RHR: Vegetarian Diets and the Microbiome | Chris Kresser
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RHR: Are Vegetarian Diets Better for the Microbiome?

by Chris Kresser

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Revolution Health Radio podcast, Chris Kresser

It is true that some studies show vegetarian diets are better for the microbiome and eating meat is associated with unfavorable changes in the microbiome. The issue with most of this kind of research is that other factors are, more than likely, what are causing this difference.

What we can learn from these studies is only that the average person who eats red meat has a disrupted gut microbiome compared to the average vegetarian. That’s the only thing a study like that can tell us. It doesn’t tell us whether it’s because of the meat or because it’s the buns that they’re eating, like, the hotdog buns and hamburger buns around the meat, or it’s the sugar, or it’s the other crap that they’re eating, or it’s a lack of exercise, or it’s that they smoke more frequently.

In this episode, we cover:

2:27  What Chris ate today
6:05  How meat consumption affects the microbiome
11:30  The biggest diet factor that determines gut health
25:28  The importance of the context in which you eat meat

Links we discuss

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Steve Wright: Good morning, good afternoon, and good evening. You are listening to the Revolution Health Radio Show. I’m your host, Steve Wright, co-author at SCDlifestyle.com. This episode of RHR is brought to you by 14Four.me. This is a 14-day healthy lifestyle reset program. Chris Kresser has put together a program here. If you’re someone who’s still struggling with, maybe, digestive issues, skin problems, low energy, maybe insulin issues, basically all these conditions, all health conditions are foundationally supported by diet, sleep, movement, and stress. Now, incorporating all four of these variables into your life can be very hard, especially if you’re having to make tweaks in all of these areas at the same time. Chris knows this, he’s been studying psychology and habit formation for a long time, and so what he’s done is he’s put together this 14-day healthy lifestyle reset program, where you’re going to actually work on your diet, your sleep, your movement, and your stress all at the same time, and by the end of the program, you’ll have incorporated the foundational pieces you need to get over these issues. Check it out at 14Four.me.

All right, let’s get on with the show here. With me is integrative medical practitioner, healthy skeptic, and New York Times bestselling author, Chris Kresser. Chris, how are you doing today?

Chris Kresser: I’m great. How are you, Steve? Good to talk to you. It’s been a while.

Steve Wright: Yeah, yeah, it has been a while. I’m recovering from a sinus infection.

Chris Kresser: Oh, man. I’m sorry to hear that.

Steve Wright: Eh, it’s OK. It happens when you don’t do those four foundational steps.

Chris Kresser: Right. You need a little 14Four spring cleaning, huh?

Steve Wright: Yeah. You try to have too much fun and do too much work at the same time.

Chris Kresser: Mm-hmm. Yeah, that’s not sustainable for very long. It might work for a short time but definitely not over the long term, as you’re finding out, right?

Steve Wright: Yep, yep. I have to make the mistake, like, every three months or so.

Chris Kresser: Right, just to remind yourself.

Steve Wright: Yeah, the body’s just trying to train me.

Chris Kresser: Yeah, got it. Well, I hope you get well soon.

Steve Wright: Yeah, I’m on the mend. It’s all good. So what have you eaten all day today?

What Chris ate today

Chris Kresser: I had scrambled eggs; sweet potato hashbrowns; and raw sauerkraut with cabbage, beets, and carrots for breakfast. And I had kind of an unusual lunch because I had a lot going on and I knew we were sitting down to record, so I just had some yuca crackers from Mission: Heirloom. A really awesome thing that they do. Sylvie loves them, and we send them with her to school for her snack at preschool. They’re made from yuca, AKA manioc or cassava. It’s grated and then pressed and dried into crackers, and I put some ghee and sea salt on them, sometimes some avocado. And I had some olives, Castelvetrano olives, green olives, which are my favorite. I had some salami, some raspberries. It’s similar to, like, food that I take with me on an airplane. A little bit of sliced chicken and some kale that we had leftover, so it was kind of almost like tapas, although there was nothing Spanish about the food but just in the sense that it was like a smorgasbord, I suppose.

Steve Wright: Yeah, more like a summer picnic.

Chris Kresser: Yeah, exactly. Got it.

Steve Wright: Have you tried the Boulder brand avocado oil sea salt chips?

Chris Kresser: No, I haven’t. Are they potato chips, you mean?

Steve Wright: Yeah, so it’s just white potato.

Chris Kresser: Oh, yeah, yeah, yeah. Yeah. Avocado oil. Yeah, those are pretty good.

Steve Wright: They’re dangerous.

Chris Kresser: Yeah, exactly. I mean, certainly they’re better than eating chips with industrial seed oils, and they’re a great snack, but if you eat, like, two bags, it’s probably not doing you any favors!

Steve Wright: Probably need 14Four.

Chris Kresser: Yeah. But we have a really great question. It’s from Dr. Akil Palanisamy, I think, is how you pronounce it. I hope that’s correct, and I apologize if it’s not. I’ve met Dr. Akil before, and he’s a functional medicine practitioner in San Francisco, and he has a really good question that a lot of folks have asked and a lot of people will be interested in, so let’s give it a listen.

Question from Dr. Akil Palanisamy: Hi, Chris. This is Akil Palanisamy, integrative medicine physician in San Francisco. I have a quick question for you about meat consumption and the microbiome. When I was reviewing the literature recently, I came across some studies that surprised me, suggesting that eating meat could have an adverse impact on gut bacteria and that a vegetarian diet may have beneficial effects on the gut microbiome and markers of gut bacteria. I’m wondering if this is related to antibiotics in commercial meats that are having a negative effect on gut bacteria. I couldn’t find any studies that looked at pasture-raised meat or antibiotic-free meat, and I wonder if that would have a better impact on gut bacteria. It’s a very important question, I think, because many patients that I see have a problem with their microbiome, and I’m trying to restore it, and if eating meat has an adverse impact on it, then that would really change my dietary recommendations for people. Thanks for your response.

How meat consumption affects the microbiome

Chris Kresser: OK, so I’m sure some of you have seen articles in the mainstream media about this or have seen some chatter in social media or whatnot, and it is true that some studies show that vegetarian diets are better for the microbiome and eating meat is associated with unfavorable changes in the microbiome. But once again, you have to understand the issues with most of this kind of research. To get a much more detailed discussion of this, go back a few podcasts and listen to the research 101 show that we did where we covered all of these issues much more extensively, but most of these studies are just comparing two groups of people. They’re comparing meat eaters and vegetarians, and then they look at the microbiome in each group and then they come to some conclusion where they say, OK, people who eat meat generally have a worse microbiome than vegetarians. The problem with drawing that conclusion is that we know from other studies that the average meat eater does a lot of things differently than the average vegetarian. They eat fewer vegetables and fresh fruits. They don’t exercise as much. They tend to smoke more. They consume more alcohol. They engage in all kinds of other behaviors that can adversely affect the microbiome, and studies do try to control for some of those other confounding factors, but they can never control for all of them.

What we can learn from these studies is only that the average person who eats red meat has a disrupted gut microbiome compared to the average vegetarian. That’s the only thing a study like that can tell us. It doesn’t tell us whether it’s because of the meat or because it’s the buns that they’re eating, like, the hotdog buns and hamburger buns around the meat, or it’s the sugar, or it’s the other crap that they’re eating, or it’s a lack of exercise, or it’s that they smoke more frequently. Those other factors are, more than likely, what are causing this difference. If you extend that, of course, it doesn’t mean that a person who eats red meat that is also eating a lot of fresh fruits and vegetables and fermented fibers, fermented foods, that isn’t eating a lot of refined sugar and industrial seed oils, that is exercising and sleeping and taking care of themselves is going to have an inferior microbiome compared to someone that’s doing all those things and not eating meat. There is no study that I’ve seen that has come to that conclusion.

Steve Wright: Yeah. I’ve looked at this stuff quite a bit as well, being something I care about, and I’ve thought about it a lot in my diet, and so I’ve tried times of vegetarianism just to kind of see what it was like and also during, like, my vipassana retreat.

Chris Kresser: Yeah.

Steve Wright: And what I think is also not being talked about in these studies besides everything you’ve already mentioned is that typically because when you go vegetarian, you need more calories and you end up eating a larger quantity of fermentable fibers.

Chris Kresser: Mm-hmm.

Steve Wright: Versus somebody who’s maybe satisfied earlier because they’re consuming animal content. They might end up eating less fruits and vegetables over time just because they need less volume to feel full and satiated during a meal.

Chris Kresser: That’s true. That’s definitely true, and of course, the question there is, does that adversely affect the microbiome? I haven’t seen any studies that suggest that it does. I mean, we’ve looked at traditional cultures that have meat in their diet but also eat relatively high amounts of plant foods, you know, fruits and vegetables and tubers and other plant parts, and they have an ancestral microbiome. So I don’t think we can say that it has much to do with the meat, but it does have to do with the intake of other stuff — we’re going to come back to that — and also non-dietary factors, like sleep and exercise, we know affect the microbiome as well.

When people read these kinds of articles or hear about them on social media or on the news, there’s a natural and understandable tendency to kind of identify with the meat eater and place yourself in that category and assume that you are in that group and are subject to those same conclusions, but it’s not true actually. Most of the people who are listening to this podcast are not representative of the meat eaters in scientific studies. That’s really important to understand. So if you ever hear of a conclusion that’s being drawn of red meat eaters in scientific research, you are not that person typically. Of course, it depends on the exact study and what they’re looking at, but most people who listen to this show are eating meat in the context of a diet that’s rich in all the things that are beneficial for gut health, and so we cannot extrapolate the results of meat eaters in these studies to all of you who are listening to the show.

The biggest diet factor that determines gut health

So if it’s not the meat, what is the biggest factor that determines the health of the gut microbiome? I think it is the type of carbohydrate that you eat, and specifically, it’s the ratio of acellular to cellular carbohydrate. Now, that sounds very geeky, I know, but just give me a chance to explain it a little bit because it’s a very useful concept to understand, and I think it answers a lot of questions, and you’ll see what I mean as we go through this.

This concept of acellular versus cellular carbohydrate and the importance of it to the gut microbiome comes from one of my favorite research papers ever, which was written by Professor Ian Spreadbury, and he’s actually going to be a presenter at the Ancestral Health Symposium conference in New Zealand, the New Zealand version of that conference, which is happening in October of this year. And the paper is called “Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity.” That’s a mouthful. The study will be in the show notes, so you can check it out. The full text is free, and you can read it if you’d like, but the basic idea is that all carbohydrates that were part of the ancestral diet, which would be tubers, fruits and vegetables, plant parts like stems and leaves, store their carbohydrates in fiber-walled, living cells, and those cells remain largely intact during the cooking process, and they also resist digestion or absorption in the small intestine, and therefore, the fiber remains intact all the way down to the colon, where it then becomes food for beneficial gut bacteria that are living in the large intestine. So those are the cellular carbohydrates, and they’re, like I said, found in all ancestral carbohydrate sources.

On the other hand, in the Western or industrialized diet, you have a lot of acellular carbohydrates. These are things like flour, sugar, and other processed starches that have no living cells. These industrial foods are much higher in carbohydrate density than anything the microbiota of our upper GI tract would have encountered during our long evolution. And these foods, because they have no living cells, they’re absorbed higher up in the GI tract, and they can stimulate the overgrowth of bacteria in the upper GI tract, AKA SIBO, or small intestinal bacterial overgrowth, and they preferentially will feed some species of bacteria over others, and that can in turn lead to an inflammatory gut microbiota.

Dr. Spreadbury makes the argument, which I agree with, that this difference in carbohydrate type could be the single most important difference between ancestral and industrialized diets. Now, notice I didn’t say carbohydrate quantity, the amount of total carbohydrate that you eat. I don’t think that’s the issue for most people. The issue is carbohydrate quality, and I know I’ve been beating this drum for a long time. I wrote about it in my book. Professor Spreadbury talks about it in the paper. He points to traditional cultures like the Kitavans and East African groups who eat from 35% to 70% of calories as carbohydrate, but all of these carbohydrates come from foods with living cells, like tubers or fruit or other plant parts, and the reason that industrialized diets are so harmful is not because of the overall amount of carbohydrates that they contain, as some people have argued, but because they don’t have those living cells, and as a result, they have a completely different impact on the gut microbiota than the ancestral carbohydrates, the real-food carbohydrates.

Steve Wright: Is it living, Chris? Or is it more of the complexity and the molecular structure of the differentiation? Because we can take those tubers and cook them. Now they’re not living anymore. But I was kind of under the understanding that you have a cell wall that contains all the parts of the cell and it’s a… complex isn’t necessary the perfect word here, but the actual molecule is still intact, whereas the processed foods, the molecule has been stripped down.

Chris Kresser: That’s right. Yeah, it’s been predigested, essentially, and broken down. And the cellular structure, like I said before, remains largely intact even during cooking, so the carbohydrates are locked into the fiber-walled cells, and that’s why in some cases the carbohydrate portion of that food is inaccessible, and that’s why it’s considered to be fiber. Fiber is not a nutrient technically for humans because we can’t absorb the carbohydrate that’s contained in those cells and make use of it ourselves, but those cells are instead nutrients for the bacteria that live in our large intestine because they survive in that form all the way down to the large intestine.

Another way to think about it is these real-food carbohydrates in these tubers and plant foods, especially the ones that are resistant to digestion, are not nutrients for us; they’re nutrients for our gut microbiota. On the other hand, the flour and sugar and processed starches, they are absorbed completely by us, and furthermore, they’re absorbed in a different part of the GI tract and they feed bacteria and can lead to an overgrowth of bacteria in that part of the digestive tract because they lack that cellular structure. And so they have a completely different impact on the gut microbiome. When you compare diets and you take one diet that has 25% or 30% of calories as carbohydrate in the form of these cellular carbohydrates, the tubers and the fruits and the vegetables, and then you have another diet that’s 30% of calories as carbohydrate in the form of flour and sugar, those are going to have a completely different impact on the body. And Spreadbury’s argument is the thing that’s mediating that difference in impact is the gut microbiome.

Steve Wright: Yeah. I love it. I believe it, too, and I think it just makes sense once you begin to actually think about what’s happening inside of the small intestine and the large intestine. When you really think about the structure of the foods we eat and what functionally is supposed to happen and then what is happening from an ecosystem in each organ, it only begins to take on just really logical sense.

Chris Kresser: I think that is a good point because we’ve been talking about this for a long time, but the contribution of this paper is that it provides a clear mechanism for why industrialized carbs have a different impact on the body than real-food carbs do. And to make it even more clear, the Standard American Diet varies from person to person, but on average it’s, I think, 40% to 45% of calories as carbohydrate, and so the low carb advocates have argued that, hey, this is way higher in carbohydrate and that’s why it’s problematic. Well, that’s not true, strictly speaking, because there are cultures, as I said before, that consumed an even higher percentage of calories as carbohydrate, up to 70%, but they didn’t have any of the diseases that people eating industrialized diets are suffering from, so that goes to show that it’s not about the total amount of calories from carbohydrate; it’s about the quality and type of carbohydrates that are being consumed.

Another example of this is that all of the studies that have been done on the paleo diet so far that have shown such remarkable improvements with weight loss and metabolic health have been done on a moderate carbohydrate paleo diet ranging from, I think, 20% to 30% or 35% of calories as carbohydrate. These are not really low carb diets that are being studied. They’re diets that restrict the quality and type of carbohydrates that are consumed. They eliminate processed and refined grains and all the dense, acellular carbohydrates that are part of the industrialized diet, and they just permit intake of starches and fruits and these cellular carbohydrates. I’m not aware of many, if any, studies on a very low carb paleo diet. Almost all the studies I’ve seen on paleo are 30% carbohydrate roughly, and you’re still seeing really remarkable reductions in weight and improvements in insulin sensitivity and body mass index and waist circumference and all that stuff, which really, again, just goes to support the argument that it’s more about the quality and type of carbs than the absolute amount.

Now, there is one thing that I want to point out, which is that — and you kind of alluded to this before, Steve — one reason I’m not a fan of very low carb, high protein, high fat diets for extended periods of time is that when you cut your carb intake, your absolute amount of carbohydrate that you eat, when you cut it down to below 10% or below 7%, which can be necessary in order to achieve ketosis for some people, it becomes very difficult to consume sufficient amounts of fermentable cellular carbohydrates to maintain a really robust and healthy gut microbiota. And I think this explains why some studies have shown that people consuming a very low carb diet may experience undesirable changes in their gut microbiota, and we have seen this in our clinic and in our work with patients. I think we need more research in this area, but again, if you understand — like you said, Steve — how the small intestine and the large intestine work and what the bacteria in the large intestine need to sustain themselves, it makes sense that if you’re on a diet where you’re eating on a percentage basis a much higher percentage of nonfermentable substrates, like meat and fat, and a much lower percentage of fermentable substrates, like the plant foods, then it very well could have an adverse impact on the gut microbiome over time.

Steve Wright: Yeah. I mean, we don’t know for sure yet, but the analogy I like to use is if you throw a scoop of peanut butter on the sidewalk in any city, you’re going to have a giant ecosystem that forms within minutes to hours, where a dog’s going to walk by, some ants, maybe a bird, maybe some humans will mess with it, who knows? And the same thing is true inside of our gut. Everything we put into our mouth, it is going to be part of the ecosystem. And some of those foods feed the ecosystem in certain parts of the body. Other foods feed the ecosystem lower in the body, in the large intestine, which is what we’re talking about here. So if you just start to think about the fact that everything you put into your body is sort of feeding this ecosystem… I don’t like getting reductionist, but it is kind of simple once you stop to think about how we do want a robust gut microbiome, and what feeds that? Well, certain types of foods. And other types don’t.

Chris Kresser: Exactly. And another angle or way to look at it is, like, in clinical practice, if I’m treating SIBO, one of the strategies that we use is a diet that’s low in fermentable fiber. We put patients on a diet that is low in these fibers because we know that these fibers can feed bacteria that have become overgrown in the small intestine. You know, there is a lot that we already know. We do need more research, but there is a lot that we already know. I mean, one of the treatments for SIBO, for example, is an elemental diet, which is composed of only simple carbohydrates, like glucose and fructose, that are absorbed extremely high up in the digestive tract and thus don’t become food for bacteria lower down in the gastrointestinal tract. And we know, studies have shown that people who are on elemental diets experience a dramatic shift in the composition of their gut microbiome. So I think you can make a very strong argument that a diet that’s low in fermentable substrates and high in meat and fat may have an adverse impact on the gut microbiome over time.

The importance of the context in which you eat meat

Now, getting back to the original question, of course, when we tell patients to eat a paleo type of diet, we’re not necessarily — hopefully not — telling them to just eat only meat and fat. I mean, that’s not what the paleo approach is about, as we’ve talked about ad nauseam. We’re telling them to eat a diet that is very rich in fruits and vegetables and fermentable fibers and fermented foods and things that support the gut microbiome that also happens to include meats because meats are very nutrient dense and have a lot of other beneficial impacts on health, even if they don’t have, necessarily, a beneficial impact on the gut microbiota.

Again, to sum this up, it’s not really about whether you eat meat; it’s about the context in which you’re eating meat and the quality and the type of carbohydrates that you’re eating. You want to focus on real-food carbohydrates, like tubers and fruits and other plant parts, that contain all the fibers that feed beneficial gut microbes. This is resistant starch; we’re talking about non-starch polysaccharides, things like inulin and FOS and arabinogalactan. And then we’re talking about soluble fibers. All of these different types of fibers feed the beneficial gut microbiome.

I know that this is anathema to some people in the paleo community, but legumes can be a really good choice if you tolerate them, if you prepare them properly, soaking them prior to consuming them, and if they don’t replace more nutrient-dense sources of food. One of the reasons that they can be beneficial is they’re an excellent dietary source of resistant starch, which is somewhat difficult to come by in the diet.

And if you have to eat a very low carb diet or a ketogenic diet for any reason — maybe you’re treating a neurological condition, maybe you’re on a rapid weight loss program, maybe you feel better doing that in most ways — I would suggest increasing your intake of fermentable fibers. Many of these don’t really count towards your carb intake anyway because the carbs in them are not absorbed. For example, if you cook a white potato and you cool it, a lot of that will be resistant starch and it won’t impact the blood sugar or carbohydrate levels as much as if you just eat a cooked potato. You can use potato starch, and that, again, is not going to have an impact on your overall carb level intake. You can use plantain flour or green plantains, dehydrated, green banana flour. You can use supplements, non-starch polysaccharides. I saw one in my store called Prebiogen, which I really like. And then there are soluble fiber supplements, things like acacia fiber, or psyllium husk is another popular soluble fiber. Glucomannan is one that I like a lot. I think I also have that in my store. It has a particularly good effect on blood sugar. You can use all these fermentable fibers to make sure that you’re not starving your gut bugs of the foods that they need to thrive over the long term.

And I just had another thought along these lines. I can’t remember if I’ve ever blogged about this. I’m sure you’ve seen this study, too, Steve, but there’s now some speculation that a low FODMAP diet, which can be very therapeutic for people with IBS, irritable bowel syndrome, and also SIBO, may not be a good choice over the long term because it removes a lot of the foods that feed beneficial gut flora. This is being discussed now even in the mainstream scientific literature. That kind of supports everything that we’ve been talking about today.

Steve Wright: Oh, yeah, definitely. And I think the ways in which you’ve mentioned, and I would echo what you’ve seen, which is that if FODMAPs are an issue for you, obviously cut them out while you fix the root causes, and it’s an indication that your gut is really messed up. The more sensitive you are to FODMAPs, it appears that you’re having some definite issues. And then over time, you want to get those foods back in as fast as possible. That’s something that’s bugged me about that entire thing, so that’s cool that there’s some research and some talk about that finally.

Chris Kresser: Yeah, exactly. And I’m sure there will be more. We’re definitely moving in this direction.

OK, so that’s it for today. Keep sending us your questions. It’s fun to be able to hear what’s on your mind and respond to it, and I’ll look forward to talking to you next time.

Steve Wright: Yeah, send those questions in at ChrisKresser.com/PodcastQuestion. And in between episodes, hang out with Chris on Facebook.com/ChrisKresserLAc or Twitter.com/ChrisKresser. Thanks for listening, everyone.

63 Comments

Join the conversation

  1. Even though these particular native cultures are eating a high carb diet, do these carbs contribute to caloric intake? If they are cellular type of carbs, from my understanding of your post, they are digested later on in the lower GI tract (nurturing our microbes).

    In this case/context, eating high carb does not equal absorbing high carb? ie. are they “really” on a low carb diet, even though they are eating a high amount of carbs?

    In contrast, high wheat cultures eat high carb and also absorb high carb…hence the whole insulin fat storing story.

    Is this correct?

    If so, it’s not about quantity of carbs, but the quality of carbs.

    If I’m reading all this correctly, and these native cultures aren’t absorbing the carbs from their high carb diet…then where are they getting their glucose needs from?

    • I mentioned this in my comment: “Even though these particular native cultures are eating a high carb diet, do these carbs contribute to caloric intake? If they are cellular type of carbs, from my understanding of your post, they are digested later on in the lower GI tract (nurturing our microbes).”

      I’ve since read that it does contribute to calories as the fiber is converted into fat ie butyrate (a short-chain fatty acid).

      I guess I was first thinking that these native cultures were on a lower calorie diet (given there carbs were being digested in the lower GI tract), but maybe the calories from the butyrate even it up to a regular calorie diet. Would this be correct?

    • Carbohydrates are the vast majority (>90%) of their calorie intake. If they were not getting calories from the root tubers (cassavas etc..), whole grains like sorghum and beans they are eating, they would be starving to death.

      They are grinding and cooking these foods, so they are well digested, and calories, as well as, essential nutrients are adequately released and bioavailable to them. Plant foods and their various types of fiber, create and grow lots of beneficial bacteria to break them down, and create high volume and bulk of stools, helping flush out unwanted toxins, cholesterol and hormones. Animal products have no fiber at ALL, and thus do not create incredibly healthful and anti-inflammatory short chain amino acids, like butyrate, in your GI tract.

  2. Thank you Chris, for the wonderful podcast! Spreadbury’s paper is a milestone. I am sure we will be benefitting from it for a long while! Here is my QUESTION: he states: “.. While fermentable fiber is able to effect certain changes in colonic gastrointestinal microbiota, these currently seem unlikely to represent a useful intervention for obesity or metabolic disease.” I have been observing remarkable recovery when individuals introduce prebiotics, after they can tolerate it. It is life changing. I appreciate any help in understanding Spreadbury’s statement above. AND if you can answer: Is potato starch acellular?? Thanks!!

    • It is my understanding that raw, unmodified potato starch is RS2 resistant starch, and does not need cellular structure to protect it from digestion. It will pass through to the colon regardless of whether it is cellular or acellular.

      RS1 is physically inaccessible starch, due to cellular structure. This physical inaccessibility is the point, here. Besides RS1, we’re also talking about all other carbs (mono-, di-, polysaccharides). These will most likely be accompanied by proportionately higher quantities of digestible carbs.

      I don’t believe cellular sources of carbs contribute a great deal to the microbiome, especially in proportion to their contribution to blood glucose. But some is better than none. And this study shows that none is particularly bad.

  3. Chiris is there any evidence that traditional people that ate a low fibre diet like the Masai Warriors had health problems due to an unhealthy microbiome? From everything I have read they were very healthy. The small amount of carbs they ate would have been mostly cellular.

    • They survived but frequently drank blood of herbivore animals to get the variety of nutrients that most of us are luckily getting from eating plants, rather than having to drink blood. One study found very few men past 50 living in their tribe.

  4. “tubers, fruits and vegetables, plant parts like stems and leaves, store their carbohydrates in fiber-walled, living cells”

    Does tubers include potatoes and other root vegetables etc?

  5. Hi Chris,
    First, Thanks for this podcast and all of the information you share!
    Second, For people with high levels of bad bacteria and low levels of lacto and bifido on a low fodmaps diet, any strategy suggestions for how to phase in prebiotics? It seems prebiotics will feed the good and the bad guys but are there any particular prebiotic foods that will favor the good guys a little more?

  6. It’s disappointing to read that us fructose malabsorption sufferers (who’s symptoms and the degree of vary far and wide) should be eating the very food that causes any number of problems to us and those around us. You give no method of how to ‘cure’ our FM or the time frame. I’ve been paleo, aip immune paleo, dairy and gluten free now for more than half a year and if I are onions I’d be doubled over in pain. It’s irresponsible to write this without substantial detailed metodology.

  7. I LOVE that you talked about the issues with removing FODMAPs for a long time. I have been dealing with potential SIBO in my 3 year old (I say potential as he’s been too young to test, but process of elimination has suggested this is likely the issue), and he improved rapidly with your and Dr. Siebecker’s approach to SIBO. However, it seemed to keep coming back if we didn’t stay on low FODMAP, and we haven’t quite reached what I’d call resolution. In the meantime, being a full time working Mom, the whole family including our 1 year old was basically eating low FODMAP. I realized that our younger son who never had any digestive issues started to display some symptoms. We made a quick decision for the summer that it was time for the whole family to transition off low-FODMAP, and I’m seeing some improvement even for our 3 year old, where we’d reached a plateau. Wondering if perhaps there needs to be more discussion about SIBO approaches that involves short duration of low FODMAP, with a minor introduction of FODMAPs, and then off and on while doing a few rounds of antimicrobials when on the diet, and then prokinetics when off the diet, interspersed with some things for inflammation and healing. This is what I seem to be coming to in the year I’ve been working with my son.

  8. I may be confused, but it seems to me that many carbohydrates, including grains, would be “cellular” until they are finely ground. So perhaps the study’s author is trying to distinguish between various methods of processing? Which is also confusing, because there are ways of preparing foods that result in a ground-up product that is also fermented or otherwise carefully-prepared and nutrition-dense.

    Could you possibly clarify the definition of cellular vs. acellular?

    Regards,
    Sarabeth

  9. Diets do NOT work. Short term means nothing. The maintenance phase IS part of dieting. Dieting FAILS. We know this from scientific inquiry into the matter. Biology is the reason dieting fails. Nobody should ever diet. Ever.

  10. What floored me in this podcast was that a medical doctor who considers himself an “integrative” doctor couldn’t figure Chris’ answer out for himself in 2 minutes! He needs to go back to audit Research Methods 101, or at least search PubMed for the keywords “data torture.”

  11. Are flash frozen fruits such as blueberries, peaches, strawberries that list fiber as one of the components cellular or acellular? They generally cost less than the fresh berries at Whole Foods.

  12. Best argument I have heard regarding studies comparing meat consumption vs a vegetarian diet. I used to be a vegetarian and developed a *lot* of irritating, but not necessarily debilitating neurological conditions. When I switched to a zone diet, my neuro health improved considerably, although it didn’t help my cognitive functions improve. When I went strict paleo, (no legumes) and cut out certain types of dairy, my cognitive function improved. I have since added legumes back to my diet as the addition of it reduced the jitters (as if I had 10 cups of coffee) and kept me from being hungry.

  13. Hi Chris, can you specifically tell me why potatoes are best eaten cooled? I’ve also read this on another website. And, what do you suggest for those that are suffer from lots of gas from most of the Fodmap foods?
    It seems like we’re screwed be it from one end to the other. Mom and I are both very sensitive to Fodmap foods — I am attempting the Keto lifestyle but w/more carbs. I have eliminated grains, dairy and wheat from my diet, but lately I am experiencing issues eliminating sugar such as fruit and a little piece of chocolate. It seems like I almost don’t know what to eat anymore and this is extremely frustrating! One person suggests one thing, another suggest something completely different! Today I heard your interview and I am even more confused! Thanks!

  14. Chris, is there a difference between sprouted grains and unsprouted? What about sourdough bread from organic sprouted rye and organic sprouted einkorn? Does the bacteria in the wild yeast used for sourdough survive baking?

    Also, you didn’t mention the difference between factory-farmed meats (CAFO) and organic grass-fed meat, and the doctor who asked the question asked about this. Wouldn’t that make a big difference in the microbiome to eat meat that has no antibiotics and all the other junk in it?

    • The process of grinding them into flour probably changes the cell structure, but imagine they would be significantly more fermentable than milled grain flours. Especially coconut and cacao, which are very high fiber.

  15. Eating meat from factory farms, from animals fed with GM crops, are likely to contain glyphosate (which is registered as an antibiotic), also other chemical residues, would have a different effect on gut bacteria than eating organic meat. The factory farmed animals would be likely to be on antibiotics – that would affect gut bacteria.
    Organically raised animals have to be genuinely free range, have plenty of space given non-GM feed, and only be given antibiotics for illness.

  16. Besides fiber feeding gut bacteria, is it also possible that raw vegetables and fruits still contain some soil-based bacteria (even after washing) which adds to the microbiome? I’ve read that people who work in the soil (e.g., gardeners) tend to have more diverse gut bacteria.

  17. Meat disrupts the microbiome?

    Were these grass-fed, antibiotic-free animals – or the standard grocery store meat that is pumped full of hormones and antibiotics from birth to slaughter (and sometimes further treated with solvents that kill bacteria once it hits the supermarket)?

    To say that meat itself is the culprit might be supportive of the vegan/vegetarian agenda – but it’s not good science.

      • Exactly what I was wondering……it appears that HMK did not even read the article. What a waste of our time.

    • Which “agenda” do you think is stronger, those of meat eaters or vegan/vegetarians. As always, all discussions of this topic avoid the moral issue of obvious increased suffering that the meat industry causes, whether it is commercially raised or free-range organic. The fact is, it is possible to live vibrantly and healthily on a plant-based diet – it does take more research and will power. But anyone who has tried it and experienced health problems has simply failed to do it properly. So if it is possible to live without causing suffering to other sentient beings, why not do so? I would say it ultimately has nothing to do with health and everything to do with people’s attachment to the taste of meat and lack of will power to enact positive change because it requires more work.

  18. I think every time you mention that people should eat meat you should always add the caveat that the meat should be free range grass fed ONLY. For many people this is difficult to get hold of or too expensive in which they would be best served by a Veggie diet. It is also an oversimplification to suggest that veggies or pagans of good habits and therefore less likely to drink or eat sugar and white flower products. I get regular invites from a local veggie society to functions but decline because the menu is quite frankly shite!. Too many veggies are like runners who think that running somehow insulates them from the ravages of high simple carbs and other poor diet input. They tend to think that being veggie somehow allows them consume other more damaging food products. If you cannot get grass fed GO veggie

  19. Any discussions of vegetarian vs. meat eating first have to take into account that lacto/ovo/flexo/pesca/polo vegetarians (sounds like Rossini) are not vegetarians, they are omnivores. Any data from these diets must be removed to defend any “vegetarian” claims. Most vegetarians eat grain based diets. This is where gut dysbiosis begins.

  20. Chris, what would be your thoughts on white rice?

    Would they be like tubers and fruit in that they are beneficial or would they be closer to the modern “processed ceaseless” type of carbohydrate?

    • White rice is acellular, but the point of this article isn’t that we can’t tolerate a moderate amount of this kind of food. It’s that we shouldn’t base our diet on it, as we have in the western industrialized world.

      • Let me expand on what I meant.

        The cellular/acellular lens is only one way to look at it. Another is how rapidly absorbed the carbohydrate is. The more rapidly absorbed, the less likely it is to feed pathologically overgrown bacteria in the small intestine (good) or beneficial bacteria in the large intestine (bad).

        For example, Jasmine white rice is so rapidly absorbed that its GI is actually higher than pure glucose. This is because it contains primarily amylopectin, which is very easily broken down. Basmati rice, on the other hand, is rich in amylase which is much harder to break down, and has a GI of around 40 (going on memory here), so it would be likely to be fermented by both SI and LI bacteria.

        This is why labs that do SIBO breath testing permit consumption of Jasmine or short-grain white rice on the day prior to the test, but do not permit any other carbohydrates. So while Jasmine rice may be “cellular”, it is unlikely to feed the beneficial bacteria in the colon.

        • I’m sure you meant to say amylose.

          I am under the impression that amylose is more likely to form resistant starch when cooked and cooled.

        • Chris, what are your thoughts on “slow fermented bread” vs “fast-fermented bread”? My own trial and error with many different types of bread and wheats lead me to this conclusion that at least for me when I consume slow-fermented bread (sourdough made in 24 hours) I don’t have any gas and bloating whereas with fast-fermented bread (using commercial yeast in 45 minutes) I get gas and bloating right after eating bread. It seems to me this difference of fermentation is key. One feeds the bad gut bacteria, the other doesn’t. That said I don’t dispute that bread is not a nutrient dense food in its current form (just like non-pasture raised meat is not!) BUT it seems to me you can eat massive amounts of it just fine provided it’s slow-fermented AND you eat enough nutrient dense food from other sources (organ meats and so on). My own traditional Armenian ancestors would eat lots of breads just fine AND supplement it by eating greasy organ meat soups for example. Isn’t it about time we have a discussion about quality of our wheat/bread and how it fits with the rest of the diet instead of just bashing white flour completely?

  21. Dear Chris,

    you´ve mentioned the FODMAPs. The studies show (for example this one: http://www.ncbi.nlm.nih.gov/pubmed/25016597) that the low-FODMAP-approach reduces the total bacterial abundance BUT at the same time installs a greater microbial diversity. Isn´t that exactly what we are after as IBS- and IBD- sufferers?

    Many studies in the past have shown a possible link between decreased microbial diversity and IBS/IBD. I wonder, if there any studies which show this link between these conditions and a increased total bacterial abundance?

    I hope you can help me with this topic, because it would help me and my clients here in GER and CZ very much.

    Thank you for your work, it´s always a pleasure to read or hear you!

    • I think low FODMAP diets may not be a good idea over the long term. In our clinic, it is always our attention to address the GI issues that lead to FODMAP intolerance, and then have the patient reintroduce FODMAPs. In almost all cases this is possible, at least to a significant degree with some, if not all, FODMAPs.

  22. I use to think evolution was real. I don’t anymore.

    Interestingly it seems all men were vegetarians before the flood:

    “I have given you every herb that yields seed which is on the face of all the earth, and every tree whose fruit yields seed; to you it shall be for food” (Genesis 1:29).

    Only after the flood did they eat meat:

    “Everything that lives and moves about will be food for you. Just as I gave you the green plants, I now give you everything.” (Genesis 9:3).

  23. Very interesting! I just skimmed the study, it seems that he is saying that grains are also acellular due to the way the carbohydrates are stored in grains?

    “Tubers, fruits, or functional plant parts such as leaves and stems store their carbohydrates in organelles as part of fiber-walled living cells.”
    “The acellular carbohydrates of flour, sugar and processed plant-starch products are considerably more dense. Grains themselves are also highly dense, dry stores of starch designed for rapid macroscopic enzymic mobilization during germination.”

    This makes me wonder if I should be eating rice or not. I do eat it because I don’t seem to have any reaction to it that I can tell, but I’m not sure if it is good for me or not.

    • Dear Kelly,

      There is ample evidence that certain grains can be a healthy part of the diet. Further, there are cultures (both hunter-gatherer and traditional) that used them as staples and experienced excellent health and could produce well-formed children. Historical observation clearly points to the fact that certain grains are beneficial. This is what I share with most people: diversity the diet (i.e., eat less grain), select wild and heirloom breeds, and restrict (or avoid) gluten-containing kinds. While this is not the usual “don’t eat grain” sound byte, it is a statement that is not contradicted by observations of healthy people. Best wishes.

    • Processing methods like blending do break down and alter the structure of the fiber and cells, but I don’t think that’s a reason to avoid smoothies across the board as long as what you’re putting in them is real, nutrient-dense food.

      • If smoothies are OK as a regular part of a diet, then mashed forms of tubers and vegetables, which also destroy the cell walls of the plants, should be OK, too. Two examples are poi, a mashed form of taro, and Russ Crandall’s root vegetable mash recipe from his “The Safe Starch Cookbook” recipe. If these are OK, then the whole cellular-acellular distinction has so many exceptions that the guideline itself becomes meaningless.

  24. Thanks Chris, Could you clarify where prebiotics supplements like potato starch, inulin, acacia fibre, and psyhillium husks fit into the acellular versus cellular carbohydrate range?

  25. Great podcast Chris. Fascinating stuff.

    It’s interesting to note that the most recent food insulin index data also suggests that fibre negates the insulin demand of carbohydrate (i.e. net carbs rather than total carbs). See https://optimisingnutrition.wordpress.com/2015/03/30/what-about-fibre-net-carbs-or-total-carbs/

    So increased fibre feeds the gut bacteria which improves insulin sensitivity, reduces insulin demand of the food as well as promoting fullness and satiety!

  26. Chris,
    What lab do you recommend for stool/parasite testing? And do you know if digestive aids(enzymes/HCL/probiotics) would affect the levels and possibly give false negatives?

    • The stool tests of which I’m familiar (Genova and Doctor’s Data) both recommended stopping use of digestive aids for 3 days prior to sampling.

      The Doctor’s Data test reported absence of undigested material, which suggested my use of digestive aids was actually unnecessary. It also recommended eating adequate fat so the measurement of fat digestion would be valid.

      FWIW, I wouldn’t spend the money for a stool test unless I also had an organic acid test and a skilled practitioner to interpret the results. I think this will give a more complete picture of dysbiosis and permeability from which you can take the most appropriate actions. If I suspected parasites, I’d go for a multiple sample test.

  27. Hi Chris i have a question on prebiotics you mentioned. I have SIBO and notice a reaction to every prebiotic or probiotic i take even if its 1/16 teaspoon of prebiotic powder or a 4th of a capsule of prescript assist. Should i just fight my way threw it so i can restore healthy gut flora over the long term? i also have no growth of lactobilcilus and bifidobacterium.

    • This kind of reaction to pro/prebiotics is one of the big red flags that leads me to suspect SIBO, parasites, fungal overgrowth, or severe dysbiosis. Those things will probably need to be treated before you can tolerate a higher volume of pro/prebiotics.

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