisms, trillions of them that live in our digestive system and assist some of our most basic bodily functions, it seems more and more like that is really true. Study after study links the food we eat to the health and structure of our gut microbes.

But what about the food we cook? Does it matter to a microbe if that sweet potato is raw or is it boiled? New research published in Nature Microbiology earlier this week found evidence that, in fact, it does. Mice fed raw diets had vastly different microbiomes than mice consuming cooked food. And at the end of the day, that could lead to a whole host of new insights into human evolution and our own first forays into flame broiling our food.

Here to explain why is Dr. Rachel Carmody, Assistant Professor of Human Evolutionary Biology at Harvard University and the lead author on this new research. Welcome to Science Friday.

RACHEL CARMODY: Thank you very much, Ira. It’s nice to be here.

IRA FLATOW: Nice to have you. So how much does cooking actually change our food?

RACHEL CARMODY: Well, cooking profoundly changes our food, as does other forms of food processing. But unlike non-thermal forms like grounding or pounding, cooking can both physically transform the food and it can chemically transform the food, and it does so in different ways for different kinds of foods. So for example, for carbohydrates like starch, cooking can actually take starch, which in its raw native state exists in a really tightly bound granule, and it can kind of loosen those bonds and allow them to swell with water and this makes it much easier for our enzymes, our amylases, to get in and break that starch down so that we can take advantage of the carbohydrate.

For proteins, it’s doing something very similar, which proteins exist naturally in kind of tightly wound balls of yarn. You can kind of think of it that way. And cooking unwinds that yarn and allows our protein digestive enzymes, proteases, to come in and cleave off amino acids that our bodies can make use of. So it essentially allows us to digest a greater fraction of the food that we eat in the small intestine. And then what we can’t digest in the small intestine passes into the colon, where it becomes the work of our gut microbial communities.

The other thing that cooking essentially does, as does other forms of food processing, is you can think of it as externalizing a part of the digestive process. And by making– by starting the process of breaking down foods our bodies basically have to do less work to complete the process. And so there’s a metabolic cost of digestion that goes down when we’ve cooked our food compared to when we eat it raw.

And these are things that we knew about the cooking process, even before we conducted this study. But interestingly, what we had found is, you know, if you take humans or you take mice and you feed them raw versus cooked food, you do see that the cooked food give more energy overall, because it’s easier to digest, because it’s less costly to digest. But when you add up the effects on digestibility and the metabolic cost of digestion, they didn’t actually make up 100% of the difference we were seeing just in terms of how much extra energy were these humans or where these mice getting. And so we really started to think there was another process happening.

And around the time I was doing this work and realized, oh my gosh there’s another mechanism that I can’t explain, work was coming out showing side effects of gut microbial community. Different microbial communities feedback into energy metabolism in the sense that you could have two different communities that return different amounts of energy back to the host. And so that’s really where we started with this project was to try to understand, is this part of the picture?

IRA FLATOW: And so you actually found that the microbiome responds differently to cooked versus raw food.

RACHEL CARMODY: Yeah, that’s right. And we– we’ve tested two different kinds of foods. We tested meat and we tested tubers. So you can think of these as potatoes, sweet potatoes, underground storage organs of plants. And the reason we chose these two foods is I’m a human evolutionary biologist, these are representative foods of types that we thought would have sustained and provided the bulk of calories for ancestral humans for at least the last couple of million years. And so we were interested in kind of understanding how cooking would have improved these particular foods, and then what that relationship would have been with the gut microbial community.

And so we said– we started with an experiment where we fed mice raw, uncooked meat and raw, uncooked sweet potato. And we just surveyed to see what would happen to the microbial community in terms of its composition, meaning the different combinations of bugs that are present in that community, as well as its function. So what particular genes was that community transcribing, and what does that tell us about what it’s seeing in its environment as well as its behavior?

And when we fed the raw versus cooked meat, we actually didn’t see very many changes with the microbial community, and I can explain why in a bit. But when we fed the raw, uncooked sweet potato, it was night and day. Within 24 hours, we saw completely different microbial communities, and they were doing very different things.

And the things they were doing differently were digesting starch and sugar, as well as producing a whole array of products for fighting off compounds that we call xenobiotics. These are things that aren’t nutrients, but things that can come in with the diet that the microbial community may treat as sort of foreign compounds, and so you can think of this as sort of a detoxification effect. And those effects were really seen within the first 24 hours, and we became very, very curious about, why those particular effects?

And if we think back to kind of what cooking is doing to food, we knew that, in the case of these plant foods that are rich in starch, that cooking would be changing the digestibility of starch. So one of our hypotheses was, OK, so you cook the sweet potato, more of it disappears in the small intestine, because our bodies have an easier time breaking it down. Less of that starch makes it into the colon, and so this fundamentally changing the nutrients that are entering that colonic environment, where the majority of the gut microbiome resides. And like in any environment, if you change the nutrient flows in, it’s going to change competition among species. And so we had a strong hypothesis to suggest that this is one of the mechanisms involved.

But that additional kind of interesting tweak that we thought was gut microbial behavior, in the sense that they were fighting off these xenobiotic or these foreign compounds, gave us an idea about a potential second mechanism, which is that when plants grow in the ground, they actually produce a whole array of natural antimicrobial compounds. And they do this to protect themselves against predation. And if you eat these plant foods in a raw state, some of those antimicrobial compounds could actually retain their activity and exert them within the gut and change the gut microbiome in that way. Whereas if you eat them cooked, some of those compounds may have been broken down outside the body, so when you eat them, they don’t really have the same kind of effect.

IRA FLATOW: So this– the raw foods are bringing in with them the ability to fight microbes in the gut like they fight it in the soil.

RACHEL CARMODY: I think that’s exactly right, although we didn’t really realize this until we started doing this research. And we said, oh– we put two and two together and said, well, of course they would be doing this, why not? They’re doing this in their native state, we’re eating them in their native state. Some of these compounds may actually still be active.

And so then we designed a series of experiments to kind of understand the role of digestibility and the role of these xenobiotic compounds in shaping the gut microbiome. And the big picture is that when we designed diets that were identical, except for the digestibility of the starch fraction, we could actually recapitulate in the gut a gut microbial community that looked very similar to what we saw on the raw versus the cooked diets, purely by manipulating the digestibility of starch. And when we tested this across other kinds of plant foods and not just sweet potato, we tested white potato and corn and pea and beet and carrot, what we found is that our ability to manipulate the gut microbial community with cooking was largely restricted to starch rich foods that were improved to the greatest extent, whose starch digestibility was improved to the greatest extent by cooking.

IRA FLATOW: Is that why you– is that why you could not get a difference in the meat, because it wasn’t starch related, so does the meat didn’t show much of a difference?

RACHEL CARMODY: Yeah, so obviously, meat does not have a lot of starch. We do know that meat– the digestibility of meat is improved to some extent with cooking, because like I said, cooking kind of unwinds these proteins, these like balls of yarn. But meat is a high digestibility food to begin with, so the net effect of cooking on the improvement of digestibility is pretty small in meat. It’s a pretty highly digestible food, even when raw.

And we all know this, you know, if you just think– take a step back and look at cultures and what cultures are doing, there are many cultures out there that will readily eat meat raw or fish or other kind of plant– sorry, animal materials raw, because historically, they’ve returned a decent amount of that energy. Whereas with things that are very rich in starch, cultures worldwide tend to cook these items, because we don’t get much out of them unless we do. And so you know, it makes sense that digestibility would be one of the drivers for the reason we didn’t see an effect in meat and we saw this profound effect in a sweet potato.

IRA FLATOW: Is there any then recommendations for whether– you know, broadly recommendations for whether we should cook our vegetables or starches or eat them raw?

RACHEL CARMODY: Well, the broad recommendation is that our bodies are not designed to eat this stuff raw. And we know this, because there have been studies of long term raw foodists who have been raw foodists for at least three years and they eat at least between 80% of their food raw, up to 100% of their food raw, and what we find is that, over time, these people have lower and lower body mass index, meaning their weight for height goes down and down.

And you would think in a modern industrialized society, oh, that’s great, this is the great weight loss tool. It is, but what you find is that among women who are consuming 100% raw food diet, they are so energy limited that they actually stop ovarian cycling. They have problems with reproduction. And from an evolutionary perspective, what this suggests is that our bodies, through a long history of cooking our food, have essentially become adapted and dependent on incorporating at least some fraction of cooked items into the diet. We don’t seem to thrive very well on 100% raw food diet.

That said, depending on people’s goals if they’re trying to lose weight, it could be a good kind of short term scenario. But over the long term, this is not the diet we were meant to eat. We were– we’re actually biologically committed to cooking some fraction of our diet at this point.

IRA FLATOW: Are you saying that that’s an evolutionary change that has happened?

RACHEL CARMODY: It is an evolutionary change what’s happened. We’ve now seen it. So my colleague, Richard Wrangham, has really been the person advancing this idea. But he kind of took it from first principles and he said, OK, well, you know, we’re human evolutionary biologists, let’s think about the things that really makes humans unique in order to understand why humans are the way we are today. And of course, one of the things that does make humans unique is that we’re the only species to control fire. We’re the only species, save for a few domesticated animals where we cook the food for them, we’re really the only species that is consuming cooked food on a regular basis.

And so he started there and said, well, I wonder if cooking has actually transformed our biology? And we know that, at least for the last two million years, humans have looked really different in the way we digest our food compared to our closest living relatives, chimpanzees, bonobos, and gorillas. We see changes in the kind of way that we chew our food. We see smaller chewing muscles, smaller molars. We see smaller teeth and dental arcade. Like our mouths get smaller in general.

We also have a smaller gut. So you can kind of imagine this. If you look at a gorilla, it’s got this enormous stomach. Its rib cage kind of flares out, because it’s containing a ton of intestines. Humans on the other hand, have a waist. We’ve got small intestines that kind of fit over a much smaller pelvis.

And we’ve got these like tiny structures for digestion, and yet we’ve got really expensive bodies. We’ve got large brains that are metabolically expensive. We’ve got relatively large bodies compared to chimpanzees, which are actually our closest living relatives, and we actually show a lot of adaptations, surprisingly, for high energy expenditure. We tend to think of ourselves as just sitting around on the couch all day nowadays, but actually, humans as a species expend a lot of energy every day compared to a chimpanzee.

IRA FLATOW: All right. I have to interrupt for a second to remind our listeners that this is Science Friday from WNYC Studios. You can finish, Dr. Carmody.

RACHEL CARMODY: Oh, great. Thanks.

So I was just saying, so this combination of features of small structures for digestion but a high energy budget means that we must have, around two million years ago, started eating a diet that wasn’t just more of the same foods we were eating. We were actually eating a fundamentally different diet. We were packing more calories into a smaller amount of space, and particularly, these small structures for digestion means that these foods must have been easy to chew and easy to break down within the gut.

And so the long standing hypothesis was, well, maybe at this time in evolution we just started eating a ton of animal foods. We were hunters and we went after meat, and this explained all these changes that we see in the human body. But we don’t actually see many adaptations that are specific for the digestion of animal foods.

And so my colleague, Richard Wrangham, really proposed that cooking and other forms of non-thermal food processing may actually have enabled ancestral humans to improve the foods that were readily available. And the single largest source of readily available calories out in the landscape at the time, would have been these underground storage organs, like sweet potato– we can think of it as a sweet potato tubers. And so that’s really set the stage. We know that the human body has undergone these evolutionary changes for a high quality diet. We think some of it may have come in from increasing the amount of meat we eat, but we actually think a lot of it would have come in from cultural adaptations, like non-thermal food processing, as well as cooking, that would have enabled us to just get more out of the foods that we had ready access to.

IRA FLATOW: Mhm. I just have about a minute left. Is there any– where do you go from here? In about 30 seconds, where do you go from– the next kind of research you’d like to do?

RACHEL CARMODY: Well, so I think what our study with the microbes actually tells us is that just as the human body has changed in response to cooking, these microbes would have actually changed in response to us cooking as well. And so this sets up a stage where we can look for signals of human microbial co-evolution.

And my lab is actually pursuing this right now. We’re looking at what is functionally unique about the human microbiome in the context of cooking, and we’re also trying to understand the fundamental nature of the host microbial relationship, the conditions under which we compete with one another versus the conditions under which we are cooperative. And–

IRA FLATOW: We have to leave. We’re going to have to leave it right there, Dr. Carmody. We’ve run out of time. But thank you for that great explanation.

RACHEL CARMODY: No worries. Thank you so much for having me and for your interest in our work.

IRA FLATOW: Rachel Carmody, Assistant Professor of Human Evolutionary Biology at Harvard.

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