The Importance of Feeding Your Microbiome - with Jeff Leach | RHR

RHR: You Are What Your Bacteria Eat: The Importance of Feeding Your Microbiome – with Jeff Leach


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I’m really excited to have a special guest, Jeff Leach from the American Gut Project, on this episode.  We talk all about the gut, which is, of course, one of my favorite topics.

In this episode, we cover:

1:00 What is the American Gut Project?
4:30 How the study of our microbiome changes as technology advances
15:22 Surprising insights from the latest gut bacteria research
22:38 What effect does diet have on the microbiota?
29:22 The effect of VLC/ketogenic diets on the microbiota
45:18 How people can get involved in the American Gut Project

Links We Discuss

Full Text Transcript:

Steve Wright:  Hey, everyone.  Welcome to another episode of the Revolution Health Radio Show.  This show is brought to you by  I’m your host, Steve Wright from, and with me is integrative medical practitioner and healthy skeptic Chris Kresser.  Chris, how’s your day going?

Chris Kresser:  It’s going great, Steve.  How are you?

Steve Wright:  I’m having a good day, too.  Boulder is having some good weather, and as long as my computer doesn’t blow up, this is going to be a great podcast.

Chris Kresser:  Good.  Well, I’m really excited.  We have a special guest here today, Jeff Leach from the American Gut Project, and I’m just going to ask Jeff to introduce himself, tell us a little bit about his background and what he’s up to, and then we’re going to talk all about the gut, which is, of course, one of my favorite topics, and I know it’s one of yours, too.

Jeff Leach:  Hey, Chris and Steve.  Thanks for having me on!

Chris Kresser:  Hey, Jeff.

Jeff Leach:  You guys hear me OK?

Chris Kresser:  Yeah, we’re good.

Jeff Leach:  OK.

What Is the American Gut Project?

Chris Kresser:  So, Jeff, maybe you could just tell us a little bit about your current position, what you’re up to, what your background is, and we’ll go from there.

Jeff Leach:  OK, great.  I’ve actually been doing archeology since the early ’90s, kind of a mixture of archeology and anthropology.  I was interested in diet from an evolutionary perspective, which kind of led me to the gut.  About 8 or 10 years ago I started getting interested in the gut microbiome, and of course, that’s pretty much when it started taking off, when next-generation sequencing starting showing up and it really started to burgeon.  There weren’t a lot of people thinking about the gut and the dietary influence from an evolutionary perspective, so I thought I could play a role there and make a contribution.  So, in the last couple years I’ve really gotten involved in gut microbiome research.  I’ve actually gone back to school, now pursuing a different degree in medical microbiology at the London School of Hygiene and Tropical Medicine, and I collaborate with a number of researchers now.  We have ongoing projects in Africa looking at hunter-gatherer populations, and then, of course, I helped co-found or came up with the American Gut Project that we’ve now launched, and that is up and running.

Chris Kresser:  Wow, that sounds fascinating, Jeff.  Can you tell us a little bit more about the American Gut Project, what its goals are, and where you’re at with it right now?

Jeff Leach:  OK.  Yeah, the American Gut Project we kind of dreamed up last summer, Rob Knight and I.  Rob’s at the University of Colorado at Boulder.  He’s a world-leading bioinformatics guys, and he’s just about on every other microbiome paper that comes out, it seems, lately.  But Rob and I got to talking, and one of the things that was missing was a huge sample of human beings, you know, 5, 10, 15 thousand people.  In order to do that project, it would take hundreds of millions of dollars and years to put together, so we decided we would pursue something this through crowdfunding or crowdsourcing.  So, we put together the project on paper, if you will, last summer, and then we approached the University of Colorado at Boulder for ethics approval to do the project.  So, we spent a couple of months getting IRB, or institutional review board, approval for the project, got that in place, and then we launched it on a crowdfunding site.  And so, as of today, we’ve got about 7000 people enrolled in the project.  It’s the largest microbiome project in history.  Our goal is about 20,000.  We just released data on our first 1000 individual participants, and the long-term goal is, are there patterns among the general population based on diet and lifestyle that may be interesting?  So, for example, are vegetarians different than omnivores?  Are people with large BMIs different than people with small BMIs?  Does the number of people in your household matter?  Do you live in the country or the city?  Does that matter?  So, putting all that metadata together with the actual sequencing results – because we send you a kit to your house where you can self-sample and send it back to us for a $99 donation – are there any patterns with that metadata?  We just started getting the initial data in, so we’re pretty excited about what we’re seeing so far, and we think it’s going to get interesting once we get up around 5, 10, or 15 thousand samples.

How the Study of Our Microbiome Changes as Technology Advances

Chris Kresser:  Right.  You mentioned earlier that DNA PCR analysis has really changed the study of the microbiome and particularly in the gut, so tell us a little more about that.

Jeff Leach:  Yeah.  If everyone remembers back a decade or more ago, or back two decades, when they sequenced the human genome, it cost hundreds of millions, if not billions, of dollars to do.  So, what’s happened with next-generation sequencing, it’s almost like technology with cameras.  The pixels have gotten better, the computing power has gotten better on laptops, and the same thing has happened in the laboratory.  You can literally take a poo sample from somebody and take a snapshot, if you will, of the DNA of the bacteria for literally just a few dollars.  You know, 5 or 10 years ago that would’ve been hundreds of thousands of dollars, so next-generation sequencing has dropped the cost and brought the cost down, and then the analytical tools have gotten a lot better as well, the bioinformatics have gotten a lot smarter, if you will, and cloud computing and big data has gotten a lot easier.  So, it’s kind of a meeting of big data, big analysis, and technology getting cheaper that makes this all possible.

Chris Kresser:  Mm-hmm.  Let’s talk a little bit more now about what the significance of all of this is because I know for some people who have been listening for a while to the show, they’re aware of the connection between the microbiota and the gut and various aspects of human health, but for some people who might be a little newer, this is, perhaps, news.  Interestingly enough, I saw a study today in Nature – or a report on the study, at least.  I’m not sure if you saw it, Jeff.  Some Japanese researchers found that butyrate, which is a compound that’s produced by bacteria fermenting dietary fiber in the gut, can actually improve T regulatory cell production.  T regulatory cells help keep the immune system in balance, and a lot of people with autoimmune disease have impaired T regulatory cell function.  Essentially the study is showing that the gut bacteria can directly influence the immune system.  We’ve known for a while that butyrate, this compound, had an anti-inflammatory effect, but this study showed a particular mechanism for how it does that.  This is just one example of many, many studies now, it seems, Jeff, that are showing a connection between our gut bacteria and aspects of health, which we may not have even realized would be related to our gut, like our mood, depression, skin, etc.  Is this something you’re following a lot, the research around this?

Jeff Leach:  Oh, yeah.  What’s interesting about this, as you know, Chris, and anybody who follows this subject, it wasn’t that long ago, just 5 or 10 years ago, before we started realizing – you’ve heard the number repeated before – 90% of the cells in the human body are not even human; they’re microbial.

Chris Kresser:  Mm-hmm.

Jeff Leach:  We’re more microbe than mammal.  That really wasn’t well understood a decade ago, and so the new DNA techniques are allowing that.  And what’s really remarkable is that not since Darwin’s concept of natural selection has something had such a profound impact on our understanding of “self.”  In our anthropocentric world, we think we’re the center of it all, but at the end of the day, the microbes are actually pulling the levers on a lot of what’s going on when you consider that at the gene level they outnumber us 150 to 300 to 1.  We’re born with genes that mom and dad gave us, and we’re pretty much stuck with those, but the genes in our gut – again, the bacteria are called the microbiota, and when you add their genes in as well, that’s our microbiome.  Of course, a biome is just an ecosystem, so we have this inner ecosystem.  So, depending on how we treat them, they can make life OK or they can make it problematic, and when they get out of balance, it’s now thought that that may be the root or the cause of a lot of disease.  The problem is working out causality versus correlation

Chris Kresser:  Right.

Jeff Leach:  People’s general take on bacteria, which is still kind of a little bit of a hangover from the last 50 years, is that bacteria are bad, so we need to kill them through antimicrobial soaps and antibiotics, which, of course, save lots of lives, and on and on and on.  We’ve improved hygiene and sanitation and really changed things, but the other edge of that sword is that we may be changing the relationship of the microbes in such a way that this imbalance is a precursor or we’ve opened the pathogen’s door, if you will, to inflammation.  Now, as you clearly know, Chris, it’s hard to be in the medical sciences now and not be thinking about how bacteria affect your particular field of study.  It doesn’t matter if it’s psychiatry.  It doesn’t matter if you’re a heart surgeon or if you deal with autoimmune disease.  Microbes are in there somewhere, and so now what everybody’s trying to do is to figure out what role microbes play in diseases as diverse as autoimmune diseases or obesity or other metabolic disorders like type 2 diabetes.  But again, it’s the early days and most microbiome researchers will tell you that.  They’re very cautious.  They don’t want to make the same mistakes that… I wouldn’t call them mistakes, but they don’t want to overpromise, if you will.

Chris Kresser:  Yeah.

Jeff Leach:  Back in the ’90s, we were all told that if only we could sequence the human genome, within a few years we could unravel disease, and of course, that really hasn’t come to fruition.  And microbiome researchers are also very cautious about dietary suggestions to nudge your microbiome because everybody’s worried about how one day butter’s good, the next day butter’s bad.  Carbohydrates are good one decade, carbohydrates are possibly bad the next decade.  So, microbiome researchers have really paid attention to what has happened to the genomics crowd with the human genome, and they’re very hypersensitive to the ebb and flow of nutrition advice, so that’s why you very seldom will hear microbiome researchers kind of go out on a limb and tell you what they really think.

Chris Kresser:  OK.  Well, I’ll try not to put you on the spot too much!

Jeff Leach:  That was a way of setting up your next question!

Chris Kresser:  Yeah, well, I may try to tease a few things out of you in a very noncommittal way, but there are a couple things you said that I just want to go back to.  This is one of my favorite topics, and we could talk forever, but there’s a quote that I actually have in my book from Justin Sonnenburg at Stanford that says something to the effect of humans are just elaborate vessels for the propagation of microorganisms.

Jeff Leach:  Yeah, spot on.

Chris Kresser:  I thought that was a fantastic quote and really does change our whole concept of self and identity.  And when you really start thinking about it, of course, it can be a little creepy, but the upside, in my opinion as a clinician, is what you mentioned:  The genes that we inherit from our parents of origin are set, and certainly there are environmental triggers and epigenetics to consider, but the genes that we have in our microbiota are somewhat mutable.  We don’t really know how much yet, of course, but as a case in point, in that paper that I just mentioned in Nature, what they found is that the bacteria that ferment the fiber and produce butyrate, that causes epigenetic changes that regulate the expression of genes that are responsible for the differentiation of T cells.  And so, it’s the gut microbiota effecting epigenetic changes in gene expression in our body, which have real and lasting effects on our health.  So, it’s a pretty exciting time to be involved in this area and even, as a clinician, for me on outside just following the research but starting to apply that in my own patient population and seeing some pretty dramatic results just from modulating the gut flora.

Jeff Leach:  Yeah, I think what’s interesting is that a lot of the initial studies over the first couple of years were basically kind of creating inventories of who’s there, what’s their relative abundance.  And this originally started off with culturing; now there are noncultural techniques.  We’re now moving from these catalogs of who’s there to what are they doing.  It would be nice if you could pin down one species or one strain that’s causing this or causing that, but in most cases, it’s the consortium, it’s the community, and so isolating one or two strains may not get you to the solution that you’re after with regards to causality.  I always kind of equate it to engineers who work on cars.  You’ve seen the wind tunnels with all the white lab coat engineers, with the smoke running over the car like it’s going 100 miles an hour, and there’s a set of engineers that work on the door handle, a set of engineers that work on the aerodynamics of the mirror, the guys and ladies that work on the slope of the windshield, and each one of these things plays into the performance of the overall automobile.  The question is, which ones are really more important than the other ones?  There are keystone species or groups of bacteria that play a bigger role?

Chris Kresser:  Mm-hmm.

Jeff Leach:  And so, right now it’s figuring out all the engineering, if you will, of all the moving parts in the analogy being the car.  In this case, it’s groups of bacteria, either phylum or species or strain level.  And there are hundreds, if not thousands, of potential studies and things to consider, and each one is important, but now we need to kind of pull back and stare at it from a distance and see what really matters the most because if everybody gets a say in it, let’s say the bumper team has a say in it, and the windshield team has a say in it, what you’re going to end up with is lots of good advice from a thousand different people, but you couldn’t possibly keep up with it all.  So, what are the big-picture things that the microbiome is trying to tell us – that’s the Holy Grail.

Surprising Insights from the Latest Gut Bacteria Research

Chris Kresser:  Right.  So, with your previous caveat in mind, what sort of things can you tell us in terms of major patterns or things you’ve observed, things that have surprised you in doing this work so far?  We understand, of course, that it’s still early days and these aren’t hard and fast conclusions and that it may change in the future, but I’m just curious to know what general trends have become apparent, if any.

Jeff Leach:  Yeah, that’s a great question, and I think it’s a question that’s asked every day.  I guess from my perspective, if I can step back a little bit, the thing that struck me the most a few years ago when I really started getting involved in this was that if you look at all the studies, you have 10 obese patients who are sequestered in a hospital ward and they’re fed this diet and they collect their stool samples and they change their diet, or even the human microbiome project where you look at 250 healthy individuals with average BMI and average age of 25, in all these studies, including the ones in Europe and Japan and Australia, hundreds and hundreds of studies, the thing that’s striking about that is that potentially, most likely, every participant in the study is compromised, in that they grew up on a Western diet.

Chris Kresser:  Right.

Jeff Leach:  We all take too many antibiotics.  We all drink too much tequila.  We all do these things to our body.  We drink water that flows through a public water supply that has things in it that are supposed to neutralize bugs.

Chris Kresser:  Yeah.

Jeff Leach:  And so, when we’re trying to get to that fountain of microbial balance or optimal microbiome, we’re never going to get there looking at Western populations because we’re all compromised.  The thing that was most striking to me was there was no data on populations that hadn’t taken antibiotics, that hadn’t wolfed down a Big Mac and Cheese, that hadn’t been drinking tequila, so that’s when I, a few years ago, said we need to look at ancestral populations, and they’re disappearing very quickly.  So, Maria Dominguez-Bello at New York University was doing work in South America, her and Marty Blaser.  The Gordon Lab was doing a little bit of work in Malawi, but they’re still looking at rural populations, which are basically just poor folks living in cinderblock houses and sheet metal homes that are barely squeaking out a living, and those really aren’t ancestral populations.  Their diet, in a lot of cases, is, like in Burkina Faso and South Africa, 50%, 60%, 70% of their calories come from grains.  That’s why we turned to South Africa, spent some time in Namibia and Botswana looking for these ancestral populations among the San Bushmen.  Of course, they’ve been fully acculturated and resettled now, so now we’re in Tanzania working with the Hadza, which are a perfect referent for what we’re after.  So, that was the most striking thing to me, is missing that baseline population of what a group might look like before the antibiotics and so on and so forth.

To kind of get back to your question, the one thing that you see and that we’re starting to see in American Gut and that you see in other large studies is that everybody kind of falls along a continuum.  A few years ago, it was thought that if you had a high level of Firmicutes, which is a phylum of bacteria, that it was more predictive of maybe an obese phenotype, and if you had less Firmicutes, you were more likely to be lean, but that turned out not to be true.  When you look at the Human Microbiome Project – and again, that’s a healthy group of people with an average age, I think, in their 20s – you had some people who had 80% Firmicutes and 20% Bacteroidetes, and then on the other end you had some people who had 20% Firmicutes and 80% Bacteroidetes.  In other words, everybody kind of falls along this continuum.   And then there was that idea that you could divide everybody up on Earth into these groups or these enterotypes, which turns out is not true either.  Enterotypes, everybody kind of falls along a continuum.  So, one of the most breathtaking things is that there is no patterning, at least based on the questions and the metadata and the populations that have been looked at so far.

Now again, this is separate from looking at certain diseased groups or dietary interventions.  Those are separate.  But when you kind of lump everybody together like we’re doing in American Gut, there are some early patterns that are popping out, but you’re not getting striking patterns that most people think exist.  I think that has a lot to do with the environment as a great equalizer.  Diet is only one piece of the formula.  Lifestyle is a big component, and again, we see that in hunter-gatherers.  Like, in Tanzania we see that men eat much more protein and fat than women, and women eat a lot more fiber and probably resistant starch, so it will be really interesting to see if their microbiomes are different.  When we look in the United States, when we look at 1000 men and women in the American Gut Project, they look pretty much the same at the phylum level.  There are the same number of Firmicutes, the same number of Bacteroidetes, so there’s no separation between men and women yet.  Evolution teaches us that more than likely men probably did consume more protein and fat than women if the Hadza are a good referent, and so we should expect, based on diet, that we should see some differences, but I think what is going to happen is that the environment is the great equalizer.  The fact that you share the same water, share the same soil, you’re covered in the same feces and blood of the animals that you consume and the dirt from the plants you dig.  I think that ultimately levels the playing field, and that social interaction and that movement of bacteria is very fluid between individuals, the soil, the plants, and especially the animals.  So, it’ll be really interesting to see how that shakes out.

But to kind of get to what you’re really asking, is one diet more interesting that another with regards to promoting a healthier microbiome, and the question then goes back to, what’s a healthy microbiome?  Because we don’t know – there are some ideas, but we don’t know – we don’t know which direction you should be nudged.  Again, that’s why I think these hunter-gatherer populations are important.  We know that people who eat lots of whole grains seem to have high levels of a group of bacteria called Prevotella.  We see that in Burkina Faso.  We see it in South Africa.  We see it in a few other places.  And then you have people like Michael Pollan, kind of who is the Omnivore in Chief, who have super high levels of Prevotella.  But then we find out that Prevotella is associated with HIV, it’s associated with rheumatoid arthritis, it’s associated with kids who have autism, and it seems to be associated with inflammation, yet you have somebody like Michael Pollan who has high levels of Prevotella that appear to be associated with whole grain consumption.  Do we really want high levels of Prevotella if it’s been associated with these inflammatory states?  And the answer is we just don’t know.

Chris Kresser:  Sure.  It’s hard to piece out correlation and causation there.

Jeff Leach:  Yeah.

Chris Kresser:  And the influence of other factors, definitely.

Jeff Leach:  Oh, yeah.  It’s endless.

What Effect Does Diet Have on the Microbiota?

Chris Kresser:  So, grains and Prevotella.  I definitely had heard of that, and I wrote about it a little bit back with the whole TAMO red meat controversy when that came out.  I’m curious, Jeff, is there any research or any observations on your part about how different types of fiber trigger different types of growth in the microbiota, for example, soluble fiber versus resistant starch?  Is eating fruits and vegetables sufficient?  Do people need more soluble fiber, like in the form of starchy tubers or resistant starch, which would be a whole different category since it’s not really that prevalent in a normal diet?  I know it’s sort of peripheral to your work in terms of getting this granular, but I’m just curious if you have thoughts about that.

Jeff Leach:  Yeah, the most interesting group doing work on fiber is probably Harry Flint’s group in Scotland.  I actually consume a considerable amount of fiber, I personally eat between 50 and 150 grams of fiber a day.  I try to consume 20 to 30 species of plants a week if I can.  So, I get a huge quantity and diversity.  I’m interested in it because fiber is the primary substrate or food, if you will, for bacteria, so if you kind of look at it from an evolutionary perspective, if I was in charge of the USDA and Health and Human Services for a day – which God help us, I’m not… for a lot of reasons! – but if I was in charge of My Plate, which used to be the US Food Pyramid, I would argue that probably the most breathtaking change in the human diet that’s had the greatest impact on not only our microbiome, but our health, I would argue that that’s the drop in the diversity and quantity of dietary fiber.  For example, you see in Africa 6-month-old Hadza kids that are being weaned onto food are getting 100 to 200 grams of dietary fiber a day, every day.

Chris Kresser:  Wow.

Jeff Leach:  And so, when you think about dietary fiber from the perspective of your gut microbiota, it’s food for them.  You mentioned Justin.  I know Justin very well.  We’re doing some work with Justin’s lab.  We’re actually taking hunter-gatherer poo and we’re humanizing mice with it, different bacteria from different seasons or different microbiomes from different seasons.  And Justin will tell you that once you start starving your bacteria, you don’t deliver enough substrates, resistant starch and non-starch polysaccharides, when you don’t deliver enough of that stuff from plants, the bacteria have to eat something, so they start eating you.

Chris Kresser:  Right.

Jeff Leach:  They eat your mucous lining in your colon, and it’s thought that maybe once you start to degrade that protective barrier, you then expose it to potential problems.  That’s interesting.  Again, I pay a lot of attention to fiber for my own health, from my own perspective.  For example, the most dominant bacteria in my gut are members of Ruminococcus.  Ruminococcus are dominant genera in things like cows and rhinoceros, things that eat a lot of grass, and so I eat a lot of dietary fiber.  I eat a lot of the whole plant.  I always tell people if you’re going to eat asparagus, the best part of the asparagus is down at the bottom, and that’s the part we tend to cut off and throw away.  We tend to think of that as stuff that kind of passes out the other end, but depending on your microbial makeup, as much as 60% or 70% of that can actually be broken down.  If you don’t have a lot of, let’s say, Ruminococcus and these other guys in there, then a lot of that stuff will pass out the other end.  So, when I go to the grocery store and I push the cart around, I look in the produce section.  I say, OK, if you put Haagen-Dazs ice cream in your shopping cart, there’s not a lot of food for your bacteria there.  There’s a lot of goodness for you, and we all like Haagen-Dazs ice cream, but when you put that bell pepper in your basket or that leek or that cassava or whatever it may be, I always look at it and say how much food in this is for me, and how much food is for my bacteria?  That math is really simple.  It’s how much dietary fiber and resistant starch is in here, and how am I going to prepare this?  How I prepare the food has a dramatic impact on the microbiota as well.

So, I typically look at my grocery cart and make sure I feed my bacteria a diversity and quantity of dietary fiber, assuming I don’t have other issues that don’t allow me to do that.  I don’t, so I try to maintain high levels of bacteria that degrade cellulose and pectin and lignin and things like that because when they do ferment, it produces short-chain fatty acids and organic acids, and we know they’re doing their job when we’re bumping and farting, OK?  I tell everybody if you’re not having two to three bowel movements a day, then you need to go back and start over, and one of them should be a whopper.  If you’re not having that kind of bowel activity, then you’re not fermenting enough – again, assuming you don’t have other issues – and so you need to increase the diversity and quantity of fiber.  Why that’s important is when those bacteria ferment that dietary fiber – and again, get it from a lot of sources – it changes the pH of your colon.  It makes it more acidic.  A lot of opportunistic pathogens are pH sensitive, and so typically as those Ruminococcus and those Blautia and those Bifidobacterium and all those guys go up, you often see the other ones go down.  It’s not always a one-for-one, but keeping your colon acidic through fermentation, frequent bowel habit, then all of that stuff leads to improved barrier function with regards to, you know, some people generically call it a leaky gut.  You know a lot about it, Chris.

Chris Kresser:  Mm-hmm.

Jeff Leach:  With LPS translocating and a lot of other things like that.  At the end of the day, I don’t think it’s rocket science.  To borrow from Michael Pollan, eat food, mostly plants, not too much.  I think that goes a lot way towards a healthier microbiome.  And again, as you know, antibiotics are lifesaving, but we now know that they’re having a hell of an impact on our gut microbiota in a bad way.

The Effect of VLC/Ketogenic Diets on the Microbiota

Chris Kresser:  Absolutely.  So, Jeff, we’re now kind of getting closer to a subject that’s very controversial in the blogosphere lately, which is low carb, high carb, medium carb –

Jeff Leach:  Right, right, right.

Chris Kresser:  This whole debate.  It’s getting kind of ridiculous, in my opinion.

Jeff Leach:  Yeah.

Chris Kresser:  What I’ve noticed – and these are just my observations as a clinician, and it’s a relatively small sample size – but almost every patient that walks in my door I do a comprehensive stool analysis, and I use different labs depending on what I’m looking for, but most of them report on the pH.  They can give you an idea of what the pH is.  They test for butyrate and total short-chain fatty acids and some other markers that give me an idea of what’s happening in terms of their consumption of fermentable fiber and the effects of that fiber on the gut flora.  And what I’ve noticed is that many people who are on a ketogenic or very low carb diet – let’s say less than 30 or 40 grams of carbohydrate a day – come back with an alkaline pH in the stool.  They have low levels of butyrate or other total short-chain fatty acids and some other markers of dysbiosis.  So, that got me thinking and wondering about the potential adverse effects of a very low carb or ketogenic diet from the perspective of gut flora, gut microbiota, and wondering is it that people who are doing the ketogenic diets are not only doing a ketogenic diet, but they’re also just not eating enough plant fiber?  And that kind of makes sense.  If they’re really trying to limit their carbohydrates, they’re going to be somewhat limited in terms of the variety of vegetables and certainly fruits that they can eat.  You can correct me if I’m wrong, but I think I read a blog post of yours a while back that was speculating maybe that 35 or 40 grams of carbohydrate may not be sufficient to reach the levels of bacterial fermentation that you were just talking about.  Do you have any thoughts about that?

Jeff Leach:  Yeah, it’s a great topic, and that’s interesting that you’re seeing the shifts in the pH in the colon.  That’s fascinating, and it’s what you would expect.  It’s an interesting topic, and it’s a pretty passionate crowd of people as well.

Chris Kresser:  Oh, yeah!

Jeff Leach:  Like Jimmy Moore and those guys.  I mean, I have nothing but ultimate respect for Jimmy.  He is all in, but I worry about it.  What’s interesting in American Gut is we have quite a few paleo dieters that have identified as paleo dieters in the study, and we need a lot more.  It’s a group of people we’re very interested in, and we’re interested in the very low carbohydrate guys as well.  We’re seeing an increasing number of those guys in the study, but we need more of them to have any kind of definitive take on the problem.  But if you just look at it from what we know from the literature – and there are not many studies that have isolated very low carb people – but when you come at it from the perspective of pH like you do, which is spot on, what happens when people go on a low carb diet – you know more about this than I do, but I always get the emails, What’s wrong with eating 10 cups of broccoli a day?  One of the big things that the low carb diets do is they really drop out the resistant starch in the diet.  And what’s interesting about a lot of butyrate producers, Roseburia and these guys and Eubacterium, they’re cross-feeders.  For example, you have certain species of bacteria, groups of bacteria that break down whatever, cellulose and hemicellulose, and produce acetate and propionate and all these things, but a lot of the butyrate producers are cross-feeders and they’re feeding off of other activities.  So, when I see a very low carb person, I often see not only a huge drop in dietary fiber, but a drop in diversity of dietary fiber and a significant drop in resistant starch, which is a huge source of nutrients for the microbiome as well.  Resistant starch is often called the third dietary fiber.

Chris Kresser:  Right.

Jeff Leach:  But I lump it all together with anything that escapes digestion in the upper GI tract and ends up in your colon and is available for fermentation, and it’s a lot of things besides just dietary fiber.  But I’m concerned about it for the exact reasons that you are.  We don’t have the data.  Nobody has done any nice clinical controlled trials, but when you starve the bacteria, you may see an increase in mucin degraders like Akkermansia and a few other ones.  That shift in the pH is going to provide opportunities for pathogens to maybe bloom up that may cause some down-the-road, long-term problems.  But again, maybe not.  Nobody knows for sure, but if you’re shifting that pH and you’re not fermenting, you’re opening the pathogen’s door.  It’s going to take a long time to unwind this, but I think the more low carb people we can get in the study, we can contribute to the conversation at least to the point where it can serve as a baseline for maybe more controlled clinical kinds of studies.  But I would never recommend a low carb diet.  I think you can eat lots and lots of healthy carbs and maintain your weight.  I’m not necessarily a paleo dieter.  I don’t eat grains.  I have a type 1 diabetic daughter, so our family is very sensitive to the effects of all grains.

Chris Kresser:  Sure.

Jeff Leach:  And I don’t eat them a lot for that reason.  I’m not really a strict paleo dieter because I eat legumes and I drink tequila.  I’m giving it up!

Chris Kresser:  That’s what I call the 80/20 rule, Jeff!

Jeff Leach:  Yeah.  The low carb thing is really terrifying to me from a microbiome perspective, but I want to couch that in saying that that’s not based on any data, so to speak.  It’s just based on what we know about fermentation.

Chris Kresser:  Mechanisms.  Right.

Jeff Leach:  Yeah, time will tell.

Chris Kresser:  This is an interesting topic, too, from a clinical perspective because there are people who benefit from ketogenic diets and very low carb diets.  For example, as you probably know, Jeff, there are several studies that suggest that ketogenic diets can be beneficial for people with neurological conditions, like Alzheimer’s and Parkinson’s, epilepsy, etc.  And then some people who have type 2 diabetes and are extremely sensitive to glucose and have poor blood sugar control and insulin resistance, leptin resistant, and don’t do well with starch and foods that contain a lot of fermentable fiber often find themselves needing to follow a really low carb diet.  In those situations, I’ve been, as a clinician, trying to figure out that assuming they’re going to stick with this really low carb diet, how can we mitigate some of the potential harm that could be caused to the gut microbiota?  And again, we don’t know that it’s harmful, but I’m just speculating based on the same factors you just mentioned as well as some clinical data, like the stool testing that I mentioned before that.  So, what I’ve been trying to do in those situations is get people who are doing a ketogenic or very low carb diet on some prebiotics and some resistant starch in the form of potato starch, which doesn’t seem to have any negative impact on their blood sugar and, in fact, actually has the opposite effect in many cases.  Richard Nikoley over at Free the Animal has been writing a lot about resistant starch, and a lot of people with blood sugar issues have seen drops of, like, 10 or 15 mg/dL of their fasting blood sugar just from taking 4 tablespoons a day of potato starch, which has, as you know, a lot of resistant starch in it.  And in my patients, I’ve seen a similar response and also with people with long-term constipation and gut issues.  Of course, it makes sense that resistant starch could play a significant role there.  So, I would say at least tentatively now that if anyone is on a ketogenic or very low carb diet, that you might consider some prebiotic fibers or resistant starch just to make sure that you’re feeding your gut bugs what they need to survive.

Jeff Leach:  Right.  I think it’s great advice.  If I was stranded on a desert island for 10 days, what food would I take with me, assuming I had water?  I would take onions, garlic, and leeks.  It seems counterintuitive at some level, but as you know, the prebiotic concept, which was created by Glenn Gibson and Marcel Roberfroid in 1995, and I’ve published stuff with Glenn before on prebiotics from archeological stuff, but I eat onions every day.  I try to eat leeks every day.  Garlic not only keeps away vampires, but it contains prebiotic fructans.  What’s interesting is – this is just a personal note – I have very high levels of Bifidobacterium because I consume lots of prebiotic foods, but I also don’t eat yogurt because it’s slimy and it’s nasty and I don’t like it, but I also don’t eat fermented foods either.  I look at a lot of people who consume lots of fermented foods, and I have higher levels of lactobacillus than they do, and I don’t eat fermented foods.  The bifidogenic effect of those prebiotic foods is well known.  Elevating levels of Bifidobacterium, which is considered a helpful group of bacteria, can’t hurt.  Now, at the end of the day, is Bifidobacterium going to save the day?  Who knows?  It’s a dominant bacterium in breastfed infants.  It seems to decrease with age, but elevated levels of Bifidobacterium from prebiotics, it seems to also suppress some groups of Proteobacteria at the same time.  It’s something that I’ve talked to Glenn Gibson about all the time at the University of Reading.  He’s the world’s leading expert on prebiotics, and he’s probably published 500 papers on prebiotics.

Chris Kresser:  Yeah.  I’ve read lots of them.

Jeff Leach:  Yeah, and Glenn’s a fantastic guy and he’s funny.  And I think from a resistant starch standpoint, the resistant starch that I think makes the most sense to me is probably lentils.  Lentils contain quite a bit of resistant starch as well.  This is your area and your expertise, but it can’t hurt by increasing and ingesting those if you don’t have other issues.  And again, the other note or the caveat to that, which you’re aware of, Chris, is that you can also cook the prebiotics right out of the onions, too.

Chris Kresser:  Sure.

Jeff Leach:  You can caramelize them and reduce them down to mono- and disaccharide and then game over.  A little bit of cooking is not a bad thing, but I think it’s time for the apple to move over.  I think an onion a day may keep the doctor away.

Chris Kresser:  Right!

Jeff Leach:  My apologies to the apple industry.

Chris Kresser:  Yeah, exactly!  One other note for people who are listening to this:  One of the things that got me thinking about this in the first place was that I had a lot of patients coming to me who had been on the GAPS diet.  I don’t know if you’re familiar with that, Jeff.

Jeff Leach:  Yeah, I’m very familiar with it.

Chris Kresser:  Yeah, and they had done the GAPS intro, which for those of you who aren’t familiar with it, it’s essentially just meat and broth for a period of time, and it can be tremendously effective and therapeutic for people who are dealing with gut pathogens and small intestinal bacterial overgrowth, and one of the reasons is that it literally starves the bacteria because they have nothing to eat or very little to eat.  But what I started to see is that people who stayed on that kind of protocol for a long period of time, they would improve and feel better, and then after a while they’d start to feel worse and worse and worse.  And I began to suspect that part of the reason that they were feeling worse is that the thing that they did, which was therapeutic initially, i.e. starving their gut bacteria because they had a lot of bad bacteria, then actually became harmful over time because they weren’t only starving their bad bacteria, they were also starving their good bacteria.  That’s when I started to advocate for GAPS being looked at as a more temporary therapeutic approach, and in fairness, even the creator of it, Natasha, has talked about it that way for the most part.  But I saw a lot of issues with people who were staying with that really extreme early intro approach and started to recommend that people add some more starchy tubers and other starchy types of plants and resistant starch into their diet as they improved in function so that they could preserve their good gut bacteria without completely decimating it.

Jeff Leach:  Yeah, that’s a great observation.  Again, if you think about it from an ecosystem perspective or from an ecosystem restoration perspective, if you take any ecosystem like the gut, the microbiome, and if you starve it, you’re spot on.  If you starve your backyard and all the diversity of plants, if you just starve it of nutrients, all ships go down with lowering water.  And that perturbation, if you will, it wouldn’t be on the same level as an antibiotic, but it is a perturbation; it is an insult.  And when you insult an ecosystem, insults like fire, drought, nutrient overload or nutrient deprivation, any of these perturbations typically result in a flourishing of weedy species, in this case, opportunistic pathogens.  I know the GAPS diet.  I don’t know the lady who wrote it, and so it’s kind of out of my pay grade to talk about it too much, but from an ecosystem restoration standpoint, it makes absolutely no sense whatsoever to starve your gut microbiome at any level.  That’s like people who do colon cleanses.  I just want to cringe.  Unless you have some very specific medical reason to do it, you might as well just let somebody hit you in the mouth.  It makes no sense at all.

Chris Kresser:  Wash out all your beneficial gut flora as quickly as possible.

Jeff Leach:  Yeah!  And again, anybody who’s ever tried to maintain a yard and had a drought or you light the backyard on fire, weedy species and opportunistic things come back, and that’s exactly what’s going to happen.  You’d probably be better off nurturing it a little bit rather than trying to starve it as an idea.  But you know, as you said, who knows?  It seems to have some early benefits, but long term it clearly doesn’t make any sense, and I would argue that it probably doesn’t make any sense initially either.  But who knows?

How People Can Get Involved in the American Gut Project

Chris Kresser:  People definitely have benefit from it up front, but there are a lot of things that provide benefit but also can cause harm, so we can’t necessarily use that as a measurement.

OK, Jeff, so we’re coming up on the end here, and you mentioned earlier that you really are looking for people who are doing paleo and specifically low carb paleo diets.  There are a lot of folks who listen to this show who probably fall into one or both of those categories, so how can they get involved?

Jeff Leach:  The paleo group and the low carb group are very interesting to the research team.  To put this in perspective, there are probably about 50 different people working on the American Gut Project right now.  They’re all volunteers.  We have over 80 or 90 total collaborators.  But there’s a big interest, and it’s an interesting dietary group because they do keep good records and they pay attention to what they eat, so if we could increase the paleo participants and the low carb participants in the group, that would be fantastic.  And people can just easily sign up.  You can go to  Just follow the links.  It takes a $99 donation to get in the game, and again, this is not a for-profit business.  It’s completely volunteers.  All of that money goes to lab supplies and mailing.  I think there are one or two actual paid positions, but not at the research level.

Chris Kresser:  Nobody’s getting rich.

Jeff Leach:  Not even close!  And I think the people who are getting rich are the fundraising sites or the crowdsourcing sites.  They get a piece of the pie.

Chris Kresser:  Right.

Jeff Leach:  So, you can go and sign up, but a way to reduce the cost is if you can get one or two other people.  It’s a donation of $99, but if you do two samples, it’s $180.  In other words, you can get it down to about 80 bucks a sample if you get a couple of friends.  And then you could have all the kits shipped to one address, and then you could distribute them to your friends.  A bug buddy, if you will.

Chris Kresser:  Mm-hmm.

Jeff Leach:  That’s a lot of fun.  We started in November.  We just started releasing results.  We’re kind of catching our stride right now, and we’re turning the samples around much quicker, so if you get a sample in, you could expect results within a few short months opposed to maybe six months.  Now we’re starting to accelerate, and so anybody that participates will do us a lot of good and really help us reach that 20,000 number.  Everybody’s going to benefit from this.  Also I can’t stress enough that if you participate in the project, it’s a huge teaching moment, and I’ve watched people go through this kind of metamorphosis of signing up.  Then they start listening to people like you, Chris.  You pay a lot of attention to the microbiome, and you’re spot on 99.999% of the time, which is as good as anybody’s ever going to be, and you talk about it in a way that people understand.  And once people get involved in American Gut, they start researching different bacteria, they start paying attention to a few more press clippings, and then when they get their results, I can tell you – I mean, I’ve been collecting my poo for a long time and keeping it in the freezer and having my own stool samples analyzed, which is a little creepy, but maybe that’s why I’m not married anymore!

Chris Kresser:  All in the name of science, Jeff.

Jeff Leach:  All in the name of science.  But it’s unbelievably empowering when you actually see this data.  It’s very different than your cholesterol level or any other kind of diagnostic.  When you see that data, it literally takes your breath away because you see what your diet and lifestyle is and how it may shift those around, and it’s literally within your control… for most of us, not all of us.  Save money on your next pair of Nike shoes, save money on the next gym membership, and get your microbiome sequence.  It may be the best thing you do for your health in the next year.

Chris Kresser:  You are what you poop, and your poop doesn’t lie.

Jeff Leach:  Hey, I’m going to borrow that!

Chris Kresser:  I got a new slogan for you!  No charge.

Jeff Leach:  And also if people want to follow along with what we’re doing in Africa, I’m headed back out in December and January.  I’m actually going to become a Hadza hunter-gatherer for two months and try to shift my gut microbiome to look like theirs.  We’ll be blogging and podcasting, if you will, from the field while we’re out there, so people can follow along and participate as well.

Chris Kresser:  That’s really cool.  Is that the as well?

Jeff Leach:  Yeah, that’s  And anybody who signs up for the American Gut Project, you’ll be able to, within the next few months, compare your bacteria to Hadza hunter-gatherers who literally hunt the same animals and collect the same plants that our ancestors have done for millions of years minus the big megafauna.

Chris Kresser:  Right.

Jeff Leach:  They drink the same water.  They’re literally walking on the ground of Homo erectus.  You could throw a rock and hit Olduvai Gorge from the study area.

Chris Kresser:  Wow.

Jeff Leach:  So, you’ll be able to compare your gut bacteria to a population of people that don’t have any agriculture, that don’t take antibiotics, they’re all vaginally born, they all breastfeed for 2-1/2 years, they’re covered in nature’s blanket, they’re connected to the gut microbiota of all the animals on the landscape through the hunting and the gathering, all the bugs associated with the berries and the tubers.  So, you really see how you compare to an ancestral population that I’m going to go out on a limb here and say it’s probably as close to a normal or optimal microbiome that we’re ever going to see in any ancestral population on Earth.

Chris Kresser:  Right.  Well, that’s amazing, Jeff, and we’ll have to have you back when you get back from that trip.  I’m sure you’ll have a lot of new insights and interesting things to share with us.  We originally tried to hook up while you were in Africa, and that didn’t work out for probably obvious reasons.  I imagine that when you’re living as a Hadza hunter-gatherer, you probably don’t have a high-speed broadband internet connection.

Jeff Leach:  Actually I’ll be the only Hadza hunter-gatherer with a satellite dish for a Wi-Fi uplink, so I am the outcast, and I’m the light-colored guy.  You can’t miss me.

Chris Kresser:  Yeah, exactly.  Well, thanks for doing this work, Jeff.  It’s so important.  I really believe that if the 20th century was the age of antibiotics and killing bacteria, this 21st century is going to be the age of probiotics, and by that I don’t mean probiotic supplements.  I mean pro life of the microbiota and the study of it and how it affects our health.  There are things like fecal transplants and what we’re learning from that and the possibility of evolving that treatment to something that can really save lives, first of all, with things like C. diff, but not only that, affect a lot of other conditions that aren’t necessarily even related to the gut.  It’s just, I think, as a clinician, one of the most exciting and promising therapeutic areas of study right now.

Jeff Leach:  I think you’re exactly right.  And one other thing – I mentioned it earlier – one of the things that we’re doing is we’re transplanting these Hadza hunter-gatherer fecal samples and we’re humanizing mice in Justin Sonnenburg’s lab.  We’re also doing it in Maria’s lab in New York.  We’re also doing it in the chemostat model that Emma developed in Canada to see if it’ll clear C. diff.  So, some Hadza poo will end up in some germ-free mice in the United States, which will be interesting.  And as a side note, I’m really looking forward to your book coming out.  I’ve followed it and your progress over the last year, and so I’m excited about seeing a copy of it.  I think it’s going to be a significant contribution to the paleo diet plus, if you will.

Chris Kresser:  Thanks, Jeff.  I appreciate that.  OK, everybody,  Head over there and make your contribution to science and also do something for yourself.  I think, like Jeff said, it’s incredibly empowering when you see what’s coming out of you that tells you more than anything else, perhaps, about what’s going into you and the state of your overall health.  So, do yourself a favor and do this evolving body of science a favor and go sign up, especially if you’re on a low carb version of the paleo diet or a low carb diet at all.  And, Jeff, I want to thank you again for coming on the show.  It’s been a pleasure.

Jeff Leach:  Thanks, Steve and Chris.  Anytime!

Chris Kresser:  Take care.


Join the conversation

  1. Great podcast – it’s inspiring to hear someone so passionate about this area. This podcast is very timely for me as I’m about to have a faecal transplant here in Sydney at the Centre for Digestive Diseases. I’m having it done for major dysbiosis including streptococcus overgrowth that caused panic disorder.

    I got a lot out of Jeff’s food ideas for feeding the bacteria – post-FMT, I’ll be looking after my new bacteria as though they are human babies.

    If I had the money, I would have had the microbiome sequencing done both before and after FMT.

    I hope this project reaches its 20,000 target. An amazing project.

    • Hi Alison, I am going to have the FMT at the CDD in Sydney soon too – just wondering how you went with your FMT? Have you noticed any improvements?

  2. Fascinating interview, Dr. K & Mr. L! Thanks again for another great piece. Certainly a lot to think about and I will be thinking more about the fibres that pass through my gut. I am now feeling a little confused though, you have always been a huge advocate of probiotics & fermented food…it seems almost as though they are being discouraged here. Was I misinterpreting this?

  3. Mary, I am very sorry to hear you are dealing with these horrible symptoms five years into a Celiac diagnosis. We all have a unique individual biochemistry and your symptoms must be addressed specifically. Hopefully you have also done testing..stool for parasites, yeast,etc. I can only offer some assistance from my own experiences. The bloating and constipation are signs for distress and inflammation. Try and be very careful with information that does not address a Celiac specifically. This can really throw you off a plan for healing. There is so much great information available to Celiacs and also for Non-Celiac Gluten Sensitivity via books and the internet. This past week the GlutenSummit offered brilliant information. Check it out as you can purchase the webinar for a listen at your leisure. Congratulations on going “grain-free”. That is a huge hurdle. (This means you should not be eating any of the processed GF products). Celiacs were once referred to as “banana babies”. Bananas are a starch when yellow, but let them develop black spots and the starch will turn to a easily digested monosaccharides. Try any ripe fruit you enjoy and keep a journal of your symptoms…no more than 2-3 servings a day…between meals if possible, to see how you react. Keeping a food journal is a key to your success. You must eliminate foods until symptoms cease before adding back in questionable foods. Also, autoimmune research has shown that these foods need to be eliminated for some time….Eggs, Nuts, Seeds,(including cocoa, coffee, and spices),Nightshades, alcohol, NSAIDS, and consider all cross-reactive foods to gluten. You can use a Cyrex test for this. Though polysaccharides have important roles to play in our health you must get your gut inflammation to calm down before considering them in your diet… if this is even possible. Sugar (honey too) and milk are disaccharides and should be avoided for now. I would eliminate all potatoes too. Vegetables are tricky but you should try some leafy greens.. spinach, swiss chard, collards,beet greens boiled in a little water till soft. If you have only a protein with a boiled green you should not experience gastric distress. Try and add a little fat to that meal with a tsp of olive oil. You might consider a Digestive Enzyme before meals. As for Probiotics I would suggest you not use any product that contains FOS (fructooligosaccharides)This form of starch (inulin) may feed harmful bacteria as well as “friendly” bacteria and may defeat your purpose. These probiotics are not easy to find. Dr. Peter Osborne at the Gluten Free Society carries a good one w/o, as does the SCD (Specific Carbohydrate Diet) supplements. I wish you the best Mary in your journey.

    • Hi Ann,
      Thanks for such a wonderfully detailed reply, it’s really kind of you to take the time. Getting some testing for parasites and other intolerances is a good idea and something that I haven’t done yet. I did do a test run of the paleo AI diet for a short period earlier in the year and did find that symptoms cleared up, so that might be the right track. I have heard mixed things about Cyrex and cross-reactivity (ie, that the scientific literature does not unanimously support it) but am thinking that it would be worth cutting them out in a 30 day trial, too. I will check out the GlutenSummit info – thanks for the recommendation and for your kind wishes. All the best to you too.

      • Nothing wrong with cutting out the Cyrex list of foods; just don’t waste your money on the test!
        I think the Cyrex test finds people who are sensitive to extremely low levels of gluten or perhaps to unusual forms of gluten. (There are 60 immunogenic gluten peptide sequences –
        If you are interested in “super-sensitvity” The GlutenZap Forum is a good resource.

  4. Chris,

    im one of those people, who went on low carb pale, felt great, leaned out. and then thigs started going down hill after about a year. My coach placed me on 30 grams or less of carbs in attempt to lean out, and instead my adrenals crashed even more, i developed terrible insomnia, fatigue. Only after adding carbs back in i started fealing better. My question is : does starving your gut flora lead to weight gain ? Or does the weight gain happen with adrenals crashing ?

    Thanks for great podcast, very informative. Keep up the great work, can’t wait to read your book.

  5. This is to address Ann and Mary’s question/comment. Current Celiac research shows that Celiacs are not healing on the standard GFD. Even if symptoms appear to resolve, the endoscopy’s show a different pathology. From The University of Chicago one of the leading treatment and research centers..”While healing may take up to 2 years for many older adults, new research shows that the small intestine of up to 60% of adults never completely heal, after treatment, especially when adherence to the diet is less than optimal”… From a 2010 study in the American Journal of Gastroenterology “Mucosal recovery was absent in a substantial portion of adults with CD after treatment with a GFD.” Finally a little green book by Dr. Sidney Valentine Haas and Merrill Patterson Haas.. the Management of Celiac Disease (which should be required reading and given proper consideration for anyone with CD) “The symptoms of CD will persist so long as polysaccharides (complex carbohydrates) are ingested and will disappear only if monosaccharides (simple carbohydrates) are used with the addition of protein and fats, the latter being well utilized if the polysaccharides are excluded from the diet. These observations are based on a clinical experience of 30 years and have been substantiated by laboratory investigation as well.” There are currently practioners and clinicians beginning to understand that the GFD is not all there is to this autoimmune and that other starches can be causing fire in the belly and elsewhere in the body. This is a short way of answering a multi-complex question but caution is the operative word and I believe a healing CD diet does not contain starches. Potatoes may be gluten free but they are the a polysaccharides.

    • Hi Anne

      Thank you so much for your detailed reply about coeliac disease and polysaccharides. I was diagnosed with coeliac disease about 5 years ago and have persistent IBS (mainly constipation, bloating) despite being on a ‘strict’ GF diet since diagnosis (I presume I get ‘glutened’ whenever I eat at a restaurant, even if eating a GF meal). At the moment I eat a grain-free diet but do eat polysaccharides from sweet potatoes/yams and white potatoes, which is perhaps contributing to my issues. Which monosaccharides are best – only fruit? Or some vegetables as well? Is there a way to get resistant starch without eating polysaccharides? Or would a pre-biotic/pro-biotic supplement be better for a person with CD? Thanks for your help.

    • Thanks for this. I have had problems my whole life, diagnosed with celiac and hoshimotos 6 yrs ago. Have been on quite a journey the last 2 years learning and experimenting. In july i did a breath test for sibo and was positive. I did a complex course of herbal antibiotics and the diet that Aglaee Jacob recommends and bought her book, Digestive Health with Real food. I am five months into following her elimination diet and slowly adding things back in and seem to be making progress, had a neg. breath test and ocerall bloating is gone. I can tolerate fodmaps in small quantities and adding more fiber back. But this whole idea of nurturing the healthy bacteria is crucial i believe for long term healing and maintaining the tight junction of the snall intestine. I did buy the bovine colostrum that was recommended on the gluten summit. So far, i am 5 days into taking the potato starch at night with a prescript assist and have been doing great, hungrier and seem to be digesting faster. I took the Colostrum with a VSL this morning and did fine. see a specialist at Univ. Of Chicago next week to see
      if she has any other ideas. Will look into the publication you mentioned. Maybe we know more about healing the gut now so wont be stuck eating simple carbs forever:)

      • Ann, I too follow Aglaee’s work, wonderful book. Can I ask which brand of colostrum you are using and where you got it from?
        thank you

        • I bought it from the, Tom O’briens website after hearing about it on the gluten summit. It is called GS-Immuno Restore Powder. I am highly lactose intolerant so started with half the dose with the vsl and so far so good.

      • Ann – Not sure if you are a reader of scientific papers, but I have been reading this one recently. (full text)

        You are definitely not wasting your time with potato starch. I think it will turn out that the biggest effect potato starch has on SIBO and a healthy gut is to ‘mop-up’ stray bacteria. Resistant Starch is a proven remedy to remove cholera from the small intestine, and it’s all been proven that all types of bacteria, good and bad, are attracted to it. When you eat or drink down a big pulse of potato starch, it is removing bacteria from your stomach and small intestine and depositing it in your large intestine where it can be dealt with accordingly.

        This little blurb from the above study, though somewhat cryptic, is probably key to all this:

        “It is striking that Ruminococcus bromii, Bifidobacterium adolescentis, and Eubacterium rectale, which showed the most substantial increases in the human gut in response to RS2, have also been shown to form highly selective associations with this substrate [35]. Therefore, the adherence of bacteria to starch granules might constitute an important first step in the utilization of this substrate, and groups of colonic bacteria might differ in their ability to adhere to granules of RS2 and RS4.”

        I hope Chris and some other really smart people read this and can make it into something big!

  6. Thanks so much for this interview- so interesting. What would this tell us about the effects of colonoscopy? Getting 30 to 40 plant species a week in our diet- can we count things we just eat a bit of, like grated ginger, cilantro, or lime juice on our resistant starch filled jicama? Extolling the virtues of intestinal gas- one of the delights of a low carb diet is gastric bliss- should we abandon that? I am going right to his website to see what wlse he has to say.

  7. Wow, what a fascinating and intense discussion, both the original and the comments. I actually found myself say ‘YES!!’ out loud a few times.

    tatertot, I was you wife! GERD, AI, IBS, possibly Chron’s, NASID abuser etc…. I actually though I was being ‘healthy’ eating a low fat/high whole grain diet until I crashed and burned and would up in the hospital. They never found out what was really wrong with me, but treated me for an hpylori overgrowth with intravenous antibiotics. I suspect now that I had SIBO.

    Since then I’ve don a lot of research and changes. I cut out grains completely, huge difference. Then I discovered HCL and that has pretty much ended my GERD. I actually had to promise my GI doc that I would take the PPIs after he did my endoscopy and said my stomach was badly inflammed (but non ulcer), but I had my fingers crossed behind my back 🙂 Then I discovered FODMAPS and eliminating them has stopped all of my IBS/Chron’s symptoms. Unfortunately I can’t eat onions or garlic or any of those great fermentable/fermented foods. And after cutting out FODMAPS, I felt great, but as you can imagine, I then became horribly constipated. Thanks to Chris I added magnesium glycinate and prebiotics with bifo. (I also cheered BIFO! outloud a few times when reading the article, LOL) Again, huge difference.

    My diet is basically grass fed beef, Berkshire pork, good quality lamb and fish. I do a lot of starchy carbs, Japanese sweet potatoes, butternut and other squashes. I love turnips and bok choy. Because of my FODMAP issues, my veggies are somewhat limited, but I am continuing to try new things to see if I can tolerate them. I’ve totally eliminated grains, legumes, dairy, eggs (I did an AIP and found eggs caused my a lot of joint pain) I also have a nightshade sensitivity so peppers, tomatoes and potatoes are out for the most part. I try to use earthy spices like tumeric and cinnamon and star anise to add flavor to make up for what I can’t use.

    I think I’m almost there. I’m thinking of doing the American Gut project. I would love to see the difference between my husband and I. He’s doing a bit of what I do, but he’s not as limited. He LOVES raw onions and now I can tell him they are very good for him. Ironically I do have a package of Bobs Red Mill Potato Starch. I will give it a shot to see if it makes a difference.

    • Jenifer – I saw that video a couple days ago and shared it on Facebook with this message: “EVERYONE, WATCH THIS VIDEO. This stuff affects everyone, whether you know it or not! Plus, the animation is adorable. Whoever made this is my favorite person for the rest of the week.”

      Just thought you might like to hear that 🙂

  8. I have learned so much, similar to what you state, from Doug Kaufman, and his tv show Know the Cause, and his website major premise is that most of the diseases/ailments that plague us are fungally related, and we should avoid fungally infested crops such as corn, peanuts, potatoes and grains along with alcohol and sugar which feed the yeast in the gut. Many people who have adapted his Phase I diet, which is essentially the anti-candida diet have seen dramatic improvement in their health.

  9. Great Info ~ It would be nice to also be able to measure the emotional/environmental impact surrounding digestion. For instance, I can eat the same exact meal {take out} at home vs. at a restaurant and have a completely different digestive experience. When I am out and engaged in social dining, a meal digests far better ~ this has been a running experiment for over a decade and always seems to yield the same results.

  10. Awesome info, Jeff!

    I was wondering two things: 1) Have you observed any differences in your health/functioning since adopting a regimen involving eating so many different plants? 2)You mentioned preparation affects the fiber, so in what way would you suggest consuming most plants? (Because I know traditionally many cultures would cook most of their plants, but nowadays everyone advocates consuming them raw)

  11. Brilliant info, including from Tatertot. Wow. The knowledge base is becoming incredible. I plan to sign on and hopefully my wife will as well, even get the kids on board. My wife has had digestive issues (as do other members of her family) forever and has metastatic breast cancer. It may be too late for my wife but this info opens up a whole new vista for building our children’s health foundations. One of my children is a very fussy eater, with some compulsive obsessive tendencies, and we have considered going down the GAPS approach but it has seemed a bit extreme. Haven’t been able to get the bone broth into his diet yet, so would love to know how to get the glycine into him.

  12. This was fascinating! Chris, do you have any advice for someone who has SIBO/ FODMAP issues but who wants to diversify their gut bacteria? Are probiotics the best bet until the gut heals?

    Since I currently eat VLC to combat the SIBO and because of the FODMAPS, I signed up for the study! Can’t wait to see the results!

    • I’ve found that starting with a very low dose of prebiotics or resistant starch and building up slowly over time helps with SIBO over the long-term, even in those with FODMAP intolerance. It seems counterintuitive, and perhaps it is, but as I mentioned on the show the key to healing the gut ultimately is restoring a normal microbiota… and that’s hard to do without these fermentable fibers.

      • Chris,

        I used to have really bad anxiety and panic attacks (after a bad diet, super stressful time in my life, and too many antibiotics). I’ve noticed cutting back on uncooked veggies, fruits and starches helps me a lot. I do eat cooked veggies and rice which my stomach does not mind. I also have Sibo. I bought some potato starch and tried 1 tbsp. one evening, and 1 tsp the next morning and morning after that. My anxiety ramped up immediately, I’d say a couple hours after my first dose, I started feeling panicky like I used to. Any suggestions? My fecal sample shows low bifido and nonexistent lactobacillus bacteria. Start even lower than 1 tsp or just not attempt it at all?

        • Hello Alex

          I have the same problem with resistant starch and anxiety attacks.

          Do you have the same problem with either l-glutamine or turmeric powder?


          • Matt,

            Not with turmeric but I haven’t tried l-glutamine in a long time. What has your experience been with resistant starch? Any experimentation with small doses?

            • When I use the potato starch I get the benefits (better sleep) but I also get anxiety attacks during the day. Some instances border on rage. I used 2 tablespoons per day. I guess it feeds both the bad and good bugs.
              I’ve eliminated all plant foods from my diet temporarily and am doing much better this way.

              I’m curious about turmeric and l-glutamine. Turmeric powder is starch. The popular theory is that gut problems are mostly likely caused by some pathogen/s. The only way to heal is to starve them out.
              I’m just curious about l-glutamine. People say its needed to repair the gut lining. Chris has mentioned that “L-glutamine I have mixed feelings about. Certainly it has some therapeutic effects and it can be beneficial, but for some people it seems to really trigger kind of a state of agitation or anxiety, and there’s some controversy about whether glutamine can end up as glutamate, which is the major excitatory neurotransmitter in the brain, and I just see that some patients have a bad reaction to it, so I would be a little bit cautious with it.”

              But I’m going to give it a shot.

              If you haven’t already, read Breaking the Vicious Cycle, Gut and Psychology Syndrome and The Management of Celiac Disease.

              • Matt,

                I tried turmeric but didn’t know much effect so I just kind of left it alone. I have a bottle of l-glutamine that I’ve been thinking about trying but for your same reasons haven’t. I’ve tried small doses of l-glutamine in the past but that was pre-anxiety.
                For my anxiety (I also get dizziness) the best thing I’ve found is enteric coated peppermint oil. I’ve tried so many herbs and supplements. . .It’s strange I just expected them to calm my stomach down but it’s done so much more. I’ve been taking 2-3 daily for the past 3 or 4 months. When I don’t take them my symptoms come back. I’ve tried googling ecpo but haven’t found why they would be helping me with anxiety and dizziness. . . Maybe they reduce the gas that the bad bacteria ferment in my stomach and that’s what causes my symptoms?
                I’ve been on a low plant diet for a couple years now and yes it helps the symptoms but I wonder, can I, and should I eat like this forever?

  13. Would you cook onions at all? If so, how?
    For people whose digestive systems are already compromised (i.e., malabsorption), would the phytates in lentils be a problem? I had not heard that lentils had resistant starch, my understanding was only onions, garlics, leeks, potatoes, and sweet potatoes and artichokes offered resistant starch.

  14. I am anxiously awaiting my results from American Gut. Am certain they wont be as impressive as yours Tatertot! I need advice. I have suucessfully treated myself for SIBO so have been avoiding RS for months. I have autoimmune issues (celiac, hoshimotos) as well and am just beginning to tolerate a tiny amount of prescript assist. I did eat lots of lightly washed veggies from my garden so maybe not all is hopeless! Anyhow, i am improving but fodmaps are still a problem if i eat more than one a few days in a row. I have been eating sushi, am not tolerating potatoes. I have been eating jasmine rice to avoid the RS. What can i do to slowly build up tolerance? Plantain chips? Cold rice, a bit at a time? Thanks!

    • I’m going to be shameless here!

      For all you ever wanted to know about resistant starch, go to and start reading…the comments are even better! Richard and I have been collaborating for months on the best sources and uses of RS. People are seeing almost instant improvements in body temp, skin problems, sleep, insulin sensitivity, and poop.

      For how to kick SIBO straight in the ass and cut it’s throat, go to
      Dr. BG and I met through Free The Animal and we are focusing on gut problems such as SIBO. We are not pussy-footing around trying to eliminate triggers of GERD, we are blasting through years of bad information and fear of fiber to completely turn the SAD gut microbiome on it’s head!

      But to answer your questions: Keep eating dirty carrots! Keep taking the soil-based organism probiotics (but you can stop soon), Try plantain chips (home made), cold rice, but more importantly, get a bag of Bob’s Red Mill Unmodified Potato Starch (not flour) and start taking 1TBS a day along with 1TBS of Psyllium Husk Powder, each week, up the amount of potato starch by 1TBS until you are taking 3-4 TBS/day. Also, eat tons of anti-oxidant/polyphenol rich foods every day–blueberries, purple potatoes, kale, oriental mushrooms, etc… Lots of fermented food–kefir, yogurt, sauerkraut, kimchi, etc… and eat several servings of starchy foods every day. Greenish bananas and rice are fine. Look into others, cooked plantains, squash, sweet potatoes, taro, etc… You need lots of buytrate in your gut–the only way to get it there is to eat lots of starchy and resistant starchy foods!

      Good luck!

      • Thanks, was hoping you would be shameless! Ok, i guess i go slow as my gut heals but persistance seems key. My repeat breath test was negative but have read how easy for sibo to come back. Am seeing a GI doc in a few weeks to see if i have motility problems that lead to sibo. I am just beginning to be able to digest more veggies so will slowly add more. Would potato starch interfere with gut healing due to the saponins or does it just go right to the colon?

        • Ann – Lucky for you I’m not a doctor…I can say whatever I want! If you had two negative breath tests and aren’t having major GERD like problems, it’s probably safe to say you have no SIBO. That means it’s time to double-down on what you are doing, don’t take it easy–kick it up a notch!

          Taking it easy may give SIBO a chance to recolonize, you need to head it off.

          With Leaky Gut, the worst offenders are vegetable oil, wheat, and anything else you may be allergic to like eggs, peanuts, or whatever. The best supporting actors for a non-leaky gut are RS, starchy foods, mucilages (psyllium, aloe vera etc.) and probiotics live and dead.

          I’m not making it up. read for yourself:

          Keep in mind, leaky gut is 100% a problem with Tight Junction Complexes while reading this and also keep in mind that when conditions are ripe for SIBO, Tight Junction Complexes are seriously screwed.

          Try this for a while: Mix 3TBS of potato starch and 1TBS of psyllium fiber husk in a cup of greek, unsweetened yogurt with a handful of blueberries and eat every day. Keep your appointment and check motility issues, but keep feeding the potato starch, it is super fertilizer for good bacteria. Potato starch goes right to the colon, and actually takes some bad bacteria from the small intestine with it.

          • Awesome reply, needed that kick in the pants! Got the potato starch last night and took a tbs with water and the prescript assist before bed. Was ready for some kind of explosion, but never happened, woke with flat tummy, hungry. Yipee! I am lactose intolerant and dont do well with coconut milk either, any other ideas of mixing the starch and powder?
            BTW, i am married to a doctor who is a researcher at a major academic med. ctr. He has not been much help with the sibo but did hear a “grand rounds” talk on the microbiome and came home with the following summary: we don’t know much yet except that the microbiome is connected to health in everyway, but what is certain is that resistant starch is the best way to feed the good bacteria. So keep up the good work!

            • Water is fine. I do that all the time. I love that your doctor-spouse knows about RS. My biggest motivation for spreading the word has been because I could see the writing on the wall. Soon everyone will be hearing about RS, but there is no real way to mega-dose with it. Potato Starch fills the void nicely. After my American Gut results I am 100% convinced of it–it erased all doubt!

              • Happy thanksgiving! Quick question if you dont mind. I have been taking the potato starch with the prescript assist and started the psyliium husk powder (tsp) too but have noticed a ringing or buzzing in my head after i take it. I have been waking up at 5-5:30 starving. Which i wish i was sleeping longer but hunger is a good sign that my digestion is healing since i was in pain/bloated mode for so long. Am worried ringing in my head will get worse if i up the amt to 2tbs twice a day. Thanks for any insight.

                • Ann – I would say that what you are experiencing is not related, but I always tell people that if they think they are experiencing things like that, then just stop taking everything for a few days and see what happens before restarting.

                  With the potato starch, you will be experiencing something that may be totally unfamiliar to your gut–producing lots of butyrate. Everyone is supposed to produce it in large quantities, but the SAD is so low in fermentable fiber that most people are starved of it. There is no shame in going slow, or taking a break. What really saddens me is when people start out with this approach and stop the minute they think something is wrong that may be totally unrelated. Give it a chance!

          • I noticed that lauric acid and capric acid both both seem to increase permeability in the paper you linked. Does that mean we shouldn’t be using coconut oil if we have leaky gut issues? A link to foods that can help tighten junctions would be much appreciated!

            • Kira – I did not catch that about lauric and capric acids…wouldn’t that be something if coconut oil leads to leaky gut! I remember a few bloggers saying it wasn’t all that great, but don’t recall specifics.

              Foods that can help tighten junctions: Anything fermented. Any fruit and veggies that you aren’t allergic to, especially colorful veggies full of anti-oxidants and polyphenols. Meat that is not burned to a crisp. Organ meats. Resistant starch and other fibers.

              While I have never seen a Tight Junction Food List, I do keep coming across the general theme that butyrate is the main player in regulating TJs.

              • If you are getting your butyrate from the fermentation of fiber or resistant starch, wouldn’t that occur in the large intestine or colon? What if you have leaky gut in the small intestine? Would you suggest getting more butyrate from butter for example?

                • See what Chris K. just wrote below…it seems strange treating small intestine by fixing the large intestine, but it all works out in the end. The butyrate that is produced in your large intestine ends up in the portal vein and gets to where it needs to go. Plus, the RS that you eat has the ability to trap pathogens in the small intestine and flush them out. Sounds like I made that up, but I didn’t.

                  Leaky gut is not just a small intestine problem–it has to do with Tight Junction Complexes throughout the GI Tract. Once you start eating right for your gut microbes it will all start to sort itself out. If you are seriously broken, like many people are, it may take some tweaking and potato starch may not be THE magic bullet, but it is a start and it eliminates a big piece of the puzzle.

          • This flies in the face of thousands of people who have successfully treated SIBO with the SCD diet.

            Any time I eat large amounts of any kind of starch, including powdered potato starch, I get severe bloating.

            Has there been any testing done on this recommendation?

      • Tatertot, thank you for this information. It’s super helpful. I am little overwhelmed by going to the website. That’s the best article to start with respect to resistant starch. I’ve had GERD for a few years. I got some recent stool tests back that indicated low Bifido and lacto bacteria, unknown parasite(s), low short-chain fatty acids, and pH was low (acidic). I also got a recent blood test that indicated Sjogren’s syndrome. My nutritionist is recommended a low carb approach (even Keto but I have been resistant). My holistic doctor has recommended a Terry Wahl’s dietary approach with WAPF focus on organ meats, broth, and fermented foods (and only 1 each of fruit per day). After listening to the podcast, I got really concerned about which approach to follow or perhaps neither. In the past when I was on a low carb GAPS diet, I got really bad dry eyes (key symptom of Sjogren’s). And now that I am low carb again (although not super low carb), I have been having the dry eyes again (which is what actually prompted the testing). Any thoughts you have approach wise would be appreciated.

        • Wanda – I am waaaaay out of my league here giving you this advice. I probably shouldn’t even do it. Chris will probably ban me from the internet after this, BUT, here’s my advice:

          The “Terry Wahl’s dietary approach with WAPF focus on organ meats, broth, and fermented foods (and only 1 each of fruit per day)” sounds perfect to me. If I remember right, Terry Wahls doesn’t eat much starch…you should. Eat a serving of rice or potatoes every day. Don’t count carbs or calories…just eat. Then, add in every day, a cup of yogurt with 1-3TBS of potato starch and 1/2-1 TBS psyllium husk powder. If you can’t eat yogurt, just mix those in cold water or in with a serving of cold rice. Eat the potato starch any way you can as long as you don’t heat it! Mix it in no-bake cookies, snort it in lines (just kidding on that one), but eat it every day.

          If you want to take a probiotic, take one that is sold as a soil-based organism(s). Also get some that say bifido on the label. Eat fermented foods every day…real fermented foods–not Vlasic Bread and Butter Pickles. Get some real sauerkraut, make beet kvass, water kefir, lots of options. Get it in you! Eat lots of anti-oxidant rich foods and colorful veggies and berries. Don’t buy a bottle of pills that says “Anti-Oxidants” and think it is the same! It’s not. Buy some organic frozen blueberries and eat to your heart’s content. Eat 90%+ Dark Chocolate as much as you want or can stand.

          Are you on a PPI? Try to get off, no matter how much it hurts. PPIs will not help you get better, only keep you from feeling bad.

          if you find a certain food like broccoli, chocolate, or potatoes make you feel bad–don’t eat them! Identify all your allergies–eggs, peanuts, shellfish, etc… and never eat them. Find all the wheat, vegetable oil, and sugar-laden food in your house and THROW IT OUT.

          Let the doctor check you for parasites, treat them any way you have to–sometimes you need to burn down the forest before it can re-grow (right, Grace?). There are options here–charcoal, clays, diatomaceous earth–look into them for your specific problems. Antibiotics it if comes to that.

          If you are overweight and trying to lose weight while fixing your gut, you will probably fail on both accounts. Fix you gut first, and the weight later–they may go hand-in-hand, but worry more about eating the right foods and then the amounts later.

          The potato starch alone is going to be a vast improvement for you, if you are eating a very clean anti-inflammatory diet, as we discussed above (no sugar, wheat oil), and it should take care of your problems with pH and SCFAs. You need to give your microbes some MICROBE FOOD, and that can’t be done while eating low carb even if you use potato starch–you need to give them a buffet, not just the main course.

          And if all else fails, set up a consult with Dr. Kresser!

        • Hi Wanda,

          I’ve been in similar shoes as you. Prior to moving abroad I did a profile on my gut via DNA 16s amplification similar to the Am Gut Project and it was accurately detected that I had both bacterial, fungal and parasitic overgrowth. After treatment with antimicrobials/anti parasitic regimens, I have banging gut function, body fat composition, happy moods, adrenal/thyroid body temps and can tolerate eating gluten and dairy again. Please refer again to Chris Kresser’s SIBO post where he advocates botanical antimicrobials regimens.

          I also advise these for all my patients as well. If we have an illness or food intolerance, I’ve found that at the crux is sibo and some kind of overgrowth.

          Here are the regimens that I frequently employ (as well as the micro biome results via GDX diagnostics which gives a wealth of information include digestive and pancreatic function, gluten sIgA, etc how GI f*kcered lol)

          Like Kresser, I prefer botanicals over Rx pharmaceuticals because they are much less likely to cause adverse effects that are commonly associated with potent manmade synthetic chemicals. By using lower doses of several botanicals, killing effects for several parasites and pathogenic microbes is achieved with less side effects or virtually none. Most of the regimens also cover fungi, viruses, protozoa and worms in case the species you’re dealing with cannot be identified or it’s missed.

          Good luck


        • Wanda, both your holistic doctor and nutritionist cannot be more wrongheaded. You need some starches in your diet, especially RS and fermentable fiber. That dry eye symptoms you got while VLCing may have been due to glucose deficiency rather than Sjogren’s; many low-carbers experience that along with dry mouth, anemia-like symptoms and dry colon. If you became postive for Sjogren’s antibodies (SSA-Ro or SSB-La) just now, it’s possible that you could be symptom-free and only antibody-positive; if that’s the case, you can still roll back Sjogren’s and become antibody-negative. Of course, those dry eyes could actually be a symptom of Sjogren’s also but they are usually accompanied by dry mouth and fatigue; joint pains may appear later.

          The worst thing you can do is go ketogenic a la the Wahl’s protocol, as that would make you vulnerable to other autoimmune diseases. You know these things come in clusters. The average Sjogren’s sufferer is afflicted with 4-7 autoimmune diseases during her life time: most common are Hashimoto’s, RA, Lupus and Scleroderma. You don’t want the last 2 conditions to piggyback on your, as they’re both systemic diseases and are potentially fatal. Your goal should be keeping your autoimmunity to ony Sjogren’s or pushing it into remission. To do that, I’d consume plenty of RS and safe starches, and stay clear of ketosis. I’ve actually personally seen ketogenic dieters develop SLE and SS; they became ANA positive soon after starting to low-carb; they were probably in the process of developing such conditions but my guess is that the straw that broke the camel’s back is ketosis, which is an invidious diet for those who’re vulnerable to autoimmune diseases.

          • Trundle, this is quite fascinating. Where do your opinions come from? Are you a practitioner? a patient? I have SLE (for 35 years). Last year I started a quite restricted diet (no grains nuts seeds legumes) and for a short time I noticed some bad breath and guessed that was ketosis. I lost about 10lbs but it was not intentional. My weight stabilised and I felt pretty well except 3 weeks into it I had a return of childhood eczema which got quite bad. This was 1.5 years ago. A few months later I started getting some joint pain and vasculitis and then by October it was clear I was having a renal flare. I managed that with lifestyle medicine and my lupus has settled right back down (surprising all my speciallists who wanted me to have immune supressive treatment). I’m still trying to clear the eczema. Anyway, reading your post I couldnt help wondering about my autoimmune disease following my accidentally ketogenic diet. I would be very interested in hearing of references and otehr information from you.

  15. What a timely, and SPOT-ON interview!

    You may remember me, I’m Richard Nickoley’s Alaskan buddy who has been pushing this Resistant Starch thing with him. Anyway, I was one of the first 1000 Am Gut people and just got my results yesterday.

    When I sent in my sample, I had been downing 30-50g of potato starch and eating another 20-40g/day of RS rich foods along with tons of fermented foods and minimally washed, homegrown veggies. I kill and eat lots of wild animals and fish, eating some raw, and digging deep in large gut-piles.

    At the same time, I sent a sample from my wife of 29 years, she has lots of health issues, auto-immune conditions, life-long antibiotic abuser and hand-sanitizer, eats no fermented food, lactose intolerant, PPIs, GERD, IBS…all that…and eats SAD with minimal fiber and no RS.

    Drumroll please……

    My results: more Actinobacteria (an anti-biotic producing microbe) than any other profile, less Proteobacteria (family full of pathogens) than any other profile. I have rare species ‘Slackia’ which is highly protective of disease and rare species ‘Limnobacter’ which is usually found in high mountain glaciers and alpine snow.

    Now my wife’s results: Lots of pathogens including Verrucomicrobia, Rothia, Eubacterium, Oribacterium, Atopobium, and a huge population of Akkermansia. Lots of these are out-of-place oral pathogens!

    I will be doing a complete breakdown and posting it soon on and

    If Jeff Leach is interested in seeing what the poo of an American H-G person’s looks like, he can check out sample 71958, first name Tim.

    • Hi Tatertot. I was wondering if you know: is there any direct evidence in humans, that more butyrate in the gut from consuming resistant starch (relative to basal levels generated on a low carb diet with plenty of green leafy vegetables) improves bowel health?

      • Oh, Gosh yes! Plenty of scholarly, peer-reviewed articles on the subject.

        Click on this:

        Then hit Ctrl-F and type in the word ‘butyrate’. You can jump to each of the 64 references in the paper, or just read the whole thing.

        If I may give you some homework: “Explain the ‘Butyrate Paradox’ in your own words.”

        If you’d like more examples, just ask. Or look at the reference section of the paper and click the PubMed links, especially the ones that say ‘Free PMC Article’.

        Seriously, though, gut-microbe produced butyrate is probably THE most important factor of gut health. Without it, nothing works right.

        • one problem I see with the article you posted is that it speaks only in broad terms of diet. The authors assume that what affluent societies are eating is high fat and high protein. However more affluent societies are also eating more refined carbohydrates and more sugars. And the cause of inflammation and cancers may be due to the simple sugars and starches that people are eating. Frustrating because it seems like yet again more sloppy work on looking at diets and the role of diet in health and disease.

            • Thanks Duck. Yes I think even Jeff Leach admits they have no or very little data on people eating a true low carb diet. More research is definitely needed.

              I don’t dispute that butyrate has benefits for colon health. I just take issue with the “diets” that are being compared. What most people are talking about is something akin to the SAD, high in refined grains and sugars, and seed oils — and they don’t even realize it. Same with the highly touted “Mediterranean Diet” which is some construct of one or two people that has only a small connection to the diversity of cuisines used among Mediterranean peoples. And I think we have to focus on traditional cuisines, foods prepared in the proper fashion, traditional “slow food” preparations.

              • Well, even if there are no studies on people eating a low carb diet, you have to wonder what those individuals are fermenting to keep their colons healthy. If someone is eating “low carb diet with plenty of green leafy vegetables” that implies a lot of cellulose—unless that person is consuming lots of raw inulin (onions, dandelion greens, Jerusalem artichoke) and some other NSPs.

                Cellulose just doesn’t ferment in most people’s guts because few humans have much if any cellulose-degrading bacteria in them.

                From: The cellulose-degrading microbial community of the human gut varies according to the presence or absence of methanogens

                Attempts to elucidate the cellulose-degrading microbial community have only been partially successful as only a restricted number of individuals appear to harbour such cellulose-degrading organisms (Bétian et al., 1977; Montgomery, 1988; Wedekind et al., 1988)”

                I’m sure cellulose helps with transit time and bulking of stools, however even if one did harbor such cellulose-degrading bacteria it’s well known that cellulose is a poor fermenter of SCFAs.

                In general, it’s very difficult to get above SAD levels of fermentable fibers when on a low carb diet—even when eating plenty of green vegetables.

                • Yes Duck, so that is an interesting path to pursue. I know that green leafy veggies are not the only veggies allowed on certain low carb diets. Onions are most definitely allowed and perhaps it’s a matter of making sure people on a LCHF diet are getting enough of the “inulin” containing veggies. I’m sure there are plenty that are included in the permitted foods. Plus there’s always resistant starch, for people who for therapeutic reasons must stay on a low carb. (20 G carbs a day) high fat diet.

                • “Onions are most definitely allowed and perhaps it’s a matter of making sure people on a LCHF diet are getting enough of the “inulin” containing veggies”

                  Sure, but the point is that it’s extremely difficult. Basically a LCHF individual would be limited to heaping quantities of raw Chicory root, raw Jerusalem artichoke, raw Dandelion greens, raw Garlic, raw Leek and raw onion just to get above minimum SAD fiber recommendations.

                  I think very few people could ever hope to keep that up long term. That conundrum is often referred to as the “Carbohydrate gap.”

                • Duck, looks like I can only do so many replies. I don’t know of any traditional cuisine that has the copious amounts of raw onions, leeks, jerusalem artichokes, asparagus, dandelion root, that you describe. Plus these things are not available all seasons of the year. I sincerely doubt there is only one formula for what is required to have a healthy gut biome. So sorry, I don’t buy it. I think there are multifarious ways to feed one’s gut biome and have a healthy gut.

                • “I don’t know of any traditional cuisine that has the copious amounts of raw onions, leeks, jerusalem artichokes, asparagus, dandelion root, that you describe”

                  Well, now you’re just proving my point. Virtually all traditional cuisines involved sufficient levels of whole foods carbohydrates.

                  The few oddball traditional cuisines that were low in carbohydrate involved raw meat and raw blood, affording them plenty of probiotics. The plentiful glycans (glycoproteins, glycolipids, etc) in the raw meats/blood/intestines/flippers/collagen were also a good source of “animal fiber” prebiotics.

                  So, it should be clear that Western low carb diets do not resemble any “traditional cuisines” whatsoever.

                  Proponents of Western low carb diets have little to no interest in gut health as far as I can tell. Many of them profess that the intestines provide mucin for bacteria to ferment/degrade. For all we know, they may be right, but I’m not aware of any indigenous cultures that avoided fibers and relied on mucin. If anything, they devoured animal fibers and plant fibers.

                • Duck, be careful of reductionist errors. Inulin is not the only nutrient for the gut microbiome, read up on pectin. But also the context of nutrients is important, we don’t want to make the reductionist error of thinking we’ve identified a single compound and that the context in which it appears — in an apple or in an onion — is irrelevant.

                • NS,

                  I’m well aware. But, again, you are proving my point for me. Pectin is typically found in carby fruits and vegetables.

                  I purposefully mentioned Inulin because it’s one of the few fibers that low carb dieters can obtain naturally without breaking their dietary rules.

          • @NS

            There are plenty of studies showing that increased butyrate levels improve colon health and if that answers your question, leafy greens and a bit of white powder do not provide enough substrate to create and deliver enough butyrate for the whole colon.

            But you are right, the great ancestral health is not only about some sugars, fats and proteins. For that we would have to go to Africa, enjoy a lot of sun, feast on the antelopes, eat a lot of baobab, dirty underground tubers and plenty of honey including larvae etc., see the latest blog by Jeff Leach:

            (Re)Becoming Human: what happened the day I replaced 99% of the genes in my body with that of a hunter-gatherer

          • OK, as long as you researched it, I’ll give you that one…but don’t try a ‘war of attrition’ with DuckDodgers, just look at this little comment he left on another blog!

            Hey, what you said about pectin…that is correct. Lots of fermentable fibers in many diverse foods.

            What my point has kind of been all along, is that in nature, the two ‘biggies’ are RS and inulin. Then in lesser and lesser amounts you find the gums, mucilages, pectin, chitin, beta-glucans, etc…

            It also seems that RS and inulin have the greatest impact on gut flora when eaten in their ‘wild’ levels. Pectin is great, but comes in tiny amounts in the wild. You could probably use it as a sole prebiotic if you bought it in a big jar, like the way they sell psyllium for fiber, but in nature, you won’t find much.

            Psyllium husk contains mucilage, a fairly fermentable fiber, but more of a bulking agent. It’s not THAT great a prebiotic compared to the others, but it doesn’t make people fart and it fits the definition, so it sells well.

            At the end of the day, I think we need to look at our gut health and immunity, and if either are failing, look to increasing the fermentable fibers in our diet.

            A proper prebiotic regimen should be top-heavy in inulin and/or RS and also contain many other natural fibers in natural amounts.

            • “At the end of the day, I think we need to look at our gut health and immunity, and if either are failing, look to increasing the fermentable fibers in our diet.”
              Agreed. Also for people in good health, eating traditional “slow” cuisines of whole foods should provide them with all they need to stay in good health (assuming of course adequate environment, soil etc. inputs). There is a lot of wisdom contained in the ancient cuisines handed down to us, erstwhile forgotten, now being rediscovered.

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