Sorry low carbers, your microbiome is just not that into you

I recently posted a scatter plot (below) on Facebook/Twitter of preliminary metadata that we are accumulating as part of the American Gut project – which includes, among other things, a questionnaire of 50 + questions and a 7 day food journal. Plotting participants self-reported height, weight, and 7 days of dietary info (recorded using an online calorie counter), we can plot low carbpercentage of daily calories from fat (all sources) against body mass index (BMI) – which we calculate from the height and weight of the participant. While the data is of the dreaded self-reported kind, the lack of any significant correlation between % of daily calories from fat and BMI, is still very interesting (note even if you remove the various obvious outliers, the correlation – or lack of – is the same). In other words, as fat goes up in the diet, BMI does not per se. (Note we just started sequencing poo samples. Will be able to see how the metadata correlates with the microbial data in a few months – stay tuned).

As I look at the preliminary generic metadata (below) and follow the conversation around the benefits of a low carb diet, I continue to be concerned about the low-carbers gut microbiota (note I eat meat daily, so my diet is high in fat, animal protein – but also dietary fiber – as I eat a large diversity and qty of plants. Though I don’t consume many grains in any form). While there is no denying the wonderful results many people enjoy on a low (and even lower) carb diet – specifically weight loss, which is well-documented now in the peer-review research – the impact on the gut microbiota is not well understood. As we can see from our accumulating metadata (ultimate goal is 20,000 participants – we are at 6,000 now – with complete metadata on ~1,000 so far), we are likely to have a decent sample of low carb dieters (hopefully). This data will allow us to compare the gut microbial communities of this population against other dietary strategies. (But again, please note we have not completed sequencing of low, low carb eaters and so are not presenting any of that data [the plot is just metadata on fat and BMI – which tells us nothing about gut health of the various dots in the plot]. The following discussion is based on some general observations based on the existing literature about fermentation, pH, and its impact on the gut microbiome).

Screen Shot 2013-06-27 at 6.34.28 AMPlease note the data in the plot above is self-reported and preliminary. As with all self-reported data, its not ideal. As data points are added over the coming months, will be interesting to see if the (lack) correlation holds. The average age of the persons in the plot is 46 – the youngest is 2, the oldest is 90. 55% are female, 45% male. ~99% are from the U.S. The point of showing this particular plot is that “these particular data” do not show any correlation with fat intake as a % of calories and BMI. Again, this has NOTHING to do with gut bacteria – at the moment – just an interesting “lack” of correlation (and should be interesting/useful for those following a HF diet).


Depending on whom you talk with, a low carb diet is many different things to many people. I think most misinterpret a Paleo or Primal lifestyle as somehow low carb. It can be, but most folks eat a diversity and quantity of whole plants that exceed that of the average American – often by a long shot. It can sometimes be a little low carb-like due the absence of high caloric foods made from grains. But I often find people who skip grains, sugar and the like as really paying attention to whole plants in their diet – which is, of course, a good thing. But a bona fide low, low carb eater is another animal all together. Whether you draw that line at 25, 50, or 75g a day of carbs, its low I’m afraid from the perspective of your gut bugs. Especially if those carbs contain a limited amount of resistant starch and other dietary fibers – food for gut bacteria.

That said, even though someone who eats as much as 200-500g of carbs a day can still be starving their guts bugs if those foods contain little to now indigestible substrates (fiber), a generic rule of thumb (albeit an ugly measure) is less overall carbohydrates – especially when you start dropping below 75-100g a day – translates into a dramatic drop in the amount of food reaching your colon where the vast majority of your intestinal microbial community resides. (There are exceptions to every rule, but follow my logic for a moment).

When it comes to the health and well being of your gut microbes, nothing matters more than fermentable substrates (You can read about here, here, here, here, here, here, here, here, here – you get the idea). As the rules/tenants of basic microbial ecology go, a reduction in fermentable substrates derived from carbohydrates means less energy sources for the microbes – who depend on host-derived substrates as well, as in the case of mucin-degraders like Akkermansia. As fermentation drops, so to does the byproducts of fermentation which include short chain fatty acids (primarily acetate, butyrate, propionate), organic acids, and gases like hydrogen. All of this can and will dramatically shift the pH of the colonic environment. As it stands in a healthy or normal gut, the pH of the colon changes from proximal to distal end, being more acidic in the proximal (front) end than the tail end – mainly as a function of more rapid fermentation as food items empty from the small intestine. As the pH shifts to being more alkaline from less fermentation, a number of shoes begin to drop (or can).

A less acidic environment means acid sensitive groups of bacteria, like those in the Phylum Proteobacteria, which includes a who’s who of bad guys like strains of E. Coli, Salmonella, Vibrio, Helicobacter, might bloom – not a good thing. You see the same blooms following antibiotic treatment. In addition, as pH shifts away from acidic, the genus Bacteroides can also bloom as well, gaining an ecological niche in this less acidic environment courtesy of a low carb diet. For those of you keeping score, many talk about the American gut in general being dominated by Bacteroides as a function of our high fat, high sugar diet. The reality is, it might have to do with what we are not eating – dietary fiber (of all kinds). The all-important butyrate producers Roseburia spp. and Eubacterium also drop in abundance as pH shifts away from acidic as well. A drop in fecal butyrate and butyrate producing bacteria was demonstrated in an elegant study comparing diets of varying amounts of carbs. Given the importance of butyrate in colonic health, any dietary strategy that potentially shifts pH away from acidity as a function of reduced fermentation, might contribute to various forms of IBD.

So, low carb equals a less acidic colonic environment due to the drop in fermentation (and I presume harder, and less frequent stools as a function of reduced biomass from bacteria – or maybe not). As pH shifts, prospects for opportunistic pathogens increase, as does opportunities for gram-negative bacteria like Bacteroides and Enterobacter. When you add this up – and a lot of more shifts in the microbial ecology of the low carb gut – you most certainly have a classic case of microbial dysbiosis – as the name implies, an imbalance. This dysbiosis can lead to issues associated with IBD, autoimmune disease, metabolic disorders and so on. But again, a large cohort of low, low carb dieters has never been looked at using 16S rRNA methods. So the jury is still out – but will be fascinating to see.

A bit of a paradox in all of this is the increased likelihood that a low carb microbial community will most certainly lead to increased gut permeability – a well-known phenomenon whereby microbial parts (lipopolysaccharides, which leads to metabolic endotoxemia) and whole microbes themselves (bacteremia) leak from the intestinal track into the blood, leading to low-grade inflammation that is at the root of metabolic diseases such as type 2 diabetes, obesity and heart disease. So it is a paradox that a leaky gut that can be triggered from a low carb (high fat) diet – and a possible increase in gram-negative bacteria and a reduction in healthy bacteria like Bifidobacterium – doesn’t result in weight gain as demonstrated in study after study in mice and humans. Weird.

I hope people do not take this as some kind of attack on low carb diets – couldn’t be farther from the truth. There is NO AGENDA. Again, NO AGENDA. (It’s worth noting I consume a high fat, high protein, high fiber diet). Just wanted to point out some obvious concerns (maybe unfounded) and that if we get a large enough sample of low carb folks in American Gut, we might be able to provide some interesting insight – or not. Who knows, maybe low carb folks have super healthy gut microbiota (whatever that is).

So to my low carb brothers and sisters out there, try and eat a little more fibrous material if you can – diversity matters –  and help your gut bugs help you. It’s what evolution intended.


**If you follow a low (or low, low) carb diet, would be great if you joined American Gut. The more people we have for each dietary group, the more we will hopefully learn.

270 Comments Add yours

  1. How do us folks with leaky guts, damaged villi and autoimmune disorders get our bodies out of the paradox? Is there a carb(s) that does not exacerbate leaky gut, enabling us to create a healthy “compost”?

    1. Jeff Leach says:

      that’s a good question! more fermentation – and grow more bifidobacterium – see

      1. Great advice! Thanks for the link. I forgot about inulin. Another good info source:

        1. Jeff Leach says:

          thanks for the link.

        2. Seymour says:

          For a significant percentage of us with gut problems, inulin is a really bad idea. It depends on what species – not families – live within. Inulin is highly fermentable by some species of bacteria, and is a major target for reduction in a FODMAP diet that focuses on reducing bloating, cramping, and flatulence for IBS patients.

          There are no panaceas. Many of us must experiment carefully, changing one variable at a time. We are not all the same, nor does our biome necessarily respond positively to the same foods.

          1. Jeff Leach says:

            yes, is an issue for some folks.

          2. sandra says:

            Yes,a big problem for those of us stuck on a minimum FODMAP diet with no way to feed our gut flora without the return of our original symptoms.

          3. Sue Carmody says:

            Eat a diet in butyrate rich foods and it will help repopulate your gut. Fodmap says we can’t eat most of the things that help those bacteria live and function so we have to help them along with butter and cheese and cream and bananas. (Not all together). Populations help those bacteria by fiber, or onion and garlic, or butter tea, or lots of cheese, fermented foods, and cream and butter.

          4. josh says:

            inulin is a horrible idea…no fiber and no carbs – its the only proven way to rid of your leaky gut symptoms. Will it repair it? There is a lot of speculation on that and everyone is different. But people with gut issues (you and I) , going no or very low carb is the only way proven way to truly rid the issues. I have been through this circus too many times, trying to find foods I could eat and nothing worked. I have personally tried every diet known to man and limited my foods to one at a time. Everyone is different, but again, if you want to get rid of the gastrointestinal issues, go zero-very low carb. Plenty of documentation online and people living this way and their lives have improved. I am one of them.

      2. Marianna says:

        I read the link that you sent this woman and it makes zero sense to someone who isn’t scientifically educated. Is there something that the everyday person can understand?. Can you please break it down for me. I’m very interested in learning about leaky gut syndrome and why it occurs and how to best prevent it or heal it. Thanks

        1. lots of people write about leaky gut syndrome – however, a lot of it is not from the perspective of the gut microbiota. a great article written by Moises Velasquez-Manoff in Mother Jones is worth reading on the subject

          Also check out Moises book: Epidemic of Absence

        2. ozob says:

          Sarah Ballantyne’s The Paleo Approach is an evidence-based synthesis of current science-based knowledge pertaining to human diet and health. Although a mostly practical guide, it is written with an -unfortunately rare level of intellectual rigor and honesty. Reading it has helped me not only understand each piece of the puzzle but how they fit together and interact in often-complex ways. I’d be surprised if she wasn’t following the projects on this site.

      3. Sue Carmody says:

        Maybe the butter teas of the Tibetans and others help supply the all important butyrate?

      4. josh says:

        horrible advice. From personal experience, I can tell you that MORE fermentation does not work. And to answer Raenne’s question bout what carbs – the answer is “no carbs”. That low-to-zero carb diet is the only way I have found that leaky gut has been fixed for myself. Saying “more fermentation” is dangerous advice and I would not listen to that, unless you want to make candida potentially worse and deal with even greater symptoms and issues that you already have.

        1. Glenn Atkisson says:

          Josh, what is your particular intestinal ailment? I’m guessing either SIBO or Crohn’s/Ulcerative colitis. In which case, yes, fiber introduced willy-nilly can cause further problems.
          But generally, for all other conditions, and to improve health, gradually increasing fermentation of fiber is the key to health, immunity, and lower inflammation.
          And this is totally consistent with a Very Low Carb diet. I eat mostly high-fiber, low carbohydrate vegetables and take in less than 50 grams of digestible carbohydrate per day, but I get way more fiber than is even recommended by Jeff. So my LC diet is quite different from yours apparently. It seems you are eating a low-fiber, LC diet. Whatever works for you is what you need to do. You are in a bad situation however. You can avoid some symptoms of gut dysbiosis by what you are doing, but you’ll never get healthy without getting the fiber in there, gradually, in greater and greater quantities, to generate a healthy gut flora, which will then help your gut enterocytes restore and seal up the junctures between cells that let all kinds of toxins enter your body.
          In my opinion, this is what you should be doing: find a way to slowly increase the fiber.
          To your health!

        2. anonymous says:

          I didn’t have issues until I ate a keto diet. Tried it for 3 months and now that I’ve stopped I feel horrible.. Never had problems before 🙁

          1. Glenn Atkisson says:

            Read Jeff Leach’s response just above your comment, when he recommend the Mother Jones article. Read the 2nd half of that article. Here it is again:

            What was the makeup of your “keto” diet? People imagine this diet in all kinds of ways. I’ve found that the ones that focus on getting a high input of fat often don’t even pay attention to the vegetables and fruits they eat, thinking that they must be so minimized that they don’t matter. I think this is a big mistake.

            Do the opposite. Eat a diet rich in very low net carbs (carbs digested in your small intestine) because they are mostly fiber of different types, you can still be on a keto diet. Adding butter or olive oil will give you enough calories that you don’t waste away.

          2. Glenn Atkisson says:

            Anonymous, what was the makeup of your “keto” diet? People imagine this diet in all kinds of ways. I’ve found that the ones that focus on getting a high input of fat often don’t even pay attention to the vegetables and fruits they eat, thinking that they must be so minimized that they don’t matter. I think this is a big mistake.

            Do the opposite. Eat a diet rich in very low net carbs (carbs digested in your small intestine) because they are mostly fiber of different types, you can still be on a keto diet. Adding butter or olive oil will give you enough calories that you don’t waste away.

            Read Jeff Leach’s response just above your comment, when he recommend the Mother Jones article.

          3. Glenn Atkisson says:

            Don’t forget that you can ingest less than 80% of your food as fat and still end up deriving over 80% of your burned calories from fat. How? You gut microbes turn fiber into saturated fat. Mostly butyrate, But also acetate, etc. This is the ketogenic diet that ruminants such as grass-fed cattle ingest. It’s all grass but they are burning mostly fat by the time the fiber gets digested. There just isn’t hardly any glucose coming out of the grass. This is the kind of ketogenic diet to aim for – high in fiber, low in small-intestine-digestible sugars and starches. Green leafy vegetables are very low on the glycemic index. You can eat a couple of pounds of this stuff a day. Start slowly though. If this hasn’t been your “keto” diet in the past, it’s worth a try. Start slowly.

    2. Odile says:

      The Specific Carbohydrate Diet, which was developed in the 1950’s to heal ulcerative colitis, Crohn’s disease, IBD (and works!), is described in Breaking the Vicious Cycle by Elaine Gotschall. This book explains exactly which carbs you can eat and which to avoid to heal the gut by restoring balance in the gut biota.

      1. Janet says:

        Thank you. I just want someone to tell me what to eat to heal my leaky gut.

        1. Jeff Leach says:

          Hi Janet. As for what to eat to help your leaky gut, should probably check with your doctor.

          1. Jeff says:

            Unfortunately most Dr.s consider leaky gut to be a myth even though there are more and more studies which show that it is not. Check out the GAPS diet book in which Dr. Natasha Campbell-McBride specifically talks about leaky gut and a diet that is suppose to help heal it. Good Luck

          2. kitinstlouis says:

            Hi Jeff!

            The Specific Carbohydrate Diet has been a godsend for thousands of people suffering with Crohn’s, ulcerative colitis and SIBO (small intestinal bacterial overgrowth). Yes, it reduces, markedly, the number of bacteria in the gut, but that bacteria has already become dangerously unbalanced with bad actors (such as e.coli) which have traveled from the large intestine to wreak havoc on the epithelial layer of the small intestine. The author, microbiologist Elaine Gottschall (RIP) recommends replacement with the known probiotics, but we are waiting for your studies to show us which bacteria really are the most useful.

            It is has been shown by prominent celiac researchers such as Alessio Fasano that the autoimmune cascade that causes Crohn’s and celiac disease can be interrupted by diet. You could potentially save a lot of human agony by familiarizing yourself with these protocols and studying how the diet works. I know this goes against your theory that cutting out food for bacteria will be ultimately bad, but for some it’s the only thing between them and the grave.

          3. Michael says:

            “Check with your doctor”, a useless suggestion. Really, we know you have to CYA, but come on, what doctor cares anything for nutrition? None.

      2. Jan Red says:

        The Specific Carbohydrate Diet is working for me and there are many similarities to protocol used by Dr. Terry Wahl to reverse her own MS and now many of her patients as well. The SCDiet is being used by the autism community as well with impressive results.

        The issue of carbs and the gut is very confusing when you review the science, but when something is finally makes sense and gets results in my life-long struggle with IBD I want to shout from the rooftops. Healing is possible, and improved overall health is the result. Sadly, the medical community is for the most part not very helpful.

      3. Jeff2 says:

        Glenn’s response above from September 2016 is quite right. Eat lots of carbs but make sure they are mostly the ones that are not digested in the small intestine, but rather make it to the large intestine intact and ready to be fermented. That includes resistant starches, inulin, dark green leafy vegetables, acacia gum, arabinogalactan fiber, soluble corn fiber, oat bran, unprocessed dark chocolate powder, the various “OS” fibers like FOS, GOS, XOS, etc. A typical meal for me goes something like this.. baked salmon (with the skin!), a huge portion of kale salad, olive oil and vinegar dressing, followed by a smoothie containing all of the above mentioned starches and fibers. The vast majority of my meal is not for me to digest, but rather to make it all the way to the distal parts of the colon to be fermented by the good bacteria. Think of the way cows eat. They don’t digest the grass. Their bacteria digest the grass and they feed off of the waste products produced by their bacteria. Try to aim for that sort of meal, where most of it ends up being digested by your bacteria rather than by your small intestine.

    3. kitinstlouis says:

      While we know that intesinal permeability is a probably actor in the development of autoimmune disease, it’s worth noting that the sheering of villi is only known to happen in cases of tropical sprue (very rare) and celiac disease, which only affects less than one percent of the population. By the estimates of clinicians in the field of gastroenterology who are informed on the existence of non-celiac gluten sensitivity, it is estiamated that at least five times as many people have NCGS but endoscopies have confirmed that the damage to the villi is absent in those with NCGS although there may be some slight epithelial inflammation. There are, as yet, no definitive tests to rule out NCGS

      The conflation of celiac disease with NCGS has been an intellectually dishonest effort by alternative practitioners at best. At worst, they really don’t know the difference.

      Intestinal permeability is also known to occur because of frequent NSAID use, capsaicin ingestion (hot peppers), certain drugs, impact injury and extreme physical training in activities such as marathon running. It’s unusual that the alternative medicine presaged the medical discovery of the role of intestinal permeability, but that doesn’t mean that every other thing proposed, yet unproven, by alternative medical practioners has scientific merit.

      1. A. Lynn Dolson, MD says:

        “The conflation of celiac disease with NCGS has been an intellectually dishonest effort by alternative practitioners at best. At worst, they really don’t know the difference.”

        I had to reply, as a pathologist (MD), turned alternative medicine practitioner, I do find a lot of NCGS. I do it by autonomic response testing, but explain that it is really unusual method, and that the real test comes from going one week STRICTLY without eating any gluten, then having a large bolus of it (such as 2 or 3 bagels). Patients are surprised how they feel better without it, and the sudden and specific return of their symptoms with it (such as sinus congestion, brain fog, fatigue, stomach upset, gas, bloating, back pain, flank pain, knee pain, diarrhea, constipation, headache, etc).

        There is a lot more to this subject than that. Grains, and particularly gluten are difficult to digest in general. Gluten is no more the problem to disease processes than sugar to diabetes and alcohol to alcoholism, but abstaining from gluten while they recover and then resuming only judicious use at the most is of tremendous and surprising benefit to many of my patients.
        A. Lynn Dolson, MD

        1. seymour brown says:

          Dr. Dolson –

          Bagels are a complex food. Some of the symptoms you list – stomach upset, gas, bloating, back pain, flank pain, diarrhea, constipation – are also symptoms of fermenting of fructans in wheat products. FODMAP challenge testing may be warranted in such cases.

          If you want to test gluten reaction specifically, try challenging with seitan – it’s almost totally gluten:

          A blind test using seitan vs chicken could easily be done.


        2. kitinstlouis says:

          Dr. Dolson, perhaps a test of pure gluten would do more to outline whether the patient benefitted from a general reduction in carbs, an allergy to yeast or is actually gluten sensitive?

      2. gh says:

        There does not seem to be any evidence of capsaicin causing damage to the gut. If anything, it seems to protect the gut. Yes, it can cause discomfort.

    4. schesche says:

      you can research resistant starch

  2. lexgravatar says:

    “So, low carb equals a less acidic colonic environment due to the drop in fermentation”
    Wasn’t less acidic environment better for our overall health?

    “This data will allow us to compare the gut microbial communities of this population against other dietary strategies. And this is likely where the problem will pop up.”

    I don’t get it. So, do you have the actual data or just speculating right now?

    1. Jeff Leach says:

      plenty of data on the importance of fermentation to microbial (gut) composition. 1000’s of articles literally. in short, varying the inputs can have a dramatic impact on the composition of the gut microbial community. while much is still to be determined, some basics are well understood. a particularly good paper on the impact of pH can be found here

      as for us, we are moving along on american gut – just started sequencing samples. we will be the first project (I think) to have a descent sample of low carb eaters. so will be interesting to see. i’ve experimented with myself. thanks for the good Qs.

      1. adventurer says:

        Hi Jeff- this is an interesting article and I look forward to your analysis of carbohydrate load vs bacterial profiles. I do hope you will stratify your analyses by the type of carbohydrate as this is likely to make an enormous difference. There are tons of scientific references regarding soluble vs insoluble vs fermentable fibers and all those vs digestible for energy carbohydrates. We’re just at the tip of the iceberg. Not all “low-carb” are created equal. Some “low-carb” are my Inuit fat-loving neighbors while other “low-carb” folks don’t discern and still include a donut a day–but just one–and yet others manage it by loading up on vegetables that are high in fibers and microbe-supporting while low-net-carb. Also the high-carb folks–are we talking processed grains or potatoes? This will likely make an enormous difference and your huge sample size could provide some great info of huge value to us practitioners hoping to heal clients so many of whom have gut imbalances.

        1. Glenn Atkisson says:

          I entirely agree with your suggestion to stratify any analysis considering the types of “carbohydrate” used in Jeff’s studies. I’m quite tired of bloggers throwing around the term “low-carb” without pointing out, as Jeff and Tatertot have done here, that the term really means next to nothing.

          Carbohydrates, defined as only that, leave every reader to define his own diet within a range that goes absolutely from maximally nutritious to abominably destructive. And a “low carb diet” thus becomes even more critical to define, as you say, carefully, as the potential for maximal nutrition can be either there in spades, or missing entirely. A person can eat half a plate full of leafy greens every meal and still be on a 75 gram per day, “low carb diet”. I’m sure this is not the image Jeff brought to mind in the title of this piece, but it was what he was aiming to explain before it ended.

          Personally, I think every effort should be made to get vegetable fiber defined as a 4th macro nutrient. Then articles on achieving good nutrition don’t have to argue a point about how many “carbs” need to be included.

          Green leafy vegetables are no more “carbs” than they are “protein”, but their primary features, obviously, are nutrient density and prebiotic qualities. There’s no reason whatsoever to call leaves “carbs”. Putting them in a category of their own frees up all the “low carb” and “Paleo” discussions from unnecessary confusion that causes stupid discussions to go on forever.

          To make this point, read this “Nutrition Data” page on Collards.

          Notice first, that Collards are at the upper bounds off “Filling” and “Nutrition”, but at the lower bounds of “calories”.

          Second, notice that for the 190 g in the sample size, 1 g is fat (9 calories), 4 g is protein (16 calories), and of the 9 g of carbohydrate, 5 is fiber and 4 is non-fiber, counting for another 16 calories that are humanly digestible — the same as the protein. So of the total calories derived from this food (49), 41 derived from macronutrients. The additional 8 calories are determined to be derived from the 5 g of fiber, probably mostly as short chain fatty acids. Well, if you add that 8 calories into the fat column, you finally come out with this serving of Collards consisting of 16 g of digestible carbs, 16 g of protein, and 17 g of fat. There is just no way that leafy greens should be considered “carbs” in the first place. They are as balanced a food as milk or nuts. That’s why I submit that the food that i think humans should focus on for health is not really any macro-nutrient so much as it is a major source of life enhancing qualities which include the fiber, plus all the micronutrients.

          So I encourage Jeff, when he writes again about this, to not even go into carbohydrates except to explain and dismiss that type of discussion as being fraught with confusion and totally unnecessary in an article that is designed to explain how to achieve health, and the part that the gut microbiome plays in human health.

  3. FakeBillyTubbs says:

    75 grams of carbs is over 6 cups of broccoli or over 10 cups of cooked spinach. Are you really arguing that’s too little dietary fiber?

    1. Jeff Leach says:

      more diversity would be preferred. not arguing anything. just pointing out some interesting microbial points. to each his own.

  4. Andy says:

    Thanks for your post. Great food for thought. How about the traditional Inuit? How would they fit into this perspective?

    1. Jeff Leach says:

      not sure. northern adaptations are more or less irrelevant if your talking about things that shaped modern Homo. that said, low gut fermentation has it’s downsides no matter where the ppl r located. but who knows!

      1. Laura Kernan says:

        I think the Inuit traditionally eat a lot of fermented fish. Maybe that replaces the effects of carbs?

        1. Sounds possible. Do they make use of any of the animal gut contents? (similar to lichen from Reindeer gut) I also wonder whether their gut bacteria may actually be different to begin with. Evolved with them for the regionally specific diet.

          1. Seymour says:


            I really think the lifespans of traditional cultures are generally over estimated. Current Inuit lifespans are short.

            What we need to know is what their life expectancy was before western culture hit them. A hundred or more years ago, their burial customs may not have included cemeteries where life expectancy can be easily established.

  5. tatertot says:

    Jeff – The paper you had published a few years ago on coprolites from the desert which contained lots of inulin and animal remains makes me think a modern-day person could thrive on a low carb paleo diet with a focus on resistant starch and fibrous veggies.

    Regarding the Inuit diet…not many people realize this, but one of the most important foods of the inuit was Eskimo Potato I’ve never seen a nutritional breakdown, but I can imagine the inulin/fiber content would be on par with what you found in the desert.

    I got my test kit yesterday–can’t wait to see what 30-50g of RS/day along with approx 150g carbs from potato/rice/plantain mostly will result in. Wish I would have tested before I started this!

    Richard N. just wrote a new piece on our experiment:

    1. Jeff Leach says:

      Holy smokes! 30-50g a day of RS.. that will be interesting. be sure and reach out to me when you get your specific results back in a few months – will be interesting to compare yours and mine. i don’t eat as much RS, i like cellulose and various inulin-type fructans. yes, in the desert paper, those groups were likely eating a diversity of fiber – but varied day-to-day and year-to-year.

      1. tatertot says:

        Yep, 30-50g, and none of it from Hi-Maize. All from real food (cold/raw potatoes, cold rice, kidney beans, green bananas, dried plantains, and raw, unmodified potato starch).

        If anyone is interested in RS, click the link I posted above…tons and tons of research papers with good summaries and personal observations.

      2. Tatertot says:

        Jeff – Just got my results. Would love for you to take a peek. Email me at akman2014 (at) and I will send you scan of charts.

        My bifido is 11X the average!


        1. Dan says:

          I am VERY surprised to see green bananas only mentioned once on this thread. Have you read the study on boiled green bananas + rice based diet vs plain rice based diet? It confirms everything you discuss as far as resistant starches fermenting short chain fatty acids, improving good gut bacteria and healing gut permeability.
          Tatortot, has proved this n=1 with his specific foods (rice, plantain, banana, potato starch) to have 11x average bifidobacteria!

          Tatortot- is everything “peaches and cream” (not literally) with your health in general since dieting this way and affirming the gut composition data?

          1. Kit Kellison says:

            I think we’re bit far away from being able to make blanket statements that it’s always a good idea to increase the amount of any given bacteria. We’re not sure what other microbes a given fuel will be feeding and until we have a better understanding of the the ideal diversity (or, more likely, the individual”s ideal diversity) of our microbiome and how to best promote that diversity, we are naive to make claims that any given diet is going to promote better health.

            There is far too much variability among the needs of different groups of people sick and healthy at a time when autoimmune disease is tripling, quadrupling and more for reasons not yet made clear, but assumed to be of an environmental cause. Remember, our biggest physical contact with the environment happens in that lawn-size surface area that is our intestinal tract.

          2. Tatertot says:

            Kit – I actually believe with the new 16srRNA testing and what we know about the beneficial effects of SCFA on colonocyte health and its effects on the immune system that some sweeping generalizations CAN now be made.

            Prebiotics, namely inulin and resistant starch, in the therapeutic range of 20-40g/day either from real food, supplements, or a combination of the two have been shown to increase bifidobacteria and lactobacillus survival, lower gut pH, and have massive antiinflammatory actions body-wide.

            These prebiotics act in many ways on the gut, stimulating healthy microbiomes that can’t be achieved without ample RS and/or inulin (mainly) in adults…especially those adults with modern, inflamed, dyspeptic guts.

            Eating prebiotics activates 3 main paths:

            -Amylolytic microbes (Many Firmicutes, Bacteriodetes, and Actinobacteria are multi-fuel creatures, happily eating starch, amino acids, and other stuff. When they get no starch, they lose their luster and produce little butyrate.)

            – Butyrogenic microbes (These are your Clostridium Clusters that contain those wonderful C. butyricum, also E. rectale, and Roseburria fellows that pump out butyrate as fast as you can give them prebiotic fibers. These gutbugs have buk genes, or butyrate producing genes, for a reason!)

            – Methanogenic Archea (These are the guys that eat the byproducts of the above activities and increase in numbers to reduce smelly farts to negligible, non-noxious toots. All the activity required to produce butyrate also produces methane…nature gave us a cleanup crew, unfortunately lots of people have lost these through antibiotics and poor diet)

            So, a diet low in prebiotic plant fiber creates a gut flora low in diversity and low in butyrate. Without butyrate, or colons whither and take our immune system with it. Feed the gutbug masses enough inulin and RS to flood the colon with life-giving butyrate and all the other SCFAs will be there as if by magic.

            Sadly, not everyone can take advantage of this little trick…your guts are destroyed. This is where 16srRNA will pay huge dividends. We identify the species needed and implant them with poop pills or FMT. For now, though, best to try eating RS and inulin…if it fails, there are lots of off-the-shelf and prescription probiotics that will help. Also, eating dirty veggies, tossing the anti-microbials, and playing in the mud will help.

          3. Seymour Brown says:

            Tatertot –

            I don’t think it’s safe to make generalizations yet.

            I have to say that some of us with disturbed biomes react very negatively to inulin. It really depends on what bacteria one has. If one has significant amount of bacteria that ferments inulin, the result may vary from slight discomfort to extreme pain and nausea due to gas. The graphic results from the American Gut are certainly not enough to determine which bacteria are the cuprit. Possibly, the raw 16s RNA data may help. I haven’t been able to get mine uploaded to find out what gold lies within.

            So obviously, we still need to test what bacteria one has in what balances (down to species and subspecies). Then, knowing that, we need a guide for which bacteria can cause which symptoms when out of balance. Also in the equation are one’s own genetics and immune system.

            I imagine there are many species that have simply not been studied enough to make such a guide yet.


          4. kitinstlouis says:

            Thanks so much, Tatertot, for your comprehensive response. As someone with SIBO due to decades of untreated celiac disease, there isn’t much resistant starch that I can tolerate without signficant discomfort. I guess I’ll have to wait for the magic poop pill to fortify my friendly microbiome. Am actually considering a fecal transplant. I’d have to completely re-learn how to manage my diet if I could tolerate long-chain starches again; have been paleo for nearly two years.

      3. Kraut says:

        If you have Sibo, eating fiber, resistant starch is seriously aggravating and problematic, sibo is an overgrowth of bacteria in your small intestine- you don’t want to feed it! See Norm robillards discussion of resistant starch.

    2. Margaret Mandell says:

      Hi, Tatertot! Paul Jaminet told me to start eating unmodified potato starch in yogurt with lunch to “kick start my gut flora.” (Rest of diet is PHD.) I have dutifully done this everyday since October 2013–take about two heaping tsp in 1/2 cup yogurt. Since February I’ve been making my own home-made yogurt from live cultures and reliable raw, full-fat unpasteurized milk, heated to the point of boiling and then cooled, from a local Pennsylvania dairy, and I add the potato starch to it and drink it, often adding cumin and cilantro to the mix. Ever since, my shit (which is completely regular and well-formed) floats. I am wondering if that occurs because of my 55% calories from fat (PHD) diet or perhaps something is going on with the RS in my colon, perhaps binding with fat prior to excretion. Dunno. Any ideas?

      1. ozob says:, discussions I’ve seen seem to focus on the interaction between an excess of fat intake and the body’s actual ability to digest that fat (ref. Sarah Ballantyne). So it could indicate either too much fat intake or problems w/gall bladder/pancreatic function (sometimes stuff like alcohol consumption around meal time can really throw off digestion, too)

  6. I am a low carber and still have not received my kit for testing.

    1. Jeff Leach says:

      When did you sign up? You can email the lab directly at – someone will check your name in the database and give you an update. Thanks for helping with the study.

      1. thanks just emailed them.

  7. Sju G. Thorup says:

    This is all speculation. I am looking forward to your reflections when you have actual data. To counter your suspicion about stool quality and frequency: Besides my personal experience, I heard that the polar explorers who started eating the Eskimos’ meat-only diet, got rid of their digestion problems and had regular smooth bowel movements. So, let’s have some real data before you judge.

    1. Jeff Leach says:

      No, this is not speculation. Lack of fermentation and its role in colonic pH and pH’s impact on microbial communities is well understood process and well represented in the literature. As is the role of opportunistic pathogens in shifting microbial communities and the role of microbes in gut permeability. Not sure about your polar explorers. And who is judging? I think you misunderstood the post – friendo 🙂

    2. kitinstlouis says:

      I agree that it’s important to have an open mind as to the multiple possible ways to insure gut health.

      For so many of us who have already got SIBO or intestinal permeability due to celiac disease, physical impact or exercise damage, too much capsaicin or excessive NSAID ingestion (to name a few), we need to know what avenues are available for us to promote a good-actor microflora.

      Those of us with that very stubborn e.coli already in our small intestine may not have the luxury to explore a high-resistant starch diet or anything else that can promote the replication of e.coli. Our only choice may be to limit the di-and polysaccharides on which it (and other bad bugs) thrive and to introduce extra-food source probiotics.

      We assume that bifidobacteria are good for us, but they do seem to elbow out others such as lactobacillus acidolphilus (both of which are often found in yogurt).

      At this point in our knowledge, we’re still shooting in the dark as far as saying which gut bacteria are beneficial. It might be that it will depend on the individual’s genetic expression, bacteria profile, villous health (and resulting enzymatic production), diet or any number of other unknown variables.

      1. Seymour says:

        I saw this on GenomeWeb recently:

        We are all like pioneers crossing oceans and mountains, with vague ideas as to what to bring, where we’re going, or when we’ll get there.

        We like to talk as if there’s good bacteria we can buy, and bad bacteria we can avoid. Nothing could be further from reality. Yogurt has only a few of the thousands of species we could benefit from. Some types of e. coli are good.There’s thousands or millions of species of yeasts, but our baked products use only a few, and we seldom know which unless we work at a bakery.

        3rd world microbiome may have diversity, but also has significant child mortality due to digestive disease. Basing our idea of normal on the biome of someone in India or a South American forest is like wearing overcoats in polynesia, or only a t-shirt in antarctica.

        Studies based on western diets have inherent biases – which may be good or bad. Defining the optimal biome will depend on the diet and vice versa. Bacterial species do adapt, and may force the host human into avoiding change, at the price of pain or malnutrition if we try to impose our intellect on its reality. There are no magic bullets yet.


        1. kitinstlouis says:

          Brilliant observation. Thanks for the link to the Genome Web article.

  8. Interesting. I use lo-carb paleo +probiotic to treat GERD successfully. Paradox?

  9. varmentrout says:

    “A less acidic environment… – not a god thing.” Surely that was a typo.

    You are probably having some sample laggards who are waiting for a day that they can be sure to eat a “good” (or godly?) diet so as to avoid online embarrassment. I’ll get to it soon, I’m sure. Oatmeal muffins, bulgar in salad – check.

    1. Jeff Leach says:

      nope, not a typo. not sure what a “godly” diet is?

  10. adinaverson says:

    hi jeff! this post leaves me confused, and i’ll tell you why… i was a vegetarian/vegan for 13+ years and suffered from IBD, then was eventually diagnosed with an immune deficiency (hypogammaglobulinemia, to be precise). i then (about 7 years ago) switched to the paleo diet, and eventually low-carb paleo- where i’ve remained for the past 3 years. i’ve stuck with it because my IBD and immunity symptoms are gone- and left more rapidly the lower carb i went.

    so, how does this line up with the research so far? help me!! just kidding. but really… i’d love to know.

    1. Jeff Leach says:

      don’t have a clue about your past and present conditions. did you consume processed carbs while a veggie (grains that is)? i also think people are confusing the line between low carb and low, low carb. i think the people on the low, low end of carb – who also don’t consume carbs with a sufficient qty and diversity of fermentable substrates, are the ones I’m most concerned about. but maybe it’s doesn’t matter. will be interesting when the sequencing data starts coming available and we can compare to the metadata. but the basics of fermentation and its effects on pH and the composition of the intestinal flora is well-established.

      1. adinaverson says:

        i did, indeed, consume grains as a veggie. nowadays, i’m off most carbs including fruit and starchy veggies… but i do crave and consume onions and garlic like cray-zay. what a complicated thing you’re exploring… looking forward to getting my breakdown in the mail and seeing the completed metadata!

        1. Jeff Leach says:

          thanks. and thanks for helping with the study. should be interesting for all of us.

    2. tatertot says:

      I have spent waaaay too much time researching and discussing fiber, resistant starch and gut microbes. The only compelling argument I have seen for the reduction in fermentable fiber is in the case of small intestinal bacteria overgrowth (SIBO). In the case of SIBO, fermentable fiber also feeds bacteria that is wrongfully living in the small intestine. Well-fed SIBO produces gas and back-pressure producing things like GERD, IBD, and IBS. There is virtually no cure for SIBO except antibiotics, which only temporarily halt it, and starving it by eliminating fermentable fiber.

      1. kitinstlouis says:

        And from what I’ve read, SIBO is extremely common in people who have had to deal with bowel bacterial colony disruptions through use of general or gut-specific antibiotics, IBS and IBD, although, there is likely some chicken and egg stuff needing untangling as to which came first. It’s the rare westerner who has gotten through life without antibiotics…

        Hopefully, studies like this will shed light on what the ideal mix of macrobiota looks like. At present, we are shooting in the dark assuming that the same probiotics are good for everyone.

        1. A. Lynn Dolson, MD says:

          Regarding SIBO, I also wonder about the importance of the factor of insufficient gastric acid. Without the acidifying gastric contents, the small intestine would be relatively more alkaline, making for a very different environment. Patients require acid replacement (such as betaine hydrochloride), with zinc replacement to sufficiency, so that that can then (hopefully, and with time) make their own. Also autonomic nervous system balance (otherwise they don’t achieve parasympathetic state to digest properly…including making acid). Also wonder about the part that bile and biliary stasis (absence) plays in shaping the microenvironment. Just curious.

          1. fodmp says:

            I agree. I have been working on SIBO and low colonic good bacteria and am on low FODMAPs diet. I’m also working on my low stomach acid and low Zn levels. My latest new addition is low dose naltrexone! Slowly increasing dose but no effect so far.

      2. Kraut says:

        Yes, only treatment, starve it, antibiotics and then fecal transplant to introduce true diversity.

        1. kitinstlouis says:

          Trying to think about how to introduce the topic of fecal transplantation to my husband and gastroenterologist.

  11. David says:

    Does the data account for low-carbers who consume bone broth, fermented foods, and clean meats without any processed LC products?

    1. Jeff Leach says:

      we haven’t put out any sequencing data. the blog post is just about some basics of fermentation and what happens when pH moves around. less fermentation, less acidic – not so good.

  12. Chris Saunders says:

    The only carbs I eat besides non starchy vegies is a banana, some berries, and a fair amount of soaked Quinoa or Brown rice with lunch. I do consume about 3 pounds of produce 47 grams of fiber, about 6 oz. fermented vegies,2 cups of Raw milk Kefir, and 16 oz of lactor fermented ginger ale. In other words lots of acidic fermented foods and tons of fiber. Does that creat the acidity in the colon, dispite being low carb, and 65% fat.

    1. Jeff Leach says:

      i have no idea. you would have to be tested i guess. curious, what’s the primary sources of fat in your diet…..

  13. daniel says:

    Hi. Very interesting and rings true. Can you give us a list of source of “fibrous material” you’d recommend? Paleo(ish) if possible, please. Thank you!

    1. Jeff Leach says:

      Any plant (sans too many grains). I don’t have a good or bad list. however, i do prefer 1) things that grow below the ground (onions, garlic) and 2) the “whole” whole plant. by that i mean eat every bot of the asparagus – not just the top.

  14. Kelly says:

    I want to make sure I understand. So what you’re advocating are more prebiotics, to feed the probiotics/bacteria? And when you say variety, do you mean a variety of fruits and vegetables? Or are you suggesting other kinds of fiber (supplements, for exmample)? Not trying to be a naysayer. I have leaky gut and am doing everything I can (fermented foods and drinks, for example) to improve the ole gut, and by extension, health!

    Missed the sign up for this study. Are you saying you’re waiting for more participants? Or just their data? I’d like to sign up!

    1. Jeff Leach says:

      thanks for the comments. curious, how do you know you have things leaking from your gut into your blood?
      people can still sign up for american gut – just follow the links at the top of the page for American Gut.
      as for prebiotic foods, i eat a lot (mainly onion, garlic, leek). my levels of bifidobacterium – which is the target for the prebiotic foods – are 5.1% – which is good. general population levels (in the US), can be much lower.

  15. Thank you all for the information and discussion. I am curious as to how the Specific Carbohydrate Diet fits into the picture. Does anyone have any thoughts?

  16. Bassett says:

    I read on Richard Nickoley’s Free the Animal blog that resistant starch can provide a measure of protection for probiotic bacteria. It somehow etches itself into the resistant starch granules and becomes encapsulated inside the RS. This allows it to traverse the upper digestive system and delivers it to the large intestine. Apparently there are many patents being drawn up to use this principle to mass-produce prebiotic/probiotic combinations of foods, but it can easily be done at home simply by combining an RS source such as potato starch with kefir or yogurt–have you ever heard of this or care to comment?

    1. Jeff Leach says:

      new to me. sounds pretty amazing.

      1. Bassett says:

        Here are a couple studies he had linked to this info:

        If you look at the pictures in the abstract, it shows potato starch granules with bifidobacteria attached to it and encapsulated by it. in the paragraph entitled ‘Resistant starch as a prebiotic and synbiotic’ as ‘There is conversion of the irregular granule to a more spherical shape with formation of a pit, which may bethe site of initiation of amylase attack…it was thought that the etched granule could confer physical protection on the LAB (lactic acid bacteria) on passage through the upper GIT. Several in vitro studies have confirmed physical adhesion of several Bifidobacteria species not only to this RS but also to chemically-modified RS starches,…”

        The other mechanism is a man-made encapsulation. This seems to provide total protection and a long shelf-life, but it’s done with a lengthy manufacturing process. This Iranian paper explains it in grueling detail.

        I found it very plausible and interesting as well.

  17. Beverly Johnsen says:

    I was surprised to see in your scatter chart that there are about twenty BMI’s under 15, and eight BMI’s under10. I’m curious to know what your sample size was, as the percentage of low BMI’s, especially single digit ones, in BMI distribution graphs is vanishingly small, although not non-existent.

    I’d also love to know the back story on some of those outliers, like 45% calories from fat on the 3 BMI line, although I don’t expect to have my curiosity satisfied on that one!

    1. Jeff Leach says:

      yup. went back at looked at all of the lower ones. once removed, the correlation stays the same. will see what it looks like when we have a larger sample.

  18. Miles says:

    Why use BMI? A lot of recent research indicates that waist circumference alone, or even better waist-height-ratio (WHtR), is a better predictor of obesity and health risks than BMI is. I’d be very curious to see if a regression of WHtR on fat intake indicates that the slight positive correlation of BMI with fat intake is due to increased body fat (shown by positive correlation of WHtR with fat intake) or increased muscle mass (shown by negative correlation of WHtR wih fat intake).

    1. Jeff Leach says:

      yes. you are correct. BMI is a rough proxy at best – but nevertheless, useful.

  19. Fred says:

    Good OPINION piece. If you can provide references for everything you mentioned that would be great.

    1. Jeff Leach says:

      the references are hyper links throughout the piece – 15+ or so references.

  20. Alan says:

    Your plot of BMI against fat intake (% total macronutrient) does not provide useful information on how people became fat or skinny–your data are only 7 days of diet information.

    Why not plot BMI against grams of carbohydrate eaten per day (given that you are interested in focusing on low carb eating)? Or perhaps plot BMI against grams of fiber eaten per day given that this was another major focus here?

    1. Jeff Leach says:

      it’s just a simple plot from some of the data we are collecting. can do 100s of different plots with the metadata. the BMI vs % of fat in diet struck me as interesting. as for the 7-days of diet, that is for the sequencing. the days of dietary info prior to taking the sample provides some rough idea of what people eat on a regularly basis – that is, do they usually eat a lot of protein vs carbs and so forth. it also appears to take some time to shift the gut microbial composition.

  21. Pam S. says:

    Now I’m very confused. I’ve been following a very low carb diet. I’ve been diagnosed with SIBO in the past by my gastroenterologist. My understanding has always been that I need to starve those bacteria of their food, so I don’t eat lactose, any kind of sugar, no grains, no starches at all. I did submit a test kit several months ago. I feel like I eat lots of plants and a good variety, but there is no way just by eating plants that I can reach above 100g of carbs a day. Not sure now if I’m doing the wrong thing. If I go to my Gastro he will just look at me like I have two heads.

    1. Jeff Leach says:

      will interesting to see how your sequencing data looks. hopefully it provides some insight.

  22. Chris Saunders says:

    Daily, 1 avocado, 2 to 3 tbls olive oil, 3 tbls coconut oil, 2 brazil nuts, 1 teaspoon fermented codliver oil,bone broth with lots of beef talow, 2 cups raw milk kefir,2 egg yolks, grass fed beef,lamb, chiken, or wild salmon. 1 lb raw butter every 3 weeks or so. All the good stuf.

  23. Adriana says:

    Any tips on how to incorporate raw onions and garlic everyday without making people not want to come near me because of the strong smell :)? I do use them cooked daily on my meals, does that count? Thank you for your project.

    1. Mara says:


  24. Elizabeth says:

    I think you need to distinguish between low carb and low fiber. One can have a low- carb high- fiber diet.

  25. Susan says:

    There are quite a few people who have difficulty eating high fiber foods. I am one of those people. I feel better when I avoid broccoli, cabbage, apples, beans, etc. One of the reasons I am interested in the American Gut project is that it seems that these difficulties might stem from having the wrong gut microbes. It seems that what you are suggesting is that eating foods that may cause pain is the way to get a healthier population of gut microbes.

    1. Jeff Leach says:

      will be interesting to see your composition. hopefully it will provide some insight.

      1. Seymour says:

        Jeff –

        How should we share I results to your insight?


        1. Jeff Leach says:

          Post if u feel comfortable doing so – but please do not post your Kit ID…. Let other ppl chime in as well…

          1. Susan says:

            Where would you like us to post results if we are comfortable? This was my post, and since I have received my results, it would be interesting to see if my composition provides insight.


          2. Jeff Leach says:

            facebook would be a good place – other ppl could weigh in as well.

    2. Cindy C says:

      Hi Susan,
      There are a lot of us that go very low carb, moderate protein,and high fat, and their digestion gets better. Some, though have to very much limit certain plants, especially raw, until their gut heals. Plants have a variety of anti-nutrients, and poisons.. After a while, your body may be able to get rid of those plant poisons, if they are lessened, and cooked well or fermented. Wheat legumes, and grains, though are the worst.

      If we had been better nourished, and had plenty of A and D containing foods, and sunshine, and never had antibiotics, then we may have been healthy enough to eliminate those plant poisons better. The discoverer of what caused Rickets found that although cereals depleted the body of D, cod liver oil would make up the deficiency. Sunshine was needed, and in Britain, the sun is not that available. Plants can reduce cholesterol,but that may not really be a good thing, as we need it to make D from sunshine. How many of us get out in the sun?.

    3. Seymour says:

      Susan –

      Seeing the foods you mention, I urge you to have a look into FODMAP testing for some clues in adjusting your diet for some relief until an actual therapy to change your biome becomes clear.

      1. Jeff Leach says:

        Thanks. Very familiar with FODMAP

  26. Mike says:

    Jeff, the chart does not look statistically correct even if the X and Y axis were flipped. Ho, pray tell, does one have a BMI lower than 10 (and at ZERO) and stay alive?

    1. Jeff Leach says:

      seems there were some outliers. checked all of the ones below 20. seems to be some errors in entries. so updated the plot. the correlation remains the same.

  27. Gabriella says:

    I’m a little worried about your data as it contains points for people having BMIs 5 and below. Considering that I am 5’7″, I would have to weigh 32 pounds in order to have a BMI of 5. What’s up with that?

  28. FWIW, since going low-carb I have been immune to the “tummy bugs” that appear from time to time with kids of school age. You need to factor in the effect of different protein intakes as well as amounts of fat, very high protein diets create a less beneficial profile. Nuts are good low-carb prebiotic foods. The butyrate in butter can supplement that from fibre.

  29. Seymour says:

    The BMI vs %fat scatter plot you posted has some obvious data puzzles – BMI’s less than 10? Were these people alive, or was it simply a typo during data entry? What’s the BMI of a skeleton, I wonder?

    Also, what sort of diet would have 70-80% fat, or less than 5%? Again, might this be a data entry issue? Surely we want to avoid cherry picking data to get a result, but we also need to qualify the data properly.

    1. Jeff Leach says:

      yup. among the 1000 data points in the simple plot their are some outliers. just a preliminary plot. will see how it looks when there are a few thousand more people.

  30. Seymour says:

    Given the comments so far, I think the project may have an atypical cross section of eaters. I know I joined because of digestive and immune system issues myself. Nevertheless, I hope for some good science from this because of the questionnaire and 7 day diet log. I do think it would be good to focus more on the longer history of dietary changes on future efforts. The biome we have is not 7 days old.

    The whole subject of fermentation is dear to me, because I discovered the Gut Project after starting an anti FODMAP regimen to reduce extreme fermentation that caused painful intestinal and stomach gas. This all happened after various antibiotics and antifungals I was prescribed to treat various infections in the gut and elsewhere.

    But I’ve always had trouble with some foods since I was a kid back in the 60s – green peppers, onions, garlic, whole wheat, bran, rye, and various polyols (usually in diet foods or mints). Perhaps I had an overabundance of biota that ferment these, or maybe my personal DNA has oddities. It’s possible that a severe “stomach flu” damaged nerves that slowed digestion, and this leads to more fermentation, or so I’m told. I did flunk the gastroparesis test, even though I studied all night 🙂

    I also discovered that most gluten free foods also have low amounts of the varieties of wheat and rye that trouble me, but discovered that some of them have inulin or sugar alcohols that cause me painful gas.

    Finally, I think fungi deserve more attention in the biome. It’s not all about bacteria. Usually, we just hear about bad fungi. I’d love to see a comprehensive list of bacteria and fungi subspecies found in the gut, and how they metabolize and interact with what we eat. The Googlebird seems to know very little about this. We hear about species and families, but there’s good E. coli and bad E. coli. Maybe I need to read back through previous posts and emails to see what gold I can find.

    1. Jeff Leach says:

      thanks for the info. 7 days of dietary is hard enough to gather – especially among a free living cohort. 7 days is sufficient to determine an individuals basic patterns as the gut microbiome doesn’t change dramatically over weeks and months so long as someone doesn’t make a radical shift in diet. yes, fungi would be interesting – but very expensive testing required. that’s actually part of the study – “Beyond Bacteria”

      1. Genova Diagnostics has an excellent webinar by Dr. David Brady, “Using Cutting Edge Accurate Identification of the GI Microbiota in the Diagnosis and Management of Autoimmune Diseases,” available for download. Registration required but well worth it. The presentation explains the role of leaky gut in auto-immune disorders, summarizes the latest research and even explores the possibility of using parasites as “probiotics” to reduce inflammation. Worth it if you have thirty minutes or so. You need to fast forward at the beginning because they started recording way before the presentation began. You can also register as a clinician or patient and obtain access to all their educational resources at their website.

        1. Jeff Leach says:

          Thanks for sharing.

    2. Sju says:

      I totally agree fungi will be very relevant and interesting. See e.g. and, and original research by Dr. Orian Truss

  31. Marc Lindhout, D.C. says:

    Give the gut critters what they need to thrive: alium family, such as onions, leeks, ramps, garlic. These all have the fiber type which bacteria feed on which produce short chain polysaccharides through fermentation. The SCP are thought to reduce chronic inflammation: the mother of all chronic diseases.

  32. J says:

    Are you breaking down carbohydrate intake further in your analysis? A lot of people who’ve read Taubes & the new Atkins diet book avoid grains but eat plenty of vegetables and count their 75 or 50 g of carbs a day as net carbs (total minus g of fiber). It seems like you’re saying 75 is too low from the perspective of gut flora. What about the low-carber who is eating lots and lots of vegetables, a bit of fruit, and no grains or beans? Also, what about the people who eat 300 g/day of carbs but don’t include whole wheat bread, fruit or vegetables? (I’ve had patients who never eat any vegetables or fruit, only white bread & rice, junk/processed/fast foods, lots of soda, and maybe the occasional serving of juice–people who state they literally don’t eat fruits & veg.)

  33. Oly says:

    Wanted to say that my and my husband’s gut flora were already destroyed causing/aggravating an intolerance to the previous high carb diet and low carb manages the symptoms. Throw in antibiotics, acid reducers and things just went downhill. I can eat vegetables and fruits fine, but my husband who was prescribed a high spectrum antibiotic a few years ago has a teacup digestive process ontop of his lifelong heartburn. Except for the free pass that soy/tofu gets, I loved “Fast Tract Digestion: heartburn” by Norm Robillard which confirmed our own ideas about acid reducers and SIBO infections — finally have a method to the madness about why some carby things cause gas/heartburn and others don’t.

  34. tatertot says:

    When increasing inulin and resistant starch mainly, a huge increase in flatulence is normally experienced. Is flatulence a normal part of eating for enhanced gut microbiome? Any tips on mitigating flatulence?

    1. Jeff Leach says:

      everyone is different. while culturally unacceptable in an office setting, ppl need not b scared of a little – or a lot – of gas 🙂

      1. tatertot says:

        Thanks. I know what you are saying! Over at Free The Animal, we have been using a lot of your research papers to convince people that a diet high in inulin and resistant starch is more ‘ancestral’ than bacon-n-eggs. The trouble is, when they start ramping up intake, they get gassy and don’t like it–one lady is an OR nurse who stands over a patient for 6hrs at a time–can’t blame her!

        We’ve been trying to pin down the best type and amount as far as gut health and ‘side-effects’, many people find as soon as they start increasing fermentable fiber, they experience very deep sleep, vivid dreams, lowered fasting blood glucose, and increased satiety. We’d love to get you to drop in and read some of the comments–and leave a few if you have time.

        We’re at

        Your work with coprolites has been very inspirational to us in trying to figure out how to best feed our ‘other 90%’.

      2. Susan says:

        Actually for those of us who have difficulty gas can be very painful. Also, if you teach 8th grade….well you can imagine. Even in a science class it isn’t a teachable moment. It has been very helpful to read these comments. There are quite a few people who have a digestive profile similar to mine – difficulty with certain carbs, heartburn etc. I was prescribed antibiotics for years as a teenager to treat acne. I try to avoid them but that is difficult after parasites from a trip to Mexico and two cases of Lyme disease. As a commenter above said doctors look at me like I have two heads and tell me that my problems are all in my two heads. I really hope that research like this project open up new avenues for understanding these digestive issues which seem to occur occur widely.

  35. Beverly Johnsen says:

    Tatertot, perhaps the previous lower fiber diet had promoted a gut microbiota sufficient to break down (by feeding on) that amount of fiber, but when additional fiber ferments in the gut and there are no organisms available to break it down, excess gas results. Since the evidence so far suggestions that the gut’s microbial profile changes very slowly, it would seem prudent to increase the fiber in your diet gradually, whereas I would imagine that most people who are convinced of the benefits of more fiber would tend to go after it wholeheartedly.

    FWIW, my husband and I eat whole grains daily and beans almost daily (as well as other fiber sources), and the only times we have unusual gas are the rare times that we over-indulge in simple low-fiber carbs (think Christmas cookies, birthday cake).

    Susan, obviously, a digestive profile like yours, and a gut microbiota influenced by repeated courses of antibiotics, is a different (although related) situation. I think that fecal transplants will probably turn out to be the therapy of choice for this condition. Have you heard of and/or considered that?

    1. Susan says:

      Thanks for the suggestion Beverly. I know that fecal transplants have been used to treat C. difficile infections but haven’t heard of protocols for other conditions. Recently the FDA has been more vocal about regulating FT so it may take longer for the treatment to become available for other conditions.

      1. Jeff Leach says:

        FT has not been shown as a viable treatment in any other conditions other than C Diff infections/blooms.

        1. eaa says:

          I’ve just discovered your blog today, so perhaps it’s too late to comment…but I think my story could be of interest to you. I went on a very strict low carbohydrate diet several years ago, and was sadly uneducated regarding the important role of fiber in maintaining a healthy microbiome & gut barrier.
          I’ve been a long term practitioner of healthy living, which has included daily exercise, a diet rich in whole, fresh, nutrient rich foods, few red meats, and a medium level of carbohydrate consumption (mostly in the form of vegetable and whole grains). Nonetheless, a few years ago I became intrigued by the concept of Low-Carb & Paleo diets as a way of maintaining optimal health. I also wanted to trim back the extra 15 lbs that had crept up on me over the last 5 years (I’m now 60). I read numerous books on low-carb diets and Paleo diets, before embarking on what I thought was the best program for me. The long story short is: I cut out all grains and reduced my carbohydrate intake to 20gms or LESS per day, and I maintained at this level for over a year. I definitely lost the weight, but I unfortunately gained a compromised gut barrier, systemic inflammation, and subsequently the auto-immune disease Sjogrens Syndrome.
          I was, to say the least, horrified and mystified, since I had NO health problems whatsoever before embarking on the carb-restricted diet. The only other relevant thing, however, is that I had been on an intense course of antibiotics after minor surgery…which proceeded the advent of my low-carb diet by 6 months.
          In conclusion, since making these discoveries about the impact this form of diet has had on my health, I have been reading voraciously on the subject of how to restore a healthy biome through diet. As a result, one of the things I’ve been doing is consuming more carbohydrates (in the form of vegetables a small amount of grains, and some supplemental prebiotics & probiotics)). In particular I’ve focused on eating more inulin rich foods, and of course fermented foods.
          At this point I’m still “a work in progress” but will keep you posted…and will be happy to participate in any studies that you may know of that are investigating your theories about the importance of the inclusion of these fibers in the diet for maintaining immune and gastrointestinal health.
          Feel free to contact me if you want to know more particulars about my experience for your research.

          1. Jeff says:


            Sorry to hear about your disease. You know your body better than anyone else, but I would say that the most important comments that you made in your post was the note about the course of antibiotics that you were on before developing your disease and maybe had very little to do with the low carb diet.

            I developed Crohn’s disease in my teens after surgery and a course of antibiotics. At the time I ate a regular western diet (read lots of sugar and other highly processed substances like white flour). I’ve come to realize that the antibiotics probably led to a major change in my microbiome, which helped to trigger the onset of my disease. Of course, there is evidence that autoimmune disease like Crohn’s aren’t only a result of antibiotic use but I really think that it may have been part of the trigger that allowed my disease to express itself.

            In my case a low carb diet has led to a great reduction in my symptoms though like you I am still a work in progress.

            Good Luck

          2. eaa says:

            Hi Jeff,
            Thanks so much for your comments…and yes, I do believe the antibiotics contributed strongly to the manifestation of my autoimmune disease. Also, having re-read my original post, I realize that I may have inadvertently sounded as if I was condemning low-carb diets. I definitely want to make a correction by saying: I’m not at all a critic of low-carb eating…in fact I am still an enthusiastic advocate & practitioner! Unfortunately, however, I made the mistake early-on of not eating enough vegetable/fruit fiber & fructans, which may have further compormised the balance of my microbiome. I suspect this, because a year into my low-carb lifestyle, I felt great, but when my CRP was tested it was alarmingly high (indicative of escalated inflammation, which of course is mediated by gut mirobes). A subsequent Spectracell test showed that, on a cellular/molecular level, my ability to process carbohydrates had dropped from normal to extremely low. It took yet another year to discover what might have been causing these changes (i.e: disruption of the balance of beneficial flora & diysbiosis), during which time I developed the auto-immune syndrome.
            In the end, let me emphatically say that I’m in no way SURE that any of the above can be implicated in the strange left turn my otherwise remarkably healthy system took. But having done a great deal of reading on the subject, and also noting (with interest) your observations about: A) how colon PH, and consumption of fructan containing carbohydrates are critical to maintaining the gut barrier, and B) the ways in which Bacteroides & opportunistic gram-negative microbes bloom in carbohydrate & butyrate deprived environments ….I am hopeful that new research will bring some revelations on this frontier.
            Meanwhile, I’ll be following The American Gut Project’s progress, as well as your (and others’) posts with interest.
            all the best,

        2. Kraut says:

          The research has not been completed is a more accurate response. It is death for drug companies so it is not funded. But talk to any specialist who completes these and they will tell you that they see it’s far reaching potential… Perhaps you should see the biome as an “organ” of the human body… A transplant is just that , an organ transplant of a faulty and failing organ..

    2. tatertot says:

      I’ve come to terms with the gas, it’s not all that bad, and has gotten progressively better. It’s just a hard sell when you are trying to convince people to up their fiber/resistant starch intake and they get really bad gas.

      Plus, I think people eating a fiberless diet have other issues that an increase in fermenting fibers only worsen. You are right, though, start slow and build up. I’m getting anywhere between 60-80g of fiber per day right now (sent off my Gut Project sample today!), I made some dried plantain chips over the weekend–they sent my flatulence through the roof!

      Anyone have experience with the Gas-X or Bean-o stuff? Good idea or bad?

      1. Susan says:

        I use Beano regularly. It only helpful with vegetables and beans. It doesn’t work 100% for me with the Brassica family or beans so I still limit those foods. I take 5 instead of the recommended 3. I have no idea how many grams of fiber I eat to compare it to what you wrote above. My local drug store regularly sends out coupons for 20-30% off a purchase. I always buy a few bottles otherwise it would be more costly.

  36. choppyskinny says:

    In the end of the day, fat is just slow burning calories.

  37. Jeff,
    How does the low FODMAP diet fit into all this, do you think?

  38. julie says:

    There is a study that has demonstrated that inulin and FOS decrease the resistance of rats to salmonella. What are your thoughts on this study? Should it be a red flag? The name of the study is “Dietary fructo-oligosaccharides and inulin decrease resistance of rats to salmonella: protective role of calcium”–in PubMed.

  39. Tim Macdonald says:

    Jeff great post! What if you have problems with fiber, but eat hi protein/fat?

  40. My flora has also been nice and healthy from my GI panels but I haven’t had a panel since starting full ketogenesis. However, couldn’t you just eat low carb but consume fermented foods + prebiotic/probiotic supplement?

  41. Dan says:

    I have been eating very low to zero carb for 1.5 years because I suffered from ulcerative colitis before that. Avoiding carbs, fiber and FODMAPs like they’re poison is what keeps me and my gut healthy now. And I’m not the only one. If you think not eating fiber will increase IBD risk, you better think again. Long and hard.
    As for BMI, my weight has always been perfect no matter how much or little carbs I consume.

    1. Jeff Leach says:

      Not fiber didn’t cause your UC – in the same way gluten doesn’t cause celiac disease. Both are environmental triggers.

  42. kikor3x says:

    I’d just like to add: Though I’m very curious myself about the burgeoning scientific understandings of gut flora, you may want to consider pointing out factors having to do with pH change. This is one of the number one reasons it’s hard to take “alternative” practitioners seriously, despite their good intentions: That is to say that we have such great control over our bodily pH. We don’t (unless you were to, say, eat a box of baking soda or something), and the body regulates this very well, as a drop or gain of tenths of magnitude simply would result in coma and death.

    Another point I’m somewhat hazy on is the usefulness of fermented foods, outside of their obvious better digestibility through the hard work of the biological critters (probiotics) who so nicely break them down for us. I think through normal digestion, the “end product,” i.e. what ends up in the colon, may be devoid of many of these critters, simply due to the power of acids of the stomach. If anything, the mass that remains may be eaten by whatever’s in the colon, but it seems that introduction through ingestion of fermented foods seems unlikely. I think that’s why once you lose the bugs, it’s very difficult to really get them back; wonder if enteric-coated probiotics perhaps help to this “end?” I think this may be a testament to the efficacy of the somewhat nasty but supposedly helpful operational procedure where someone with ostensibly healthy gut flora has their feces surgically implanted into the colon of someone who has bowel issues.

    Anyway, a novella; but something to think on!

  43. Heather says:

    I would love to see a chart plotting fructose intake with BMI.

  44. Randy says:

    low carbers may not have a microbiota shortage per se, they may just need less of the kind that we consider to be beneficial. check out the work of weston price

  45. Gail says:

    This is all interesting reading. Regarding gas – Since cutting out most dairy (and all cow’s milk), I have noticed a significant reduction in gas – has anyone else found this?

    1. Susan says:

      Lactose intolerance??

        1. Susan says:

          I was wondering if Gail was lactose intolerant. If she is, dairy products would cause gas. Stopping consuming dairy would relieve it.

    2. Chris Saunders says:

      I had almost no gas before adding Resistant Starch, (Mostly Bob’s Red Mill potatoe starch) The first week gas and bloating was signifigant. Now it’s much less, but sill a lot more than before. The other thing I’ve noticed is my stool have been pinkie diameter or less since adding the RS. Has anyone else noticed that?

  46. A. Lynn Dolson, MD says:

    Hi Jeff,
    I am venturing into the realm of shifting the microbiome with a few of my patients. I found a few “weed and feed” protocols that are quite different. The basic concept is to “weed” between meals (antimicrobrial with Interphase – a mixture of enzymes (Klaire Laboratory), that breaks down biofilm, alternating with “feed” with a meal, with prebiotics and probiotics. One protocol calls for daily 1 or 2 doses of each, in ever increasing doses, and another for weeding on the weekend and feeding during the week. I would love to hear any thoughts that you have, particularly about the timing. How long after things are stirred up would be optimal to introduce the solution (and hopefully repopulation tools)? What aspects would be necessary to make this successful?
    Thank you!
    A. Lynn

    1. Jeff Leach says:

      good Q. not sure anyone knows. so you are charting some new territory. only way 2 know what’s going on would be to do longitudinal sampling of the gut microbiota throughout your intervention.

    2. I am very interested in what you are doing. Do you have a website link? Thanks!

  47. Chaya says:

    Hi Jeff,
    Really fascinating stuff.
    Can Canadians participate in the gut project?
    Also, can you tell us your recommended daily amount of carbs and examples of the best ones? And would berries, other fruit, and veggies count?

    1. Jeff Leach says:

      Not accepting international participants at the moment. As for recommended daily intake of carbs – no idea. Just do what you think makes sense for you. At the end of the day, just eat more natural, human food.

  48. G. says:

    If one is eating a sensibly laid out ketogenic diet high fibre is naturally a part of it as you end up eating a TON of greens. As the carbs present are bound in fibre they won’t knock you out of a ketogenic state. Great blog but honestly seems like a lot of guess work on this one.

    1. Jeff Leach says:

      Yes, we don’t a whole lot at this point. The post was just to point out some interesting things worth considering. However, mounting evidence is revealing that we have “unwilded” our bodies in the modern world and in doing so, reduced the diversity of gut bacteria. The rules of ecology 101 suggest that a reduction in diversity in any ecosystem is problematic.

  49. capen76 says:

    Hello, I read this only recently and feel concerned. I have been drinking alkaline water in order to help chronic health issues (autonomic neuropathy resulting in chronic fatigue and fibromyalgia), and diet too has been important to management. I did the GAPS diet for some months, but it’s hard. The health of my gut is paramount. Is drinking alkaline water detrimental to my gut biome? I couldn’t tell from the information referenced here.

    1. Jeff Leach says:

      no body knows for sure.

  50. Leigh1964 says:

    Look, I drink milk kefir and water kefir EVERY day,love the stuff. I have found in my culturing these two that they eat sugar! My whole family drinks them as well,my husband drinks the water kefir,and my daughter drinks milk kefir with breakfast. We are healthier now than ever before most chronic illnesses have gone away:) We started drinking kefir a few months ago and have seen healthier habits come with it. I think it’s funny how we now get excited in the produce department of the store.LOL My child had ASD and has started to come out of her shell now as well as other signs that she is healing. We can’t say enough about my husband and his heart disease, everything is starting to show that his body is healing it’s self! We indulge like most people in the U.S. with the sweets and a BBQ sandwich every so often,but the kefir seems to keep us on the right track:)

  51. Jo says:

    I grew up eating a standard south-Asian diet, with no health problems whatsoever. My diet mainly consisted of white rice, legumes, fruits & veggies, lentils, sea food and some meat. I decided to experiment with an Atkins type low-carb diet about three years ago in order to lose some weight. I developed Ulcerative Colitis in the distal colon within three months of switching to this diet. I did not have enough information at the time in order to connect the dots – also my condition was mis-diagnosed for quit a while. When it was correctly diagnosed this year, I switched to the SCD, which did alleviate some of my UC symptoms but they were not all gone. I did a few FMT’s, which got rid of all the symptoms, now I’m back to eating the south-Asian way. I’m trying to rebuild my gut with a variety of supplements, while trying to incorporate more soluble fiber and resistant starches in my diet. I know the lectins in grains and legumes are a problem, so I pre-soak them and cook them at a high temperature. Wish I knew then, what I know now. Jeff, your article perfectly summarizes what happened to me. I’m trying to incorporate lightly cooked onions, garlic and leeks in my diet. Besides the gas, are there any other problems with incorporating these – I understand that a proper sulfur-fiber ratio needs to be maintained in order to reduce oxidative stress in the colon and to keep a check on the sulfur reducing bacteria. Doesn’t eating too much red meat tip this balance? As red meat is high in sulfur compounds?

  52. Trundle says:

    Jefff, this makes a whole lot of sense. I’ve been noticing that a whole bunch of low-carbers are developing food allergies. Many embark on such a diet to become healthy and some, to treat their autoimmune conditions. Some actually ended up with more autoimmune conditions. In fact, some of them actually ended up with autoimmune diseases that are not proximal to the conditions they already have — like Lupus and UC, or MS and Crohn’s, or RA and autoimmune hemolytic anemia. I’ve always wondered about that: how could they end up with such combo. I could understnad RA and Lupus, but RA and UC?

    It is ironic but tragic: there were signs that the VLC/ketogenic diets were potentially dangerous because of its pathogenic effect and immmune deficiency. You’ve brought up the microbiome angle and the medical literature is now teeming with the immune function our gut microbiome plays in autoimmune conditionsl ike RA and T1 diabetse. But even prior to all this, we had severe concerns about VLC/ketogenic diets: the very low triglycerides that these ketogenic dieters attain were being implicated in autoimmune pathogenesis in an Italian study; the mucin deficiency that you mention were also being linked to immune (Secretory IgA deficiency); the T-lymphocyte dysfunction was being linked to ketosis and its effect on thymus; and the general leukopenic effect that a VLC diet has on everyone — this was being attributed to inflammation reduction but we were seeing WBCs fall into the 2s in many people. Some of these people actually ended up with serious immune conditions like CVID and SID where their immunoglobulins and IgAs are in deficit.

    Among Dr. Bernstein’s patients who do VLCing, 100% have autoimmune diseases, 90% are hypothyroid, 80% have Raynaud’s, which overlaps with connective tissue autoimmunity, and 33%+ have serious immune deficiency issue like CVID. He’s been ascribing this to diabetes but I always suspected these were due to his ketosis-level diet. You’ve shed light on the underside of this diet which has been responsible for untold suffering of many, who fell prety to its trap unnecessarily.

    1. kitinstlouis says:

      Can you give sources for your info? I’ve never heard that autoimmune disease is more prevalent among those on a low carb (50-150 grams daily) or very low carb diet (under 40-50 carbs daily), would love to look into this. Would like to see something about this Dr. Bernstein, as well.

    2. Raphi789 says:

      (restraining my sarcasm…..sooo…..difficult…!)
      Those pesky hunter-gatherers, if only we could make 99% of our history as great apes vanish to fit our preconceived dietary notions, dang it!

      1. kitinstlouis says:

        I’m still puzzled when dietary recommendations dismiss all but the last 10,000 years of our eating habits. I don’t get why so many are so close-minded as to the possible damage done by eating 600-800% more carbs than we did in the (historically recent) past.

        1. Raphi789 says:

          “everyone is a special snow flake” – this cop-out is resonating very strongly in the online health/nutrition/exercise blogosphere at the moment. I think it is because it allows everyone to hold onto their beliefs without honestly challenging them ===> It is OBVIOUS that DIFFERENCES exist. It is also OBVIOUS that SIMILARITIES are shared. Saying everyone is special gets us NOWHERE (as it is so axiomatic to all domains of life).

          For example: there is good evidence that humans do NOT need ANY dietary carbohydrates (look at traditional populations, metabolic pathways in the body, the apparent superiority of alternative fuels etc..)
          —BUT, there is also good evidence that humans DO need dietary carbohydrates (a possible role in adequate mucus production, a role in glycolitically demanding physical activity etc…).
          Here is where the science gets interesting – resolving contradictory views.

          Those with intellectual integrity/honesty holding a willingness to advance their knowledge – EVEN if it maybe means being proven WRONG – will ACTIVELY TRY TO DISPROVE their hypothesis/view…..those who do not attempt this will prefer to accumulate supposed evidence for their hypothesis and wilfully ignore the ‘other side’, resulting in dogmatic thinking – they’re fundamentally unscientific.

          When is the last time you saw someone publish a blog post with evidence supporting a view they hold to be false? VERY RARELY…why? because it requires a lot of work and it means going out on a ledge…

          1. kitinstlouis says:

            Quite true. Even the most liberal among us fall into the habit of only giving credence to evidence that supports our world view, no matter how strong the counter argument is. Common habit of mind that also may have some evolutionary social reason…?

  53. saga says:

    Low carb can mean so very different things. This image of vegetables contains 30 gr carbohydrades. I’d say it’s more vegetables per day than most people eat.

  54. Hi there! I know this article is several months old, but just reading now and reading with interest, as a person who is currently following the keto diet–and loving the results that go far beyond weight loss.

    Question regarding the diversity and health of the gut flora on such a diet: I eat lots of high fiber (any vegetable that grows above ground except for corn–5+servings a day), my meats are either free-range or grass-fed, dairy generally comes from the same source and tends to have natural probiotics, organic as possible, multivitamin and mineral supplements, in excess of a gallon of water a day, and a probiotic supplement once a week to give the little fellas a boost–all while staying below 50 grams of net carbs per day.

    Do you think these practices will help with the concerns your article states?

    Thanks! Very interesting!

  55. Kennen Neil says:

    With all due respect, the title of this blog post is rather disingenuous for two reasons. First, reading the post makes it clear that both low and high carb diets can have a negative impact on the microbiome if they are low in prebiotic fiber. So the title should really be “Sorry Low Prebioticers, Your Microbiome is Just Not That Into You”. Even a person eating 75 grams of carbs per day could get plenty of prebiotics if they’re carbs came from the right plant sources (ie onions, garlic, chicory, etc.)…but I guess that headline isn’t so good for blog traffic.

    Second, in a world where 250-350 grams of carbohydrates per day is considered “normal” by USDA/MyPlate standards…100 grams of carbohydrates should be defined as “low”…in fact anything less than 175 grams of carbohydrates should be considered low because a plurality of the those in Western Cultures consume more than 300 grams per day. The levels you’ve used should be called “carb restricted”.

    Moreover, the evidence is now overwhelmingly in favor of a low carb diet (75-120 grams per day) as being the best for overall health. In fact, Dr. David Perlmutter recently recommended a diet of 80 grams of carbohydrates per day as being the best for overall brain health.

    Low carb-high prebiotic is best for health.

  56. Alexandra says:

    Hi Jeff,

    I was one of the first to be analyzed (sent in my kit in January 2013, I think) and have my results. I have been VLC Paleo for 3 years (less then 30 gms of carbs). I am now now adding 30-50gms of resistant starch to my diet daily in the form of unmodified potato starch.

    Question: may I test again to see what changes?

    Thank you!

    1. Jeff Leach says:

      hi alexandra. yes, lots of folks are testing again after changing some aspect of their diet… what were your results?

  57. ambimorph says:

    I think it’s quite plausible that the main benefit of probiotics is not that some bacteria are good per se, just that they are better than some others they out-compete.

    In this article, we show that mice without any gut flora may be better off than those with normal gut flora. Butyrate eliminates the positive effects. Reducing gut flora may actually be part of why low carb diets are good for you in the first place:

  58. Nina Birnbaum says:

    Jeff, how do you account for the health of cultures eating a traditionally high fat, high protein, very low carb diet such as the Inuit? Per Wikipedia, “Traditional Inuit diets derive, at most, 35-40% of their calories from protein, with 50-75% of calories preferably coming from fat.” Although the Inuit diet lacks fiber from plant sources, the Inuit consuming a traditional diet are free from the “diseases of civiilzation.”

  59. Raphi789 says:

    can someone explain to me why we are comparing apples and oranges?
    Dietary carbohydrates come in a form that our bodies can absorb – by definition – otherwise they are some type of fiber. According to Tatertot & Nikoley’s blog, RS is a carbohydrate that is not absorbable, thus fitting the definition of “fiber”. Since fiber does not “count” as a carbohydrate because it doesn’t fit the definition, why are we lumping in “low carbers” (whatever that means) with people who consume “low amounts of fiber”? What evidence is there that they are mutually exclusive?

    I thank Tatertot and Nikoley for their research and I genuinely hope their results keep coming back as positive – I for one will try their RS experiment and have purchased a glucose meter for this reason. But why bring in the “low carb” / “not low carb” discussion when what we’re actually talking about is something else – fiber!

  60. JMD says:

    Gut diversity is low in IBD and in particularly some species of beneficial bacteria are absent or nearly so. What are the keystone species in a healthy gut? Without them, which species will overgrow if food (fermentible carbs) is abundantly available? These are my questions. Many people with IBD do better on a low carb diet. Why? Are they missing keystone species of gut bacteria? It’s not surprising that advice for treating a damaged gut might need to differ from advice for optimizing a healthy gut. Regular vigorous exercise is good for our health in general – but not immediately after heart bypass or spinal surgery….right?

  61. twitchyfirefly says:

    I have been on a zero-to-very-low-carb diet for three years now, aiming for ketosis as much as possible. I was never overweight but have a degenerative neuropathy that is thought to be autoimmune. Ketones are supposed to be neuroprotective and neurodegenerative. Anyway, I have recently gotten very interested in the whole gut biota subject. From what I can tell resistant starch is similar to, or the same as, soluble fiber. I have always used konjac noodles in my cooking. Konjac is one of the highest soluble fiber content foods in the world, and has zero carbs. And it should be a good prebiotic. But I never see it mentioned in your resistant starch articles.

  62. Macrobe says:

    A few comments to consider:
    1. BMI does not represent an accurate indicator of body composition. It’s greatest albeit limited uses are for insurance companies and as a too-convenient scale for scientists. 😉
    2. As a biologist and a former ‘unofficial’ (unpublished study) participant in low-carb (aka ketogenic and cyclic ketogenic) diets, there are many issues with methodology, conclusions and extrapolation of current studies in ‘low-carb’ diets. Some of these issues are stated in your post.

    One unaddressed issue is spacial-temporal: changes in the organs or tissues of the body relative to duration of dietary intake. The most controversial is changes in energy source in the brain (funny how most scientists forget that ketone bodies serve as an alternative energy source….), which requires time for full upregulation of brain enzymes to stabilize metabolism in this organ. Most low-carb studies are of short duration, often limiting their extrapolation, especially in physiology.

    Another is the immune system; most participants of a ketogenic diets universally report reduced or absence of allergic reactions, especially chronic allergies (e.g. rhinitis, Crohn’s disease, rheumatoid arthritis, etc). We suspect humoral and cell-mediated changes in the immune system. But no published research has been conducted on such changes. Although immune suppression is suspected, most participants also report a significant reduction in contagious seasonal colds, flues, etc. Changes in tissues can vary greatly. e.g. enzyme changes for energy substrate in the brain take 3-7 days for stable energy substrate conversion. Changes in allergy symptoms vary: symptom reduction ranges from 3-7 days, whereas increase in symptoms during reintroduction to dietary carbohydrates usually occurs within 24-48 hours.

    I posit that a long-term very low-carb cohort study and associated fecal sampling would provide a larger and more accurate data pool for conclusions of gut changes over time. I am glad to see that you provided explanations of the various types of ‘low-carb’ diet, which are very objective (aka relative) and susceptible to erroneous interpretations.

    A candidate pool for long-term dietary and gut microbiota associations with ketogenic diets are epileptics for whom dietary treatment is prescribed to reduce or eliminate seizures. Another, albeit non-conventional pool is bodybuilders that use modifications and variations of low-carb diets to prepare for competitions. They are typically obsessive about their dietary records and regimen, and the duration of their diets usually span for several weeks to a few months.

    We can talk about this in more detail over a glasses of red wine sometime at the Starlight. 😉

    1. Cindy C says:

      Thanks. I have tried to research that subject, by going into such groups as Matthew’s Friends and the Charlie Foundation. It seems that those are only put on the diet for a few years, as usually that is all it takes to change how the the brain is working, and then they go back to a more normal diet. Also there are different types of ketogenic diets being used and studied. My diet was mostly using a lot of coconut oil so I was able to eat more carbs and low/moderate protein and see a benefit, After 5 years, I may be able to now add more starches, as long as i still have at least 3 tbs of coconut oil a day as well as some animal fats. On the diet my pain level was reduced, and my social anxiety was much less. So I will have to see if those come back.

  63. Paul Sacco says:

    Are Low Carb diets really low carb or are they low grain or are they low refined grain? I would think that there’s a significance between the carbs in beans and those in wheat. Why don’t you eat grains?

    1. kitinstlouis says:

      It’s difficult for me to tell whether you are asking me, personally, but I don’t eat grains for the simple fact that they disagree with me. Although I subscribe to the paleo diet it might as well be by default since nearly everything proscribed by that diet makes me ill. I have been dealing with SIBO since my celiac disease diagnosis and find that if I cut out most carb sources I feel a whole lot better.

      For instance, I baked and sampled a gluten-free cake for a company party yesterday and was miserable by the time I went to bed last night. The same happened last month at a friend’s house who was kind enough to buy me special gluten-free ciabatta bread so I could eat a sandwich with everyone else. Normally I just don’t eat bread. I’m still bloated and shaky from the cake. I’d be an idiot to keep trying to eat that way even if I had not been officially diagnosed with SIBO.

      There is a lot of debate right now about whether the percentage of our diet which is carbs is healthy and there is a separate debate about whether wheat is healthy and what portion of the population can benefit from abstaining from it.

      Apparently, the test of whether one feels better staying off of it isn’t good enough because of the placebo effect, but calling into question the validity of another’s dietary choice isn’t something I feel informed enough to comment on, in general. There is a lot still unknown about the role of food in human biology (as this program demonstrates) and I become skeptical of anyone who can make strong pronouncements that they believe apply to everyone. I know that my experiences with the medical profession have led me to believe that too many practioners believe that absence of evidence equals evidence of absence. Heh…this is likely more than you wanted to know….

      1. Elzi says:

        Another variable that can convolute distinction of intolerance is yeast. Many grain products contain yeast, which can induce intolerance in a population subset. A prolonged and complicated process of elimination and reintroduction of specific dietary components can help discern the sources of symptoms. As one that has a relatively high intolerance to yeast, I just avoid most grain products, especially if they contain yeast. But it took decades of experiencing various symptoms and finally a strict MD-supervised elimination dietary process to identify the culprit.

        As a biologist, I find all of the testimony here valuable in many respects. Too often, academic scientists (myself included) are guilty of disregarding anecdotal testimony. But when n=many, then its time to consider that anecdotal evidence.

        1. kitinstlouis says:

          >Another variable that can convolute distinction of intolerance is yeast. Many grain products contain yeast, which can induce intolerance in a population subset. A prolonged and complicated process of elimination and reintroduction of specific dietary components can help discern the sources of symptoms.

          Point well-taken. It’s unfortunate that the massive media blitz over the pop-health yeast book of ten or so years ago has produced such a backlash that yeast is not taken as seriously as it should be. Before paleo, yeast was a problem for me. I couldn’t stand the yeast diet (no fruit??? ever???), the die-off was just too difficult for me to handle. I tried Nystatin and other killing remedies (oregano oil, other presciptions, other herbal extracts, etc.

          You might be aware of the B12 backlash decades ago that still has an impact today. Too often B12 deficiency goes undiagnosed because of a terribly inaccurate reference range and the association with quackery because of physicians who prescribed B12 injections they (allegedly) over-administered at inflated prices. Now, B12 deficiency in the U.S. is rampant due to a lot of environmental factors including the over-use of proton pump inhibitors and antacids that reduce the stomach acid that’s necesssary to cleave B12 from animal protein sources. This just illustrates that medicine is almost as reactionary as the fine art and fashion worlds where fads swing back and forth simply because some idea has gone in or out of vogue.

          Back to your point: Even after yeast is arrested, people can become allergic to it, so that even the dead yeast in baked goods causes an uncomfortable immune response and residual systemic inflammation.

          I react to just about all carbs, though, besides fructose. I have had the lactulose breath test for Dr. Leonard Weinstock’s IBS/SIBO study
          that confirmed SIBO (very common in newly diagnosed celiac patients like me at that time). I tried the rifaximin antibiotic regimen and it reduced symptoms for a few weeks, but they came roaring back. I was prescribed probiotics, but that was…some 7-8 years ago before we had the information we now do about the microbiome. I’m convinced that carb control (SCD or GAPS diet) is the best treatment, still, for SIBO and that SIBO and fructose intolerance contributes to a lot of bowel issues no matter the diagnosis.

          1. Elzi says:

            My daughter has fructose malabsorption, first manifested as a baby. As a diabetic (familial), I avoid fructose, too. It permeates processed food to the point it’s ubiquitous in everything.

    2. Elzi says:

      The problem here is semantic: what defines ‘low carbohydrate’? Objectively and scientifically, the answer is easy: the total number and/or proportion of calories of carbohydrates in the diet. But not all sources of carbohydrates are the same, just as not all fat calories are the same because they are digested, excreted differently and their bioactive and physiological profile is different. Add to that an individual’s tolerance or intolerance and what appears as a simple question demands a very complex answer. So, in short, ‘it depends’.

  64. DameLiberty says:

    How do you know what the optimal pH is for a colon? How do you know that more microbial diversity is better than less? Are there studies showing humans are healthier due to these conditions?

  65. ryn says:

    seriously, what is the point of even talking about “carbohydrates” in this context? it pushes the discussion in the wrong direction from the get-go – i mean, here you’ve got yourself differentiating between “low carb” and “low, low carb”. it’s awkward and it obscures the relevant distinctions between fiber[s] and “simple carbs”.

  66. Alison says:

    My gut biome is into me a plenty, thanks for your concern!

    It might be worth noting the distinction between fermentable vs. non-fermentable forms of fibre. It is not clear to me that health-conscious low carbers actually would be getting less food for their gut microbiomes than grain eaters….

    I eat on average about 6-8 different types of fibrous vegetables a day and include them in every meal I eat, but more than 70% of my calories come from fat (BMI 20.8). I struggle to crack the 50g of CHO unless I include tubers, but most vegetables just don’t contain that much glycolytically metabolisable CHO, though they do contain a lot of fermentable fibres and polysaccharides. My gut health is better now than it has ever been in my life.

    I got a lot more absolute “fibre” (= roughage) back in the days when I lived on mostly whole grains and sugar treats, but my gut was a mess and I paid for it with a lot of autoimmune problems.

    1. Jeff Leach says:

      It’s also worth noting that the distinction between fermentable and unfermentable fiber is a bit misleading and a tad useless. It’s not much of a stretch to argue that the amount of so called unfermentable fiber in the human diet has taken a hit in our modern world. Don’t have the references in front me, but the poorly fermented fiber extend metabolic activity deeper into the colon (think organic and short chain fatty acid production in the distal colon). The amount of fermentation of poorly fermented fibers correlates with the gut bugs you posses. If u r deficient in said bugs than very little of those structures will be degraded. However, if u are flush with ruminicoccus and cousins, then u posses the ability to degrade portions of those fibers – and thus benefit distally from their activity and byproducts 🙂

  67. James says:

    Looks like carnivorous cultures like the Inuit were actually eating 10-20% carbohydrates, prebiotic glycans, and fermentable animal fibers. A new way at looking at these very old diets:

    If true, that means that every indigenous culture was getting lots of prebiotic fibers.

    Curious on your thoughts, Jeff.

    1. Jeff Leach says:

      Don’t know enough about it –

  68. Catootje says:

    Hello Jef,

    I am Dutch and trying to read all the information on ‘Resistant Starch’. I already started to use the Starch (and my family along with me). SinceI have had a lot of antibiotics in my life I think I need more ‘friendly bacteria”. I remembered a website with micro-organism products and I am wondering what your thoughts are about it, it is called EM (Effective Micro-Oganisms), these products are promoted on this website:
    http: //

    I have bought (long time ago) an activator to make my own micro-organisms for my plants. 🙂 They claim it can be used to make your own fertilizer which can be used for almost everything; environment, lakes, ponds, agriculture and home plants. On this website they also have ‘cleaning products’ which can be used around the house. And for internal use they sell EM-X Gold (, but is quite expensive. The founder is Professor Teruo Higa, his ideas have been published in the books ‘An Earth Saving Revolution’ volumes 1 and 2.

    1. expertlearner says:

      Eat 200grs of carbs, lots of leafy greens & probiotics (greek yogurt) daily, add some ginger, lime, garlic, cinnamon and coconut oil as often as possible (daily). Important, omega 3 (salmon, tuna, linaza, chia seeds, etc) daily in a ratio 5:10 with other good fats. 2 to 3 lts of water daily. 150 to 200grs of meat, poultry or fish daily. Cicle with one week every 1 or 2 months reducing to 50grs of carbs daily (clean liver). Exercise at least walking 30 minutes daily and eat most of the carbs after the exercise. Add more carbs in days of more exercise.

      1. kitinstlouis says:

        If I ate that much carbohydrate I’d feel like hell. Not only would my blood sugar swing madly, but I’d be too bloated to wear any of the clothes I now have as well as enjoy significant malaise, headaches and poor concentration. What is good for one person can’t translate to good for everyone.

  69. Having tried several diets, I have found that lots of variety in the the raw and minimally cooked veggie range seems to really agree with me. I graze the farmer’s market. That was after I eliminated all gluten – all the time. It took years to convince me, but it worked when I finally took it seriously. When I hear of people dabbling about with gluten-free and then complaining that it didn’t work, I cringe. It takes weeks to clear the system of the gluten and then more weeks for it to heal. It means brown bagging it all the time.

    1. kitinstlouis says:

      It doesn’t take any longer to expel gluten than it does other foods; that’s about 30 hours from ingestion to bowel movement.

      As far as it’s role in ramping up inflammation that may take weeks to resolve: we know that there are systemic manifestation of non-celiac gluten sensitivity (as there is, of course, in celiac disease) because of the many neurological manifestations of NCGS.

      It is thought to be a problem in the innate immune system, however, but we don’t have studies that confirm that hypothesis yet. Look for research done in the future by Fasano and/or Catassi to answer these questions

  70. Kate says:

    Is there a link between hormonal changes and gut microbiota? For example, during different stages of the menstrual cycle?

  71. JE Young says:

    With the increased use of Ketogenic Diets for weight loss, not only for nutritional therapies, an update of the microbial data with the long term use of very low carb diets would be appreciated. Thank you for your important work on this project.

  72. Beth Emma says:

    This is such an important page for all low carb dieters. I developed sibo due to a combination of acid suppressing drugs, antibiotics, a high carb diet and diverticulosis. I thought it would be a great idea eat a low to none existent carb diet for a month or so to get things back on track. About two weeks into the diet I developed severe stomach cramps and diarrhea, lost a stone in weight in the space of a few weeks and got very unwell until finally the doctors found out I had a c.diff infection. I strongly believe this was because I deprived the healthy bacteria of their food supply so much there was not sufficient numbers to keep the c.diff bacteria I already had in check and as a result they overgrew. After taking antibiotics I have since started taking probiotics and eating a higher fibre and carb diet and the diarrhea and stomach cramps have gone although I still think bacteria is accumulating where the diverticula is and causing sibo. I am still trying to find a way to feed the bacteria in my colon but not in my small bowel, I will possibly try more fruit and veg to keep the small bowel clearer. Thank you for your post!

    1. Glenn Atkisson says:

      Beth, it seems like your entry into the realm of “low carb” was quite like many other people – totally unaware that a truly healthy low carb diet includes lots of plants with fiber. Not even necessarily resistant starch. Most people living successfully on low carb diets have restricted the human digestible component, and are just eating veggies that are mostly fiber (soluble and insoluble). These don’t count for much in terms of “carbs” if the fiber is indigestible (think green leafy veggies), but they can be a considerable component of the diet in terms of bulk.

      Jeff is careful to point out the value of fiber, and not just focus on resistant starch (RS). Other writers on this such as Richard Nikoley and Tatertot focus on RS and imply that it is only RS which can bring gut health in the lower gut. I think this is misleading. The big mistake Jeff makes is in sticking a sensational heading on this article which implies that a low carb diet can’t bring gut health. I maintain that if the carbs you DO eat, say 50-100 g / day, are mostly green leafy veggies, then you can be just as healthy as someone who focuses on eating 100-200 g of RS per day and excludes all above-ground veggies.

      Richard Nikoley’s 2nd article on the subject of RS (“Now we’re getting somewhere”)

      cites lots of studies, many of which tout the importance of vegetable fiber, but he tends to ignore anything that isn’t RS. I think he’s making a big mistake. With intake of a lot more fiber than is present in a small daily dose of RS, one can insure that all the RS gets to the lower gut where the RS needs to be worked, as the additional fiber (insoluble) moves the meal along. If one just ingests RS, exclusive of other fiber, they may only encourage the critical gut organisms to creep up into the small intestine to begin their work, thus shorting the colon of valuable nutrients and allowing it to fall nearly into as poor health as if the person had eaten zero carbs.

      BTW, I just received my American Gut Project results, and am happy to share these. My profile is quite different than that of Tatertot whose profile is shared on Nikoley’s blog.

      1. Tatertot says:

        @Glenn – The ‘Potato Starch’ deal was our intro into the world of prebiotics. Back when I first started exploring all this, AmGut was not accepting outsiders and Jeff Leach was not blogging to the lay person looking for ways to improve gut health. About the only written on fiber was a stupid book called “Fiber Menace.” All I had was PubMed and a bag of Bob’s red Mill, lol.

        So much has changed in the last 2 years it blows my mind!

        Not tooting my own horn, and I think you will see Jeff’s influence, but I have written a series of blog posts about fiber (amount, types, etc…) that I think everyone needs to read (everything there is free, not even an ad!).

        In Search of the Perfect Fiber, Parts 1-5

        Hey, if you email me (email found on my blog) I will send you a quick tutorial on how to find your AmGut sample in the European Nucleotide Repository and you can then go into a free metagenomic diagnostic site (MG-rast) to see species levels and diversity scores along with tons of other good info about your sample that doesn’t show up on your AmGut report. It will blow your mind!

        I did a couple blog posts also showing this type of dissection of AmGut and uBiome samples if you look around my blog over the past couple months.


        1. Glenn Atkisson says:

          Thanks Tim for your input. I did link to your blog article “In Search of the Perfect Fiber (Part 1)” and enjoyed reading it. I can see that you, as well as Mark Sisson, are “not afraid to change course” as you say, when more knowledge dictates.

          In general, to all, I must say, my comments that criticize your earlier emphasis on resistant starch, should be taken as just that: comments on someone’s earlier, less informed point of view. In no way do I consider that what I mentioned as your point of view then must still be your point of view now. That’s the problem with comments on blogs. They cause points of view to appear permanent. A person staying on top of the issue such as yourself may find it necessary to go around correcting their self image. But at least you are doing it with remarkable links to your updated work. I respect your work and will follow your writings. Kudos.

          Yes, thanks for the offer! I will email you so I may find my AmGut sample in the European Nucleotide Repository. That’s fantastic.


  73. Mary Taylor says:

    Hello Jeff,
    Just now I am reading the post. Very interesting article.
    The results are valuable.

  74. shar says:

    What about food processing? The food industry is so wasteful. There is technology to help them significantly reduce waste water but it’s easier for them to dump on the fields

  75. Rachel Brewer says:

    If the microbiome ferments to produce acetate and butyrate. I find it interesting that two of the three ketone bodies are acetoacetate and betahydroxybuyerate. Has anyone studied this obvious connection?

  76. Vicki says:

    What do you consider “low carb”? That is usually the issue. For those of us that follow some individualized food plan of fat+meat+veggie…. No problems. This is not a low fat nor all meat way of eating….

    1. Susan Carmody says:

      What about the role of genetics? People might have differences in the gut that initially encourage or discourage certain types of bacteria. And no matter what they do,they cannot build a healthy microbiome.

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  79. Tana Thurman says:

    Interesting. I low carbed for many years and my health only declined.
    At the beginning of this year I went into see my naturopath for a GI effects stool test. I showed a severely reduced butyrate concentration as well as low Lactobacillus spp., Rosburia spp., bifidobacterium spp., bifidobacterium longum.
    Granted I do understand this is a fairly new scientific terrain. But of the little we understand now these early findings are interesting.
    I have theorized now for quite some time that we will find that we actually need grains and fibers in our diets more than we currently understand. I also theorize that in the future, our microbiome will be considered another organ.

    1. Glenn Atkisson says:

      Tana, It would be very educational for us here to know in some detail what your diet was for the many years you were utilizing a low carb diet.

      Will you please share that with us?

      If you’ve ever talked to many people who have been on a version of a lowcarb diet, I’m sure you have encountered vast differences. It would help me in particular to understand exactly what type of low carb diet led you into your situation. Were you using a diet that was also low fiber, for example?

      Thanks for your help on this!

  80. Autompd says:

    “While the data is of the dreaded self-reported kind, the lack of any significant correlation between % of daily calories from fat and BMI, is still very interesting (note even if you remove the various obvious outliers, the correlation – or lack of – is the same).” – means it is meaningless and not “In other words, as fat goes up in the diet, BMI does not per se. (Note we just started sequencing poo samples.” 7 Days means absolutely nothing when it comes to measuring BMI. My goodness, a person is still likely burning sugar and it they actually were going low carb would have lost a few pounds of water weight.

  81. John Vella says:

    I had severe Crohn’s Disease that was eliminated by a low carb diet.

    1. But you now have a poor microbiome.

  82. Arpan says:

    I believe fibres are what important for our GI microbes. Especially if its plant based cellulose (with least hemicellulose and lignin) for example green veggies. A bowl of salad is sufficient to feed your gut microbium. Keep the fats and collagen based fibers for yourself. As you can gain wholesome amino acids and essential fatty acids from them.
    Donot keep your microbes unfed, especially overnight when they are working out.

    Note: Remember dietary fiber based sugars aka salad and berries (atmost) are sufficient. Add meat and healthy fats they are really helpful for both.

  83. Canan Canpolat says:

    The problem is with our gallbladder and pancreas.not appropiate bile and pancreatic juice .İt will leed to maldigestion and malobsorption.This insufficiencies can be due to exposure to exotoxins like herbicides and insectisides,antibiotics,surgeries,use of NSAID and corticosteroids and other drugs,which all can lead to SİBOand SİFO that can Ascend to gallbladder and pancreas leadin to chronic infections of these organs.The Liver will get infected to.chronic infections of these organs can lead to Neurodegenerative disease like alzheimers disease and other chronic degenerative disease ilke rhomatoid arthritis,diabetes and much more.İf we want a healthy population we have to change our aggriculture and health politics.And unfortunatily not a single step is being made toward this.

  84. Thomas says:

    I know what my gut feeling is : low carb & low sugar. I have never felt better. I do supplement w/ occasional probiotics and do have kefir once in a while and other fermented items too. Also, low doesn’t mean no. And it depends on which microbes and how many of them, some might be bad (at certain times and places etc.).

  85. david says:

    The butter doesn’t make it to the microbiome, fiber does.Please ignore the bulletproof quack Asprey and his homies.

  86. lozgod says:

    The studies showing bad gut health correlated with a keto style diet aren’t an example of a healthy keto diet. One of the largest studies done used animals and fed them a diet of primarily lard and corn oil. They are two of the highest oxidized omega 6 containing fats you can consume. There is evidence that omega 3 fats protect against the inflaming effects of certain gut bacteria. Polyphenols do this as well (olive oil os loaded with polyphenols, same with cacao which is very high in fat). A healthy keto diet will have fatty fish and grass fed meat which contains high amounts of omega 3s along with high omega 3 plant foods like chia seeds and walnuts.

    A true healthy keto diet has lots of fiber as well. It should actually have the most fibrous green vegetables that humans eat if done correctly. Those same vegetables are loaded with antioxidants as well.

    People blasted the guy that said a solar eclipse wasn’t the result of an angry God. The Keto diet done correctly is the best way a human being can eat.

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