Wednesday, July 15, 2015

Researcher "Pulls a Wilbur."

Research finds diversifying your diet may make your gut healthier
He created NM504, a formulation of inulin, beta glucan and antioxidants, and tested it in a pilot of 30 individuals, half of whom received the formulation twice a day. The remainder received a placebo. Those who received NM504 saw a shift in the makeup of their microbiome and, consequently, health benefits that included improved glucose control, increased satiety and relief from constipation.

Well, there you have it folks!

I have to laugh just a little. This researcher is concerned that the modern diet is lacking diversity, saying that most people are "...consuming only five animal species and 12 plant species. Of those 12, rice, maize and wheat contribute 60 percent of all the calories."

Adding two simple fibers (inulin and beta glucan) showed improvements in several health markers. One of these days, researchers will find Wilbur and his like, those consuming well over 100g of various fibers daily. Of course, we've also seen that the complete opposite approach also leads to increased diversity with my little potato diet experiment.

As the above researcher mentioned, and I truly believe:

Like any ecosystem, the one that is most diverse in species is the one that is going to be the healthiest," Heiman said. "In almost every disease state that has been studied so far, the microbiome has lost diversity. There are just a few species that seem to dominate.

I'm starting to believe that maybe this loss of diversity could be caused by the modern diet of preservatives, artificial colors and flavors, added "nutrients" like iron and vitamins, enzymes, and whatever else they invent to make foods tastier.

I have not seen the full text, if anyone can find a copy, or even the title of this study I would like to see.

To the gut bugs!


  1. Not a study, but this press release had a video by the researcher discussing the supplement and diversity. There are links to his company at the bottom of the article.


  2. A lack of diversity - and a lack of quality. You could eat only 3 variety of animals and still get very high nutrition - eg. some grass fed ruminant animal (muscle, fat, liver, and bone broth), some type of free range fowl and more importantly it's eggs, and some type of oily fish. Species-wise that is low diversity but exceedingly healthy esp compared to the average SAD. I guess you could call that (food diversity) versus species diversity. Eating nose-to-tail as they say is still eating diversely compared to SAD. So what is the equivalent of this with plant foods? Certainly high diversity is not enough since there are many types that are not very nutrient rich or which have a significant difference in it's prebiotic content.

    Here's something I was just pondering: Who is likely to be overall and long-term healthier, someone who has high gut biodiversity but is fat and out of shape, or someone who is fit and trim but has sub-optimal gut flora? Obviously it's better to have both, but sometimes I wonder how many people have their priorities right. Then again, they could be not independent things. Eating for higher gut diversity may make (contribute) to being more lean? But... if you are not "moving often" you're gonna degrade functionally and metabolically over time, no matter what else you do.

    It seems to me if there is any link between gut bug diversity and ancestral diet it would come from Mr. Grok eating all manner of digestible plants he could manage find during those periods when more caloric foods could not be obtained. Basically to keep him from starving.

    Just some meandering thoughts.

    1. I'd think Mr Grok would be using those plants for seasoning on his more caloric foods as well.

    2. Brad,

      I have no special expertise, but I can mention my case. I've worked out and exercised nearly constantly for over 30 years. I started out as a powerlifter/bodybuilder, got injured, and then worked out to stay in shape. I drove a race car for a while - it's very common to see old(er) guys striving to lose weight in the bid to go faster (and it truly matters) - and got to my lowest weight. I was often "in shape" in that I could move your body as needed. But I don't think I was ever really healthy. I had autoimmune issues, constipation, and whatnot.

      Now, I feel healthy. I became healthy while I was out of shape and fat. I lost weight. I lost my sluggishness and energy problems. My joints quit aching, making me able to move. I recover very quickly - unbelievably quickly - from workouts. Moving has become easier, and I'm in better shape as a result. I want to move. After a six-mile walk, I commented to someone that when I got back I felt the same as when I left. So, without eating, I repeated the walk. And still felt the same. I am stronger. For the very first time in my life, handstand push-ups are within grasp. Maybe a year, but soon. My goal is 5 on my 50th.

      So I guess I'm saying someone can look good but be unhealthy. I've looked better, but I've never felt healthier.

    3. "high gut biodiversity but is fat and out of shape"

      Not likely to happen. Excellent gut health promotes all sorts of good things (sleep, energy, metabolism, etc).

  3. Question: If I ate only using my hands and hardly ever washed them, wouldn't my gbiome be more diverse regardless of the foods I ate? Is that necessarily healthier?

    1. Brad, my hunch is it's not either/or, it's both. If you don't feed them right, they won't hang around. And if you're too clean, you won't pick them up in the first place.

  4. Good discussion. I don't know if it's even worth considering how our ancestors ate and lived, it was so different from now. I read lots about the Hind's Cave paleo-Indians, there are well preserved coprolites that chronical the eating habits there for 9000 years. During that entire time, they ate mainly prickly pear cactus, pads in winter, fruit in summer, but also their dried poopage was full of scales, bones, feathers, seeds, stems, etc... These are the guys that Jeff Leach figured were eating ~140g/day of fiber.

    At any rate, we still have gut bacteria that is trying to help us out. It will adjust to any diet, but I am pretty confident that unless the diet contains a goodly amount of fermentable fibers, then the gut flora and gut environment will be substandard as far as having a healthy colon, healthy immune system, and whatever else knock-on effect gut bugs are good for (sleep, blood glucose regulation, etc...).

    I have no doubt that people can live a long life without giving a second thought to their gut bacteria. A long, healthy, life, I'm not so sure about. Modern foods just don't have what it takes to make gut bacteria happy.

    Sure, there is also a genetic component. Some people may just thrive on pizza and Coke. But for my money, I'm betting that a healthy gut can be accomplished in a variety of ways, but they all require lots of fiber.

    For instance, Wilbur's massive, varied fiber load appears to have done him a world of good. Assuming he is not just a person I made up and post under, his approach is exactly what I thought would be a good one back when I started digging into all of this several years ago. I have a feeling that a gut test would show lots of butyrate producers and great diversity.

    Another approach would be a guy like Brad who eats a good, clean "paleoish" diet and works out and maintains healthy habits without getting near as much fiber as Wilbur.

    I'm also seeing that once dysbiosis sets in and autoimmune diseases get established, it's not quite so easy to reverse even with an impeccable diet and gut reports that look perfect.

    Lots of gurus will create amazing protocols to cure whatever problems you have, promising fast fat loss and reversal of AI disease. Call me skeptical on this approach. But I think everyone owes it to themselves to eat a lot better than the way 90% of people are eating. It's not very hard to do.

  5. So I'm one of those who have dysbiosis (bloating and all that), and over the past 2 years I've tried all manner of fibers. Pretty much every time, the result is more fiber == more problems.

    Your little potato diet n=1 study inspired me to try a mono-ish diet. It makes sense in a lot of ways: Pre-industrial cultures surely had less dietary variety than modern. I was a lot healthier many years ago when I ate the exact same breakfast and lunch every day. Kempner's old rice diet was apparently very effective for some people.

    Of course, plausible does not mean true. So, I'm doing the experiment, and using the most evil food on the planet -- refined wheat. I picked wheat because it seems to be the only staple that I don't get completely sick of in a few days. It's not completely mono -- I merely use wheat as the main ingredient in most meals. So a typical day will be reheated pasta (with a bit of some sauce) for two meals, and maybe a sandwich or other wheat-based meal for the third. I'm assuming reheated pasta will have about as much RS as your reheated potatoes.

    It's been about 5 days, and the seas haven't parted yet. But I'll keep going for now.

    1. I could fully get behind your experiment if you could find wheat or wheat products that are whole-grain and not fortified. Bleached, fortified wheat just makes me cringe.

      Let us know how it goes!

  6. Hi Tim

    I have ankylosing spondylitis and am currently in the process of trying the SBO probiotics, inulin and psyllium - in the hopes of flushing out the overgrowth of klebsiella (considered to be one of the root causes of this condition).

    In initially started with raw PS and Probiotic 3 (as per Art Ayers recommendations), but a week or so in, I saw Dr Grace's post warning to stay clear of RS2 if you have an autoimmune condition and therefore stopped the RPS and have gone for an inulin and psyllium mix instead.

    To be honest, apart from the wind problems (which subsided within a week) the RPS approach seemed to be going quite well for that short period, and I don't think I'm getting the same results from my current approach.

    I wanted to ask therefore, would you consider RPS along with cooked/cooled potatoes a solid approach for myself? I'm just a bit apprehensive as I don't want to make my klebsiella situation worse.

    Many thanks

    1. Most of dr. Grace's warnings about RPS are unfounded, as far as I'm concerned. Not sure what she says about AS, but that does seem to be a special case. Commenter Harriet has AS and has used RPS, I'll make sure she sees this and gives her opinion.

      Did you see the Perfect Health Diet articles on curing AS with a starchy diet?

    2. Hi William
      Sorry about my slow response but I'm travelling and this is the first time in a fortnight I've cleared my mail.

      I did the potato starch, starting with just 1 tbs at night. By the time I got to 4 tbs in 4 days I was starting to feel distinctly sorry for myself with a flare up - the worst I ever had but fortunately my AS isn't too bad. However, and this is interesting, that 4th day (if my memory serves me right) was the worst and the pain and symptoms started to subside after that. By another few weeks from my bad day I was just a bit worse than when I started. By 6 months or so I was no worse than when I started. I've not had any flares since then despite various experimental things tried.

      I undid my various good works by agreeing to my doctor's suggestion to go on antibiotics last January to clear a streptococcus infection. She is an experienced nutritional medicine doc so I trusted her judgement but while I got rid of my worst symptom of alzheimerish memory loss it caused huge other problems including a return of depression and food intolerances I had previously eliminated. I am currently working at returning to my previously improved condition. However through all this I've not had any flares of my AS. As long as I keep moving as I have always had to I'm OK.

      Basically potato starch has improved my overall health immensely after the sore start to the process. Two bad days, a year and a half improved.

    3. Thanks for the info Harriet.

      I've decided to cut out the potato starch for now until I get my pain levels settled a bit.

      I definitely intend to give it another go in the future though.

  7. Thanks for the quick reply Tim.

    I did see the PHD articles, but to be honest, they don't really seem to address feeding the good stuff... more a focus on starving out the bad a la paleo.

    I'd certainly be very keen to hear what results Harriet has experienced with the RPS.

    Just one more question if I could, do you think psyllium is worth taking? I don't think the combo of it and inulin are working too well for me. Perhaps the inulin powder and RPS would be better?

    Thanks again

    1. I like to think that inulin and RPS is a nearly perfect pairing. But don't be afraid to drop either if it does not agree with you. Inulin and RPS are the two most common prebiotic sources in the natural world, and found in the amounts typically supplemented with (we could probably go up to 150g/day and still be within natural limits).

      I sent a note to Harriet, hopefully she will see and reply here. Unfortunately, you guys are kind of on your won when it comes to trying this for AS. Conventional Wisdom says to avoid most starches with AS, but CW probably is also the reason you have AS to begin with.

      You know your body better than anyone, you'll have to trust it to let you know what it likes.


    2. As a side note, I'd like to add that not all inulin is the same. RPS is fast fermenting. Whether that is good or bad for you I do not know. Psyllium, I believe, takes longer to ferment and will do so deeper into the gut.

      What your inulin is doing depends on the brand. Most likely, it's a mix that mostly ferments at about the same rate as the psyllium. So pairing those two would very likely have a very different effect than RPS in terms of comfort and gas! You're hitting a different part of the gut that might not be ready, especially if you start too fast. Give yourself time to adjust.

      If you are using the Jarrow FOS/Inulin or Synergy1 then my hypothesis above is wrong in the details but maybe not the conclusion.

      I agree with Tim about the pairing of inulin and RPS. I started with inulin, and RPS was my second. Psyllium was an early one too.

      Make sure you are drinking plenty of water, especially with psyllium. It absorbs a lot of water. I only drink when thirsty, but a lot of the time people ignore their thirst.

    3. Dang, I forgot to suggest that you look into berberine, especially if you do not eat lots of raw onion and garlic. I give my dogs it as part of a supplement (Para Gard) that cures them of digestive issues very quickly. I think it's important to have something that selectively antimicrobial to the bad guys during the healing phase. Of course, decide for yourself.

      For those who might rember, I had my dogs doing a Wilbur with stellar results - until I went on vacation and subsequently fell out of the habit. Both dogs reacquired their colitis. I'm using berberine, pumpkin, banana flour, and apple pectin, and both have been fine for a few weeks.

    4. "In conclusion, our findings suggest that marked modulation of gut microbiota by berberine, namely inhibition of a wide range of intestinal microbes and enrichment of some SCFA producers, helps to alleviate systemic inflammation, at least in part, by reducing the antigen load to the host and elevating SCFA levels in the intestine and contributes to the beneficial effects of berberine against insulin resistance, obesity, diabetes, and other metabolic disorders. Functional metagenomic studies and molecular dissec- tion of the host-microbiome cross-talk are needed to further elucidate the mechanisms of action of berberine [3]. This study also suggests that pharmacological or nutritional modulation of gut microbiota is an effective approach for preventive healthcare."

      They also provide evidence that berberine is selective at the species level.

  8. Thanks for the advice Tim and Wilbur.

    The whole thing just requires a lot of tweaking and fine tuning.

    My main goal is to hopefully crowd out the klebsiella by increasing the numbers of the beneficial stuff.


    1. Hi all

      Just a quick update regarding the above for anyone interested (and hopefully of use to any other AS sufferers out there) - I have since been consulting with a nutritionist and have had the Genova test with parasitology, the SIBO breath test and an IGG/IGA antibody blood test (used for detecting leaky gut) and I have to say I'm somewhat surprised by the results.

      From the Genova test, it turns out that klebsiella isn't a factor for me at all (so much for that widely held theory) but I do have citrobacter and enterobacter.

      As expected, I tested positive for SIBO and leaky gut, although my leaky gut case was described as relatively mild.

      I'm now on a 30 day program supplement program of ADP Oregano, Berberine, Allimend (allicin extract) and Whole GI Wellness.

      The plan is to get the SIBO levels down and then follow this up with probiotics and RS.

      I'm currently 2 weeks in and starting to feel the 'herx' reaction which, hopefully means things are moving in the right direction.

      Thanks again for reading, and I'll post another update once I've completed the probiotics round.


    2. Best of luck - hope you see some improvements.

      I'm very interested in your mileage with any intervention. I think one of the problems with people posting issues on forums etc. is that once they recover, they rarely follow up what worked - leaving everyone guessing.

      Tim - we could do with a longer recent comments list if possible. I try to get on here once per day, but when work is manic (I did 79 hours last week), such comments as this are easy to miss, especially if they appear somewhere other than your most recent blog post.

      Just my thoughts.

    3. Hey Rob,
      Rmember a while back when we were discissing garlic and I said that it made me wake up in the midde of the night or way too early in the morning o move my bowels? Well here is my follow up to that. Ibelieve that the capaules I have been taking for Lyme disease were confusing the issue. At that point I was increasing my dosage weekly and did not appreciate how much fiber they contain. I am now pretty much adapted to all those capsules. (48 daily) so may try the garlic again, especially since some people advocate garlic supplements for Lyme.

    4. Thanks, William! Keep us posted. Remember, the ultimate goal is to increase what you can eat, not eliminate everything until you are only eating a few things. Glad you are working with some professionals.

    5. Elliebelly - you'll know how powerful garlic can be, my only comment would be to take it slow. Even Wilbur appeared to have issues taking garlic neat. I had some issues with it originally (stomach feeling uneasy mainly), but am fine now - unless I take too much. 1 clove, crushed, rested for 10 mins, then swilled down with water is fine. 2 large cloves and I can have quite bad toilet issues.

      48 tablets is some going - really hope it is paying off for you

  9. Tim,

    Have you ever heard of Donna Pessin? She is a lady who has developed a program and written a couple of books about her Unique Healing program. I have not purchased her books, but she has many videos on youtube that describe her program. The basic idea is that she believes in a twofold approach to healing your body. You should remove toxins (what she calls acids) out of your body using huge doses of bentonite clay. Simultaneously you should heal your gut (bowel bacterial environment as she calls it.) What is interesting is that there are two different ways to heal the gut. One method is by taking high doses of probiotics daily (as in 400-500 billion cfu per day.) She feels like anything less than that will not be enough to make a difference. The other alternative is to take a product called Bowel Strength which contains Berberine, grapefruitseed extract, garlic, and other things to heal the gut. The interesting thing is that she says both approaches do the same thing. She says that probiotics do not colonize the gut, but instead they feed the good bacteria in your body. She also says that the berberine and other things in the bowel strength do the same. And she says that it is much less expensive to use this approach than to purchase expensive probiotics. I am including a couple of links that describe her theory.

    I would love to hear what you think, Tim, as well as the other regular commenters on your blog. Wilbur just spoke of using Berberine occasionally, and I know others have as well. Is it possible that there could be some truth in this? Could using these antimicrobials possibly be just as beneficial as using probiotics? Many times we are cautioned about the dangers of using antimicrobial substances.....too harmful on the good flora.

    I really would like to hear your opinions.



    1. I think Donna Pessin has some really good ideas. Probiotics have never really been on my radar, but maybe she has a point.

      My only problem with people like her, is that her methods are just ideas that may or may not work, and certainly won't work for everybody.

      I would not begrudge anyone who followed her advice. But if it does not work as planned, don't give up, but keep trying. I think everyone has a secret combination that only they can decipher. No one-size-fits-all when it comes to the gut. Well, except for the fact we need to feed our microbiota a fiber-filled diet, sleep well, exercise, etc...

      Berberine, turmeric, onions, garlic, and lots of other natural foods are undoubtedly super-foods for the gut.

    2. Thanks for the reply, Tim. I'm not interested in doing her program. Sorry if I gave too much information about it and made it sound that way. I was just more curious about the thought that antimicrobials could be equally as effective as high dose probiotics. They certainly are less expensive.

      There are so many cautions on the internet about these antimicrobial substances harming your good flora, rather than feeding it. I had just never heard it put that way and wondered if anyone here had ever heard of any research or had any personal experience that might back that up.

      Instead of staying on long courses of antimicrobials, I just might try Wilbur's approach. Use them for a short period of time and then use prebiotic fibers and foods to feed the gut.

      I have enjoyed reading your blog immensely and appreciate the time and effort you invest in keeping it going.


    3. A big part of her success might be the bentonite clay, and PrescriptAssist also uses an earth-based (Leonardite) material in the formulatuon.

      Bentonite Clay has some very interesting properties, one being that it seems to preferentially only remove pathogens and leaves beneficial bacteria alone. I would not believe that if I read it on a product label, but seems to be a well-studied phenomenon, as in:

      "Although the antibacterial clay minerals discussed herein are natural substances, they are not produced by microorganisms and are not considered antibiotics. In an ideal situation, antimicrobial agents disrupt microbial processes or structures that largely differ from those of the host. The majority of known antimicrobials function by affecting cell wall synthesis, inhibiting protein and nucleic acid synthesis, disrupting membrane structure and function, and inhibiting key enzymes essential for various microbial metabolic pathways."

      I think we often overlook bentonite and other clay in the fight for a healthy gut.

      The quote above about clay's antimicrobial effect is probably similar to what you mentioned about other antimicrobial substances. They are not 'antibiotics' per se.

    4. Joni

      I have done a lot of reading regarding antimicrobials, especially garlic, onion, and berberine. I guess I'll need to add things like blueberries in light of the patent application mentioned elsewhere.

      I have read nothing indicating that natural antimicrobials are harmful when taken continuously. Garlic, for instance, is a very natural food. It's antimicrobial effect seems to select the bad guys, and at worst fo nothing to the good guys but at best actually improve the action of the good guys.

      See the link above I have for berberine. It selects at the species level, which is amazing. The reason I cycle berberine is because, as an American, it does not seem to be a natural food. Onions, garlic, turmeric, and ginger are to me. i know a lot of people who eat the latter every day for lifetimes, so I do not worry about eating them myself. The only negative I've seen about berberine has to do with muscular atrophy, and I know from my own experience that is wrong.

    5. Wilbur, You posted a study the other day that dealt with food diversity vs gut diversity. I cannot find it. Could you please repost it?

      For anybody who has taken garlic in largish quantities, I was getting sick a few weeks ago and took an old Italian remedy. A quarter cup of chopped garlic in tomato juice twice a day . I did this until my throat felt better and I could tell the virus and been subdued. That was 5 doses. Or roughly 2 and 1/2 bulbs. Could that much in such a short period of time have made a difference to my gut species? I have been doing a number of different things lately (more exercises less supplements), so it is hard to pin point but I definitely feel calmer. Anxiety is an issue I've been wrestling with for the last year.


    6. Here's a link to a popular press article that references the study. A lik to the study is in the article

      My understanding is that the gut microbiome changes very rapidly in response to diet, within 24 hours. I would guess certainly the proportions could change very quickly. Keep eating the garlic!

    7. Thanks, Wilbur! I will try. I am trying to find the amount that will be effective by not make me so aromatic and slowly build up from there.

  10. Tim, In the link they refer to a presentation by Mark Heiman. By googling it I found the following link. It doesn't mention where and when the presentation was given. Maybe you can contact Heiman direct to ask him for a copy of his presentation.

    Jo tB

    1. Thanks, Jo tB. I'm searching him on Google Scholar, and found this fascinating patent application. I'd cut and paste, but there is so much that I find interesting that it would take forever.

      Checke out the Detailed Description of the Invention. If it works - and I've found some anecdotes by Heiman that it seems to - then this is something easy and cheap to do at home.

      I am especially floored by Heiman's statement that something is needed to suppress certain types of bacteria to improve ratios. He uses blueberry extract. I've long wondered if my insatiable craving for raw garlic and onion played a role, and this is another suggestion that it did.

      Here is a case report.

    2. "A cobiotic, consisting of purified inulin, sugar-free blueberry pomace extract, and an oat preparation of purified beta-glucan was developed for twice a day (bid) consumption as a smoothie drink to repair the gastrointestinal dysbiosis in type 2 diabetes"

      I wonder what would happen on just the cobiotic without the Metformin? What do you think?

    3. I replied too quickly before reading the patent you suggested. For those who haven't read it, this is what happens:

      The present invention relates to weigh control and metabolic fitness. More particularly, the present invention relates to compositions and methods for increasing desirable microbiota in the human gut and reducing therein undesirable microbiota to achieve a healthy glucose regulation, metabolic fitness, inclusive intestinal health, and a healthy body weight.

    4. Wilbur

      I love reading patents :-)

      So much new to learn, LOL

      "What is claimed is:

      1. A method of treating a patient for diabetes, comprising:
      a. administering to a patient in need thereof a pharmaceutical composition comprising a biguanide; and
      b. administering to said patient a therapeutic composition, comprising:
      i. insulin;
      ii. β-glucan; and
      iii. at least one polyphenolic compound."


      "A preferred indigestible carbohydrate is insulin and can be found naturally in banana, asparagus, garlic, onions and wheat flour at low levels"

    5. Gemma - surely a typo.

      "FORMULA A is made of 4.7 g dried blueberry pomace extract powder from Milne Fruit Products (Prosser, Wash., product no. FG20155), 9.22 g Oat Well 22®beta glucan from CreaNutrition (Sweden), 4.4 g agave insulin (Inufib) from The Iidea Company (Tiaquepaque, Jal, Mexico),"

    6. Never mind...I see you already knew that and were just teasing us.

    7. Looks to me like Mr. Heiman is the original Wilbur, lol.

      Quite the concoction he's come up with, makes the patent almost meaningless. All he's missing is eye of newt.

      But, no doubt effective. A massive fermentable fiber blast. Where have we seen this before?

    8. Ha! I missed the typos. But you know that if you want to patent existing knowledge, you can't waste time proofreading! Gotta be quick.

      Did you notice his list of fibers that might feed the gut? The list is do exhaustive that it makes my Wilbur drinks seem ordinary. I think he has beaten me to patenting the Wilbur. He even includes my concerns about adequate feeding of the gut without excessive caloric intake.

      Nah, I just hope this helps people. The "invention" is very easy to do at home. And the effects seem rather remarkable.

    9. Okay, so there was the probiotic. Then the prebiotic. And now there's the cobiotic.

      That last one I first ever read it here. Hm, "google? What's a cobiotic??"

    10. I am proposing that if you take antibiotics, to rebuild the gut you will need RE-biotics . And, if you use larch, birch, or maple to feed gut bugs, these should be called TREE-biotics .

      Don't even get me started on FLEA-biotics and PLEA-biotics.

    11. What about biontics?

      Actually, I see a company has bacbots and virubots.

  11. What? No 'Walking Dead' Zom-biotics?

  12. Tim's tatter tampering with his gut microbiota showed that if you are florally flush, then a limited source of prebiotic fiber can let the biota bloom and a few keystone species produce a cascade of cross feeding and diverse flora. But this scenario obscures that the tatter feeding reveals underlying, preexisting diversity. Putting the patent prebiotic cure in this context yields the harsh reality of haves and have-nots -- those like Tim with preexisting diversity will respond to potatoes or patent prebiotics, but the dysbiotic will not respond to potatoes, because they are floral failures. If you feed them, they still will not come. We can talk and talk about the best way of feeding gut microbiota, but the bottom line is the gut microbiota has to be adapted to the diet. If the bacterial species are not present, then the diet cannot compensate. If antibiotics push a couple of key species to extinction in an individual, then diet and/or commercial probiotics cannot fix it. The gut ecosystem will collapse. There is no medical solution (except off label FMT.) All I've got is muddy veggies and questionable hygiene, and people who go that route have to live in Alaska.

    1. Hi Art - You were the first to propose that a simpler diet would lead to increased diversity. Seems counter-intuitive, but it appears to be very correct.

      I've talked to lots and lots of folks behind the scenes that try in vain to reverse AI and other gut dysbiosis related problems to no avail with fiber, fermented foods, and probiotics.

      We need a plan that works quickly and in most people. All of the "10 steps" type protocols offered by gut gurus never really seem to come through and the blame is placed on the patient, never the protocol.

      I wonder how much "F" is needed for an effective DIY FMT, and what the best way to administer would be? Does there need to be a thorough PEG cleanout first, or could it be delivered in suppository form at any time?

      I was reading about some time-released capsules...same questions: how much, what prep is needed?

      This seems like a biotech dream, take the grossness out of DIY FMT and provide a lab-grown culture that anyone could administer.

    2. Tim,

      I've been thinking about that patent I mentioned before. Did you read the description of the invention? As I recall, there were three parts: 1. Fermentable fiber to feed the bacteria 2. Beta-glucans to make bacteria prefer dietary fibers over food produced by the host (not sure I described this right) 3. Massive polyphenols to suppress bacteria that contribute to dysbiosis.

      I seem to be somewhat unique in how I reversed AI and dysbiosis. I don't think my starting condition was anything special. I don't know how I fit into Art's information. But I followed all 3 steps. Fiber, of course. Beta-glucans too as part of my diversification strategy and because of their purported immunity benefits. You might remember my insane cravings for onions and garlic some time ago - there are are the polyphenols in part 3.

      Do you have anyone who might be willing to try all 3 parts, plus maybe fermented foods and dirty veggies? I'm very curious. Maybe I got lucky, not in my starting condition, but in stumbling on these 3 parts. The patent has the recommended dosing.

    3. You may be onto something, there, Wilbur. As part of my health transformation, I started drinking tea made from chaga mushrooms, very high in polyphenols, and 'mega-dosing' wild blueberries and dark chocolate.

      A good diet should be high in polyphenols if one eats lots of berries, spices, and plants in general. Here is a list of top 100 foods for polyphenols:

      I eat lots of those from the top 10. Maybe this is a missing link.

    4. When I think about beta glucans, I always jump to oats, but they are also a big part of fungal and yeast cell walls. Chaga also high in beta glucans. hmmm

      And what will Gemma think of this?

    5. And aren't mushrooms high in beta-glucans? I don't know about tea though. I'm guessing that you ate a fair amount of mushrooms anyway.

      I have some sympathy for the patent saying insulin instead of inulin. Autocorrect is making my miserable with beta-glu cams.

    6. Polyphenols have far reaching effects. It starts in plants :-)

      My favourite paper on catechin:

      The Impact of Microbial Biotransformation of Catechin in Enhancing the Allelopathic Effects of Rhododendron formosanum (2013)

      "Rhododendron formosanum is distributed widely in the central mountains in Taiwan and the major allelopathic compound in the leaves has been identified as (-)-catechin, which is also a major allelochemical of an invasive spotted knapweed in North America. Soil microorganisms play key roles in ecosystems and influence various important processes, including allelopathy. However, no microorganism has been identified as an allelochemical mediator. This study focused on the role of microorganisms in the allelopathic effects of R. formosanum. The microorganism population in the rhizosphere of R. formosanum was investigated and genetic analysis revealed that the predominant genera of microorganisms in the rhizosphere of R. formosanum were Pseudomonas, Herbaspirillum, and Burkholderia. The dominant genera Pseudomonas utilized (-)-catechin as the carbon source and catalyzed the conversion of (-)-catechin into protocatechuic acid in vitro.

      In this study, 2 viewpoints have been investigated with respect to the role of (-)-catechin in the rhizosphere of R. formosanum. Firstly, (-)-catechin acts as antibiotic to suppress the growth of certain groups of microorganisms that are sensitive to it. Secondly, (-)-catechin increased catechin-utilizing bacteria in the rhizosphere of R. formosanum. Catechin, one of the major flavonoids, is widely found in natural fruit, green tea, wine, and traditional Chinese medicine [34-36]. Many plant flavonoids exhibit the functions of both antioxidants and free radicals whose role is to undertake oxygen cleaning in biological systems. They may also have antimicrobial characteristics [37-40]

      Catechin inhibited growth of some, but not all, of the soil bacterial population tested in the root zone of spotted knapweed [19,41]. Microorganisms are hypothesized to be most important for the productivity of nutrient poor ecosystems and a reduction in microbial diversity could reduce growth of plant species and plant diversity [42]. In this study, the population of total culturable bacteria was suppressed as the concentration of catechin increased in the soil. The dominant bacteria in the rhizosphere of R. formosanum were restricted to the gram-negative proteobacteria. Thus, it is concluded that catechin generated the selective pressure that drove microbial diversity.

      Catechin acts not only as an antibiotic to suppress the microorganisms, but also as a carbon source for microorganisms in the rhizosphere. Catechin-utilizing bacteria can transform (-)-catechin into glycerol, a common carbon source for bacteria without passive transport system. Glycerol is one of the few compounds that can enter bacteria by facilitated diffusion without the need for energy. Therefore, microorganisms can directly utilize glycerol without any transport system [43]. The results of this study strongly suggest that catechin was the carbon source for catechin-utilizing bacteria in the rhizosphere of R. formosanum."

    7. I'd sure like someone to experiment with this, especially someone who has had no luck with just RPS or inulin. From the case report I linked above, it seems that some effects might be very fast, as in days. We,ignite want to buy stock in Heiman's company!

    8. I should have some time. Let me put together a blog post on this this week.

    9. Beta glucans?

      I've been telling everybody to eat mushrooms and yeasts (alive and heat killed). Wilbur knows.

      Everybody thinks fermented foods have bacteria only, but there are many tiny tiny fungi too. And I think these are much more important health wise.

  13. Tim and others - I don't recall seeing any discussion of this here (unless I missed it)....was wondering if you have any thoughts on inulin propionate ester? Thanks

    1. Propionate is one of the big 3 short chain fatty acids produced by gut bacteria. I see no reason it should be supplemented if you are eating plenty of fiber.

      From the link above:

      "These data demonstrate for the first time that increasing colonic propionate prevents weight gain in overweight adult humans. "

      This is best done while increasing also butyrate and acetate. I would think an unnatural imbalance as would be seen with a propionate enema or supplement that increased just propionate would be counterproductive.

    2. I've read several places that pectin fiber tends to stimulate propionate-producing bacteria.

      Here is a quick link

      So, eating more fruits ought to do it. Baobab is very high in pectin, and you can buy Apple pectin. I suppose you could eat straight pectin, but I haven't.

  14. Wait a minute. Let me give you a summary of some of the molecules that you are thinking about using as supplements.

    Beta-glucans are a diverse group of polysaccharides that differ dramatically in properties in those made in fungi and plants. Cellulose is the most abundant biopolymer and contributes to the digestibility-challenged polymers in soil humus. The beta 3,6 glucans of fungi/mushrooms/yeast are the hallmarks of fungi and kick off human inflammation via a devoted fungus-detecting receptor. The seed glucans (3,4?) are typical prebiotic fiber. Cellulose passes, fungal glucans (hormesis aside) cause stress by turning on inflammation, seed glucans are floral feed.

    Plant polyphenols are natural antibiotics. They kill gut flora in general and are detoxed by the intestines and liver, so we don't die when we eat plants. There is no reason to believe that phytochemicals kill only bad bacteria. Purified single plant polyphenols are individual antibiotics and select for antibiotic resistant mutants in bacteria with sensitivity. Fungi also produce antibiotic polyphenols, e.g. statins, and they also select for resistant mutants among gut flora. Mixtures of antibiotics don't select for resistance, except in the unfortunate calamity of multiple drug resistance plasmid specific for all of the drugs present. Plants always produce multiple antibiotics simultaneously, hence usually no resistance. Purified berberine, resveretrol, curcumin act just like medicinal antibiotics. Common medicines can be used as antibiotics and antibiotics have the physiological impact of the common medicines (since most act via antibiotic impact on gut flora.)

    I would avoid purified plant products as supplements and learn from the potato. In diversity is danger as well as desirable mystery. There is little point in searching through phytochemicals to find which ones are uniquely toxic. Whole foods with some mystery.

    1. Art - Help us out here! We are seeing that some of the people most helped over the past year to recover from significant guy dysbiosis and AI disease, were those that used these crazy blends. Looking at them, we see they probably contained a good mixture of beta glucans, polyphenols, and fiber. Many others who were not so helped, focused more on just fibers.

      We then came across this patent with several case studies that showed a blend of blueberry, inulin, and beta-glucans was very effective at modulating gut flora.

      If we try to emulate such a blend, what would you recommend?

      See patent here:

    2. I don't think we are talking (or promoting) supplements. At least not me.

    3. And you know, I don't like supplements, but I do "supplement" with some fiber, as I don't think I can eat enough fiber rich foods. Would eating 1/4 cup of raw oat bran be considered a supplement? Or would eating blueberry extract or cocoa powder be considered a supplement?

    4. I just ordered some oat bran on Amazon, it said 'people who buy this also buy:" and next to it was the Dukan Diet book, the French diet that swept Europe a few years ago. Apparently oat bran features heavily in this diet.

    5. I certainly prefer real foods too. Garlic and onions were my primary polyphenols, but now that it's summer I'm enjoying lots of blueberries and blackberries. I have no need for supplements.

      I eat mushrooms frequently for their beta glucans (Gemma, I remember - plural!). Dark beers are supposed to be a good source - Men's Fitness says 1.3 g per 12 ounce.

      I am puzzled by Art's statement about mushroom beta glucans.

      I don't think I'd ever advocate something that would suggest purified polyphenols for long term usage. But what if - and this is just uninformed speculation - somebody with IBS issues can't eat large amounts of polyphenol rich foods? I couldn't have myself when I first started. A pint of blueberries would have had me in the bathroom all the next day. Red wine too. Would a short term correction with extract correct things so that person could eat enough real food to sustain the benefit? We need a trial!

      Maybe the IBS I had was actually the effect of polyphenols doing their job - every food that I was super sensitive to was rich in polyphenols that I can recall. Maybe it's enough to slowly ramp up these foods and not blast them at the beginning. Maybe the effect would be more gradual.

    6. "I eat mushrooms frequently for their beta glucans"

      Well, if I remember well we discussed beta glucans back then, because they were found in your supplement, and I told you to eat mushrooms, which you avoided first. There's chitin and who knows what else, depending on the source, all contributing to synergistic, immunomodulatory effect of mushrooms. People have been eating mushrooms for eons. And truffles :-)

      Nice reading:

      Mushrooms and Truffles: Historical Biofactories for Complementary Medicine in Africa and in the Middle East (2013)

      "From early stages of civilization, desert macrofungi in forms of mushrooms and truffles have been used as food and medicine. Originally, these types of organisms were associated with Mediterranean region and were first recorded as poem in Egyptian temples as follows: “Without leaves, without buds, without flowers: yet they from fruit; as a food, as a tonic, as a medicine: the entire creation is precious.” Thus, macrofungi were considered as food and medicine for royalty, and that no normal citizens were allowed to consume this precious food. During Greek and Roman eras, they were imported from Libya and sold in southern part of the European continent [1]. In the southern part of African continent, the nomadic people of Kalahari Desert used truffles for millennia [2]. "

      "I am puzzled by Art's statement about mushroom beta glucans."

      So am I. What does Dr. Ayers eat, I am thinking sometimes...?

  15. I don't think that there is any new information in the patent. It is merely formalizing eating dehydrated vegetables, a couple of cheap prebiotic fibers and some polyphenols. There is no comprehension that the groupings of beta glucans and polyphenols define vastly different molecules that are metabolized by different groups of bacteria. They are essentially defining all plants as covered by their patent.

    The traditional solution to developing gut flora is to make kids open to their family, avoid antibiotics/too much hygiene, and stick to culturally defined foods, herbs and spices. Of course the dirt floor helped. Now we try to define the role of each food and bacterium. Also notice the big farce, that the named bacteria actually have the expected genes or existed in more than one individual. People ignore that the very nature of gut biofilms is to construct bacteria to fill gut niches. Gut species are not stable, but are continually formed from available genes.

    The question then, is why people fed plenty of the same vegetables/prebiotic fiber do not get their gut flora repaired. Why do they remain dysbiotic? The answer is that their starting biofilms are dysfunctional and they do not have adequate access to candidate gut flora. It is all about the access to bacteria and little to do with prebiotics outside of basic needs. Any type of fermented vegetable should be adequate as a source of prebiotics. The problem is that all of the commercial probiotics and fermentation liquors lack the bacteria to repair dysbiosis. People that have minor amounts of the needed bacteria can get their gut flora reoriented by prebiotics, that is Tim's response to potatoes. People lacking the requisite bacteria remain dysbiotic no matter how many potatoes they eat.

    So, oat bran is fine, inulin is fine, and blueberries are fine (but not because of polyphenols), but they are not different from what you are already doing. You need to take up mud wrestling, a la Marine basic training. I think that facilitating 50 distinct sources of freeze dried gut microbiota for oral FMT is the answer. Maybe it is just ten oral capsules of FMT plus a potato diet. That should be an improvement on the patent protocol.

  16. I don't think that the polyphenols added anything. They are treating all polyphenols the same. That is identical to treating all drugs as the same. After all, most are derived from plant polyphenols.

    My comments on beta glucans is that the term is too inclusive and fungal beta glucans are as different from plant beta glucans as starch is to cellulose. The fungal beta glucans are the fungal version of the bacterial LPS and the body responds with inflammation in the same way. If the glucans just pass into the colon, they act as prebiotic fiber and no big deal. When they are said to stimulate the immune system, that means they are inflammatory and that is not good.

    1. Thank you for the insight and education Dr. Ayers. As the species are being formed in the biofilms, filling gut "niches", how is that process driven? By need or opportunity for example? And is the point of the 50 sources of gut microbiota just to make missing DNA available?

      I'll do a quick search for patents on Marine mud wrestling.


    2. "There is nothing new in the patent"

      True, but not many people ever get this combination in a bolus dose, in the amounts discussed. Well, until Wilbur and I came along.

      My focus has always just been to increase overall fiber. I lumped RS and beta-glucans, and all the other fibers together. Most people following my advice would not be getting much beta-glucans from oats on the same days the get a big dose of RS from potatoes.

      In the patent write-up, the inventor says something like, "the polyphenols act as an antibiotic to reduce overall numbers of bacteria, and then the beta-glucans and inulin preferentially feed beneficial bacteria, increasing their numbers."

      Is this such a bad plan? I think it seems logical. The conventional approach is to use retail antibiotics and give no thought to rebuilding the flora afterwards. And this sometimes works for gut dysbiosis.

      I should think that the antibiotic activity of blueberries is much preferable to, say, Cipro.

  17. Barney,
    The process is driven by the division of the bacteria able to metabolize what's available and the constant depletion of the populations by the rapid flow through the gut. It is a machine that cranks out diversity by mixing and matching across species using transformation systems triggered by the biofilm environment (quorum sensing/signaling). The mutation rate is staggering and the selection pressure is intense. The result is extraordinary Darwinian evolution that produces new species on a daily basis. It is beyond the capacity of sequencing systems based on 16S rDNA to make sense of the generated species.

    1. That is so cool yet scary at the same time. Mostly cool though. I can picture the churning chaos of a machine when it runs amok. Like Lucy working at the candy factory, who knows what's coming out of the kitchen next.

      I hope your FMT pill becomes a reality someday.

      Thank you for helping me learn about this complicated system. And thank you for probably saving me some money too.


    2. I find it greatly perplexing and fascinating too. I wonder, though, if there is not just dynamism in terms of composition but also function. That is, maybe two very different compositions can provide very close functions. So someone with a gut missing some microbes can, somehow, develop a gut that provides all the healthy benefits of someone who started with an 'ideal' gut, yet never attain the composition of said 'ideal' gut. Function is key, not form. I think I'm just echoing something others have said.

      In my case, there is no reaon to think that I had an initial condition suited to all the AI and other benefits. I had two rounds of ciproflaxocin and flagyl, plus other antibiotics. Most dinners, I'm embarrassed to say, were frozen Salisbury steak with Mac-n-cheese. Lunch was cheese melted in a tortilla or a sub sandwich. Breakfast was skipped. Lots of diet soda. I ate practically no vegetables. When I did, I had diarrhea. This was for many years. What on earth made my gut the initial condition that provided my astounding results? Maybe I had just a little of the good guys alive. Maybe then a lot of other people do too. Maybe the bugs I had left morphed into something that provided me with what I need to be healthy. I dunno. But I refuse to believe that I somehow started from an advantaged position. Something I did worked. I d like to learn what it is. And the information in the patent says that something very similar to what I did has proved effective in cases and randomized trials. I hope it's true, even if the reason is unclear. To be rid of ALL AI is amazing by itself.

    3. And that is why I still hold out hope that it is not impossible to recover. I was subjected to 6 months of weekly high dose cipro while in the military in 2003. Within 5 years I was fat, bloated, and on a sack of pills feeling 80. Within a year of a new diet and exercise, I was a new man off all the drugs.

      My diet was like yours up until about 2010. Donuts, McDonalds, and Hamburger Helper were my go-to foods.

    4. I hope it's always possible to recover. I live in the DC area, and one day I was in a store when a guy from the USDA was there. He was impressing the ladies with his knowledge of food safety and hygiene. He talked about how he bleached this and bleached that. Kill everything.

      I was thinking, what do you do when you step outside? It's in the air, on everything you touch, on your food, so on and so on. How do you avoid it? But they were distracted by their horror that I do not use color-coded cutting boards. Seriously, can anyone explain this? (Assuming a healthy gut.)

      Like I said, I believe this has been said before, but maybe there is no ideal gut composition. There might be ideal gut function, but this can be achieved via several (infinitely?) compositions. What we need is all around us, but it needs to be nurtured, cared for, and protected.

    5. I know you guys have written mountains already, but is there a concise summary of the Wilbur / Tatertot road to recovery? I ask because it's extraordinarily encouraging to know that it's _possible_ to recover a bad gut, but I really don't know what to try next [my mono-diet experiment, so far, has led to more headaches, creakier joints, and little relief].

      Here are some questions that'd be nice to try to resolve:

      - Did you have any lifestyle changes before recovering? Did you take a job where you shook more hands, or started working outside? Did you get married or have a new person or pet enter your life?Maybe good bugs came from them?

      - How did you prepare your foods when recovery started? If the simple act of cooking / cooling food can make RS3, is it impossible that other food preparation differences might affect how it affects the microbiota? Maybe frozen, microwaved, or canned foods have subtle differences?

      - Did you exercise before or after starting to feel better (or never)? If so, what was the nature of it? I have read small studies (w/ mice) suggesting that exercise is an independent modifier of the microbiota, which implies that it's better to try to do that as well as modify the diet. However, every time I try exercise, I end up feeling spent and miserable within a few days.

      - Did you know when you were recovering? How long did it take? How did you feel during recovery -- was there a period of feeling worse first? One of the main problems that I face during self-experimentation is that I don't know how to interpret things. Headaches and fatigue could be die-off (a positive?) or just more inflammation.

      Obviously you guys don't owe me your life story, and I'm not trying to pry. :) I'm just trying to come up with new hypotheses.

    6. For me, the transformation started in 2010 at age 45 when I was drinking heavily, 250 pounds (at 5'11), physically weak, terrible gout, high bp, high chol, high trigs, hypothyroid, fatty liver disease, and graduated from pre-diabetes to T2D with a prescription for Metformin in my hand.

      I was doing everything the doc said. Whole grains, low fat, take your pills!

      First, I decided to try Atkins for a month or so. Lost some weight but just could not reconcile all the fried foods were healthy. Then I found Mark's Daily Apple and read everything. I stopped drinking and started trying to do a pullup (couldn't). I ate low carb, no wheat or veg oils, no sugar. LOTS of meat and coconut oil, basically the whole 9 paleo yards.

      Within a month or so, I had lost about 25 pounds of bloat, could do a pullup, was walking 60 minutes per day and working out on a treadmill and elliptical machine 60 minutes a day.

      At two months, I was doing a couple pullups, lost more weight, and stop taking all of my pills. I had a checkup at about 4 months in: bp, chol, trigs, normal. No gout in months. Liver labs normal. Thyroid was still a little off. Doc said, 'good job, don't see this often.'

      I stayed off thyroid meds for about a year as my TSH slowly crept up out of range. I reluctantly started taking Synthroid again, and have ever since. No Hashi's AI, just high TSH. Who knows why?

      Anyway, I kept on this path from 2010 til late 2011, I was down to 170 pounds and wanted to get to 160. I went very low carb, keto and felt terrible. My FBG was creeping back up to 120s, not sleeping so great, and looked too skinny, but still had some flab.

      In Jan 2012, I started the Perfect Health Diet path with lots of starchy foods. Gained about 10 pounds, but have stayed around 175-180 ever since and feel great.

      Moral to story, I got healthy ditching the SAD but got even healthier eating a gut friendly diet. Now FBG is 80-90 and everything seems just great. Labs all look good. Still taking Synthroid, low dose 50mcg/day, could probably stop, but not pushing it for now.

      During this transformation, I started gardening, raising chickens, and never took back up the drinking. I try to get as much sun as I can in summer and take Vit D in winter. I make my own fermented foods. Kill lots of fish and game and process it myself.

      I never thought at all about gut bacteria, probiotics, prebiotics, or gut tests when I was getting healthy. I was just lucky, I guess. Once I realized how important gut health is, it kind of became an obsession and I felt the need to spread the word since no one else was talking about these things.

      How was that?

    7. Extremely useful! A couple of clarifying questions, if you don't mind:

      - Did you have gut issues that you know of, either pre- or during the recovery?

      - Would you say your paleo recovery diet had a fair amount of fiber in it from veggies? That is, there was no period of gut bug starvation?

      - Would you describe your paleo recovery diet as reasonably monotonous?

      - The lifestyle changes you mentioned -- gardening / chickens -- sound like they took place after you started feeling better. So they may have accelerated the recovery, but weren't likely the initial change. Is that right?

      - When you started exercise, do you remember if you felt worse before feeling better? Every time I try exercising, I get floored with fatigue within a few days.

      The dietary interventions you mentioned don't sound too different from things I've tried. The biggest difference probably is the 60 minutes of walking / day. If exercise does indeed modify the microbiota, then maybe this is necessary in addition to the healthier diet. For a sufficiently deranged biome, there just might have to be a period of low-intensity exercise and dealing with the fatigue to bootstrap to a better gut.

    8. OK, then it's to bed for me (another health hack I picked up!):

      - Did you have gut issues that you know of, either pre- or during the recovery?
      -- Really, really bad gut problems after I took antibiotics in 2003. Heartburn, diarrhea, skin problems. really, really bad heartburn! Lasted until I started with diet and exercise, has not returned.

      - Would you say your paleo recovery diet had a fair amount of fiber in it from veggies? That is, there was no period of gut bug starvation?

      -- No not really. In fact, probably less fiber than I was eating before. I went 'full paleo' which is low carb, little fruit, no grain, no potatoes. Fiber was minimal and from green veggies, so almost no fermentable fiber. I think the success of this diet was in getting away from SAD oils, sugars, fake foods, etc... and exercise, even if it starved gut flora. But long-term, caused problems to surface.

      - Would you describe your paleo recovery diet as reasonably monotonous?

      -- Yes, I guess. I was counting calories/carbs, so I pretty much had about 10 foods I ate for a year. Chicken breasts, fatty beef steaks, salmon, cheese, coconut oil, butter, salad bar stuff, almonds, dark chocolate (these last two, incidentally, are great gut food!).

      - The lifestyle changes you mentioned -- gardening / chickens -- sound like they took place after you started feeling better. So they may have accelerated the recovery, but weren't likely the initial change. Is that right?

      -- Right. I credit these hobbies with healthy long-term benefits, but had no real part in my recovery. I know plenty of people who garden and have animals that eat bad SAD and are very unhealthy.

      - When you started exercise, do you remember if you felt worse before feeling better? Every time I try exercising, I get floored with fatigue within a few days.

      -- Not really. I remember feeling good. The only time exercise became impossible was my VLC/keto phase. I was up to 10-15 pullups, but on keto diet could not do even one. I was so sore, I could barely walk. Yes, some will say I was "doing keto wrong" or not "fat adapted", but Christ, I was SORE. Carbs are your friend when you work out! My minumum seems to be about 100g/day, but most days I eat 150-200g nowadays.

      If you are 'floored with fatigue', examine diet...make sure you are eating enough carbs and protein to support the activity. just too many other variables to guess at here: thyroid, adrenals, age, weight...I know nothing about you! Is Zogby a 12 year old ballet star or a 49 year old ex-cop?

      Great questions!

    9. I would sure like to know what if takes for the gut flora to go awry! I was never on any antibiotics before I developed RA and I ate whole foods with the exception of maybe using canola oil but not on a regular basis. I ate carbs, bread, pasta, & cereal and some lunch meat but always cooked dinner and no fast food. Never have been overweight and have always been active. I had a paternal grandmother who had RA. Maybe that was enough to get the ball rolling. Although Art says not likely. I sure would like to know!

      On and by the way, I have been adding wild blueberries in my kefir for years. :) I have since added ginger and some green banana too.

      Tim, I remember you saying you ate cocoa nibs but then stopped. But can't remember why you stopped.

    10. Ok, the fact that you had gut problems as well is encouraging. Though it sounds more like D and less like C, and I do sometime wonder if those are two sides of the same coin or more profoundly different.

      It's interesting to me that you were eating moderate-fiber, but with dark chocolate, which is very high in polyphenols. The semi-monotony, high-polyphenic chocolate, and exercise may all have been excellent gut biome modulators, without you consciously trying to fix your gut.

      As for my fatigue, I really don't think it's due to a lack of anything, diet-wise. I haven't restricted calories in a long time (which didn't work, either), and I eat plenty of all macronutrients, including carbs.

      Zogby is a 43-yr old office-working male. 5'10" and maybe 220, mostly in the belly. I go through bouts of extreme inactivity due to fatigue. Health workups have always been "fine". That is, there's usually a thing here or there out of whack (FBG, liver enzymes, BP), but never anything actionable. I've had a few doctors say things like "you're fine; go and live your life." Which is great in a way, but I still feel like garbage. I was a very healthy & active person up through my early-to-mid 30s, so I know the difference between health and not.

      Thanks again for all the info -- it's very much appreciated. This, plus your most recent post, have given me some ammo for my next self-experiment. I'll post there!

    11. Navillus - That's the great mystery. Could be a variety of things that we don't even know about yet. Heredity is not out of the question with gut issues and AI as far as I know.

      I was eating cocoa nibs last summer, lots of them, seemed to cause me some joint pain in my big toe which felt suspiciously like gout. Happened twice separated by several months, must be something in the raw nibs that does not agree with me.

    12. Zogby

      It's hard to answer all your questions! I alternated between C and D. I used to be a college professor, and teaching and presenting seminars made me nervous. That caused me to get D right before every presentation. Other times I'd have trouble going when I felt I needed to. But lots of food would give me D. I felt bad quite a lot. I love to walk, and more than once I got caught miles away from a bathroom. It was misery.

      I was hypoglycemic.

      My low point was going to the ER for an anal abscess. I had two more. A gastro was planning to test for Crohn's.

      I had avoided doctors for several years. I hated mine. I found a new doctor who is nonjudgmental and supportive. She gave me six months. I'd tried other diets like SAD vegan, but I just gained weight. I was close to 210 at 5' 9".

      I had energy problems. Some days I woke up and just sat in a chair.

      It was about this time that Pollan's germ article was published. I was hooked. I started studying stuff. I found Jeff Leach's stuff about eating diverse plants. I thought, why not diverse fibers? I found his article suggesting 130g/day. Why not? I kept reading stuff by a guy named tatertot about resistant starch. I'll try that too.

      At some point I started losing weight. Fast. 2 lbs per week without fail. A big part was getting my blood sugars under control so that I didn't need to binge eat. I had no idea what a good diet is, but suddenly I had intense needs for certain foods. Like onions and garlic. Raw. Lots of it. I eat half a bulb every day for breakfast. I needed liver. Foods I once liked, like whole wheat and brown rice, I cannot eat anymore. I now have a sense of what is and isn't right for me to eat. I never had that before. I think it is a personal thing, because I couldn't follow Tim's diet. I'm sure he feels the same about mine.

      The first thing I noticed was that my knees and hand joints no longer ached. No cramps. Then I noticed my horrible seasonal allergies were gone. I've had them since a teenager. Gone. The intestinal issues were. It immediate. Perhaps it was die off. I don't know. I got acne, not bad. These are all gone now.

      I felt so good that I knew my blood test would be perfect. It was stellar, and yet it gets better each time.

      I have all the energy I want. I don't need to eat to have it. There are no up or down days. I feel really good, every day.

      It was the last to go, but I lost high BP too. I think it took time to heal all the vessels.

      There's lots of other stuff too.

      Good luck!

    13. A couple of clarifications.

      Tatertot is Tim, in case you are unaware.

      Whole wheat and brown rice do not cause me digestive problems. They smell bad to me. I can't get them past my nose.

    14. Wilbur

      you should write a book :-)

      You also move quite a lot, don't you?

      And if I am recalling well, you have remarked somewhere that your approach corresponds to iron overload reduction methods described in Duck Dodger's post at FTA.

    15. Gemma,

      Yes, I love to move. I used to have to take days off though because of joint pain or intestinal issues. I work out most days. I swim. I love to do 40 yard sprints in the shallow part of our pool (I have to turn around a few times) to get my breathing going. I walk about 8 miles. I listen to history and other nonfiction audiobooks.

      Yes, I've forgotten now what the method was, but there was significant overlap.


      I don't know what happened, but that sentence about intestinal healing should say something different. The healing wasn't immediate. It improved immediately, but I'd still go periods of mainly D. Some foods, like mushrooms, dandelion root, and yacon root, I had to finally just push through. I'm glad I did because I now have zero problems. I can eat anything.

    16. Wilbur,

      Thanks so much for the response! I know you and Tim are different (and that he's Tatertot) -- I was addressing both of you. Perhaps unclearly. :)

      Ok, so it sounds like you had well established gut problems at the start -- there can't be much dispute about that. While I tend towards C, so many of the other symptoms (HBP, low energy, painful joints) are all there.

      Like Tim, it sounds like the clear intervention that made a big difference for you was diet. And it sounds like you were always active and exercising as much as you could.

      So my only followup question is whether or not you think your diet intervention had any 'staple' foods that you more-or-less consistently ate. I know you ate a diverse set of fibers, but a diet can be both diverse and contain staples.

    17. Zogby - Maybe more important than what you eat is what you don't eat.

      When healing your gut, and wanting long-term happiness, DO NOT EAT:

      - Deep fried, breaded foods
      - Flour or Bread, gluten-free or not
      - Vegetable oils
      - Processed foods with many additives
      - Processed sugars, artificial sweeteners, or energy drinks
      - Fruit juice, unless fresh squeezed by you
      - Too much of anything
      - Anything after dinner
      - Anything between meals

      Later on, you'll find periodic cheats with these are not totally damaging, but keep this list handy, it will keep you healthy!

      Did I miss anything?

    18. I've tried tons of elimination diets, and none of them have ever done anything for me. I ate a very clean paleo diet for a while (cooked almost everything for myself, no grains, vegetable oils, little or no processed food, no milk, no fructose). Maybe 3-6 months, IIRC.Nada.

      Besides, the 'staple' diet will probably crowd out most of those anyways. I'm wrapping up the initial experiment design (gosh that sounds so formal) and will post it shortly.

      The 'too much of anything' is kinda interesting. I do wonder if a semi-monotonous diet will spontaneously cut down on eating too much just because you get a little sick of it. That is, you eat when actually hungry.

  18. Tim,
    They are essentially producing blue diarrhea that is little different than a dose of PEG. But it is still just half the picture and ignores the potential lack of critical bacterial genes. This is a shortcoming of all of the diet based attempts to repair gut flora. I think you should just add mud wrestling, if you have already started with boluses of prebiotics and blue diarrhea.

    1. Dr Art, Tim, anyone! I feel silly for asking, but what do you mean, Dr Art, when you say "blue diarrhea"?


    2. Annie, I don't think blueberries make poop blue. More like a reddish colour.

    3. I've eaten plenty of dirt in the past year or two, and it hasn't appeared to make a difference. For the most part, it's been random dirt in the middle of a park, rather than veggie dirt, which could be a factor. I've also eaten plenty of fermented veggies, kefir, and probiotics.

      So I've done enough of that that I feel I've gotten exposed to a fair number of genes. So why hasn't it helped?

      - The 'bad bugs' have too much of a head start in my gut. The small amounts of incoming genes can't make a dent. This might suggest reducing fiber intake until the dysbiosis is fixed.

      - The environment in my gut (from diet, exercise, etc) does not select for good strains/genes. This could respond to behavior modifications on my part, which is why I'm curious to learn more about how Tim & Wilbur made their recoveries.

      - I have bacteria that are both pathogenic and able to compete. Therefore, even introducing new genes via dirt / FMTs is unlikely to succeed until the bad actors are somehow removed. This is an unpleasant scenario, but I think unlikely (a healthy gut environment likely rewards bugs that do good things).

      There is enough conflicting / incomplete information to make it hard to say. We know that some people have made great improvements in their health, but we don't know for sure if they've changed something in their lifestyle that shifted the selection of their gut bugs, or they hit the bacteria jackpot (e.g. a healthy person shook their hands right after leaving the restroom....).

      I've heard (purely anecdote) that some people have had disappointing results from FMTs. This suggests (but does not prove) that it's more than just the mere presence of genes.

    4. Gabriella, Thanks lol..But then what does Dr Art mean by "blue diarrhea". He mentions is several times in his post above mines.

    5. N=1, sorry if TMI...

      Last night after a light dinner, I had a large smoothie made with 1 cup of wild blueberries, 1/2 cup of rolled oats, 3TBS of potato starch, 1 green banana, 1TBS of chia seeds, beet kvass and ice.

      This morning there was no blue diarrhea. Just a very normal colored Bristol Scale Type 5, "Soft blobs with clear cut edges (passed easily)."

    6. Tim,

      I just now noticed the rearrangement of Tim to TMI. Hmmm.

      Anyway, I've been curious about what normal transit time is. Mine seems to be 18-24 hours, probably closer to 24. I know that diarrhea speeds things up to maybe 12 hours, but I don't have that problem anymore. I usually poop twice per day, morning and evening. The morning one is usually anonymous, but the evening includes traces of seeds or skins from the previous dinner.

      Just curious, because your post suggests that you consider something like 12 hours to be your normal time.

    7. OK, but I warn you this is Too Informationally Much.

      I go once a day, in the morning. I suspect there is flotsam and jetsam from 12-24 hours old in there, if corn is a guide.

      Average stool weight .5 to 1 pound
      Average stool pH 5.5 - 6.5
      Bristol Type 4/5
      Color varies with diet
      Smells of aged cheese or yogurt
      Requires minimal paper products
      No "skid marks" in years

      You ask, I tell, lol

  19. Annie,
    Sorry to be confusing. I am just poking fun at the patent assuming that blueberry polyphenols, as general purpose antibiotics to kill gut flora, are a panacea. That is no different than using the common PEG laxative. That was just a vague reference to one of my areas of research, phytoalexins, and to one of my pet peeves, assuming that phytochemicals are safe and healthy, because they are natural. The patent did clarify a significant point that polyphenols are antibiotics.

    Thanks for reminding me that the blue polyphenols will change color in the pH environment of the stools.

    I believe that damaged gut flora can be fully repaired.

    I think that the approaches taken by Wilbur, Tim, et al. provide simple cures for most people and Tim's gut microbiota analysis shows that the gut flora are repaired. Many other people are going to have more severely damaged gut flora and/or additional damage to other body systems. Autoimmune diseases progress beyond fully reversible to treatable to untreatable. The population needing help and not getting it from medicine is very large and very diverse.

    Some complex disorders involving gut flora, e.g. chronic fatigue syndrome, autism, have not been well studied and may involve interactions between gut flora, body and brain that have not been identified. There is still broad resistance to FMT studies, since they would result in very cheap, non-medical interventions.

    I emphasize the point that diet proponents tend to ignore the impact of gut flora and now we are at the point where signaling between host and gut flora needs to be examined. I think that you guys are asking all of the right questions and have answers that are sufficient to resolve the most common problems. Now you are at the level of those who are not fixed by the solutions presented by Tim and Wilbur, and the rest of us have to come up with new processes to point to as the additional problems.

    I think that your comments on the dynamism of gut flora are consistent with my thoughts. There are many ways to a healthy flora and each individual has to find a unique solution. The only limit is that it is difficult to evolve a new enzyme, e.g. a pectinase, and it is much faster to pick up an enzyme from a new bacterium.

    I do not think that the gut/microbiome system is fragile. It is robust, but modern assaults in the form of purified, individual phytoalexins, aka antibiotics, and elimination of dietary prebiotic fiber and extreme hygiene are outside of the realm of human evolutionary history.

    Fermented vegetables should provide the lactobacilli/dairy probiotics sufficient for a healthy immune system and prebiotic fiber to feed gut flora. Thus, regardless of the health of the gut flora, with enough fermented vegetables, the immune system, especially immune tolerance, should be sufficient to block progression of AI diseases. If it is not, then further damage must be repaired for diet and flora to be the path to health.

    1. Art:

      I'd like to understand your position on this a bit more. From a couple of the posts in this thread, it sounds like you feel that non-isolated phytochemicals will invariably have broad-spectrum antibacterial action. Is that a fair characterization of your view?

      But intuitively, it feels to me that phytochemicals could exert positive selective pressure.

      Here's an article claim: "It is clear that dietary polyphenols and their metabolites contribute to the maintenance of gut health by the modulation of the gut microbial balance through the stimulation of the growth of beneficial bacteria and the inhibition of pathogen bacteria, exerting prebiotic-like effects". I didn't read the whole thing very clearly, so maybe this line doesn't characterize the article correctly.

      It's possible that the phytochemicals and flora need to be matched. For example, if you're going to eat a lot of potatoes, maybe it's best to eat the soil a potato grows in, as it's likely to have bacteria compatible with potato chemicals.

      On the other hand, maybe it doesn't matter so much as long as somewhere in your gut are genes that are compatible with potato phytochemicals, since gut bugs are so promiscuous. But then again, the success of FMTs indicates that at least some people are missing necessarily genetic material. Ah, it's so easy to argue both sides.

    2. zogby,
      I think that a mixture of phytochemicals, most of which have the adaptive advantage associated with their antimicrobial activities, will selectively kill particular bacterial that the host plant experiences. So, the selective advantage to the plant to produce the phytochemical is to kill particular fungi or bacteria.

      People eat plants because they can get away with it, i.e. the toxicity of the plant's phytochemicals provides a burden less than the benefit of the protein, fat and calories supplied by the plant.

      The phytochemicals produced by a plant reflect adjustments to its secondary product enzymatic pathways. A mixture of intermediates and branched pathways results in the suppression of most bacteria and fungi that encounter the plant, i.e. a mixture of antibiotics. Any one of those phytochemicals would select for resistant mutants, but the mixture does not.

      The gut microbiota are different from the organisms challenging a plant and the phytochemical mixture from each plant will have a different impact on the gut microbiota of each person. It will be mostly empirical, but familial, since people in the same family share gut flora and food.

      I think that it is nonsense to expect everyone to respond the same way to a mixture of phytochemicals, e.g. blueberry extract. Prebiotic fiber may provide similar experiences, because the various polysaccharides are metabolized by different individual bacterial genotypes that occupy equivalent niches in different people, i.e. the niche definition of bacterial species as opposed to the genotype definition. Pathogens tend to have parallel niche and sequence definitions, unlike commensals.

      I do not believe that phytochemicals, in general, contribute to gut health, nor do they preferentially stimulate beneficial bacteria and inhibit pathogens. I also don't think that it is possible to match food and phytochemical gut flora manipulators. Gut flora can adapt to phytochemicals, just as they adapt to commercial antibiotics, aka purified phytochemicals.

      It seems to me to be easiest to adopt (FMT) gut microbiota adapted to a general diet, e.g. potatoes, and then subsequently eat that diet until the new bacteria are established. This approach would reveal people whose gut cannot communicate to maintain an interaction with a defined diet/microbiota. This would provide access to the variability of the host physiological state. I assume there is no individual genotype impact, since there is so little impact of human genes on major diseases.

    3. Art:

      There are parts here that I agree with, and some things I'm not yet convinced on.

      The things I buy:

      - The whole mix of phytochemicals prevents bacterial resistance. After all, plants are still around while being constantly challenged by bacteria, so they must ultimately be able to defend themselves pretty well.

      - Gut bacteria is different from those encountered by plants in soil. Further, gut bacteria varies from person to person. So I buy that different phytochemical mixes will affect individuals differently.

      - (not from this discussions) Reduced diet diversity can lead to improved microbiota diversity and strength.

      But I'm not sure I agree that phytochemicals are incapable of benefiting gut health. Here are possible arguments:

      - Consumed plants contain a fixed set of phytochemicals. A consumed plant can't engage the pathways you refer to in response to the gut flora, as they might when growing in soil.

      - Some gut flora are able to metabolize polyphenols, conferring an advantage to bacteria possessing the right genes. Indeed, there is speculation that the by-products of polyphenol metabolism in the gut is needed for them to be beneficial.

      - Some plants form symbiotic relationships with bacteria, while presumably holding pathogens at bay. That implies that the broad spectrum phytochemicals they produce still allow for some species. Now, perhaps this is very specialized to the natural conditions of the plant, and thus is irrelevant to gut health, but given how chaotic nature is, I'm not sure.

      So, if consuming plants means that the phytochemicals' antimicrobial action is incomplete, then it seems reasonable to me that some bacteria will be selected against. And if so, it seems likely that we, as plant eaters, are more compatible with the bacteria that thrive.

      To some extent, this is academic, because I think we'd mostly agree on the right course of action. For example, your posts on decreasing diet diversity, and Tim's results from his potato mono diet, have convinced me to try eating a diet primarily composed of 5-6 ingredients, at least for a couple of weeks, as an experiment.

      But I do include polyphenols (dark chocolate, green tea, blueberries) as an extra nudge towards a beneficial microbiota, in case it actually helps. :)

    4. Zogby

      good points. We really need to talk the polyphenols more.

      And someone smart speaking dog language needs to explain to my dog that blueberries (billberries?) contain deadly toxins. Silly, silly dog. Here she is, feasting on polyphenols. Video (low quality, sorry).

    5. And it will be such a shame to see these giant bears in Alaska go extinct. It seems they recently discovered the wild blueberries and have been eating them non-stop. I suspect soon they will fall asleep and not awaken.

      Maybe we can spray fluridone, diquat, and 2,4D on the berries to save these stupid animals that know no better than to eat blueberries!

    6. And here some science on deadly polyphenols, comfortably collected by Duck Dodgers in this post: (links to the studies and papers in the linked post)

      "And just like the glycans in fibers and polysaccharides, polyphenols have glycosidic linkages that can be metabolized by gut bugs. This explains why red wine polyphenols can bloom certain kinds of bacteria.

      In fact, polyphenols, fructans, and fibers like RS appear to be synergistic. One study showed that tea polyphenols modulate RS to produce a more slowly digestible starch that is beneficial to postprandial glycemic control. Fructans are not only prebiotics, but when combined with co-existing phenolic compounds they too can exhibit anti-inflammatory, antioxidant and immunomodulatory properties.

      And it seems that plant-derived polyphenols can act in collaboration with whole saliva, human red blood cells, platelets, and also with catalase-positive microorganisms to decompose reactive oxygen species (ROS). Amazingly, polyphenols can adhere to mucosal surfaces, and are retained there for long periods to possibly act as a "slow-release devices" capable of affecting the redox status in the oral cavity."

    7. Are you saying that the patented smoothy blend that has been talked about might actually have scientific backing, and that when looking at the chemical structure of polyphenols, B-glucans, etc... it might not really apply that they have seemingly harmful properties, when looked at in the context of a whole-body ecosystem?

    8. I would say that polyphenols bind to glycans, since they share hydrophobic domains. The inherent toxicity of the polyphenols is reduced by being immobilized on the glucans and transported to the colon. Some of the polyphenols must be transported along with bile salts. All along, the polyphenols are killing gut flora that favors lean vs. obese.

  20. This is a really nice post. Thank you for writing it.

  21. Hi all

    I'm afraid I have to conclude that resistant starch, inulin, psyllium etc hasn't worked out too well for me in trying to treat my AS thus far. This is undoubtedly due to my gut lacking some of the necessary bacteria at this point.

    My pain/inflammation level has shot to it's highest point in a number of years and indeed, now appears to have spread from my spine to my shoulder joints as well.

    I stepped on the scales today and was shocked to find that I've lost 14lbs in the last month - which I certainly didn't need to lose. Would it be fair to say that this is due to the RS and fibre feeding the undesirable stuff in the small intestine and the resultant malabsorbtion of nutrients?

    I guess my focus at this stage has to return to healing the gut first, whereupon I can then start experimenting with RS etc again.

    Thanks again

    1. My hat is off to you folks with Ankylosing Spondylitis for trying this. I'm glad to see that you are going against conventional wisdom, but I have no better advice for you. You just have to listen and feel your body as it guides you along.

      Let us know how it works out!

    2. I'm indeed grateful for the advice offered by yourself and others anyway Tim.

      I'm going to give Wilbur's berberine suggestion at try as apparently it can be very effective against klebsiella.

      I'll keep you posted.


  22. I've been really thinking hard about Wilbur's spectacular results. He includes so much garlic in his diet, and I have been reading about how powerful it is as an antibiotic, and as a prebiotic. I have taken it intermittently, but not at large enough doses.

    Have any of you heard about using a raw garlic clove as a suppository? I know it sounds crazy, but there are people that swear by the results. The idea is that digestive juices can destroy the effect of the garlic, so it would take very large amounts by mouth to actually reach the large intestine. The rectal wall is supposedly very permeable, and the effect is immediate. Just wanted to ask if anyone thinks this might be a viable option for those who have a hard time stomaching large oral doses of garlic. I first read about this here:

    1. I didn't really finish my line of reasoning from above. I have had enough antibiotics in my day to know that I have dysbiosis. (recurrent UTI's, vaginal yeast, etc.) What if the garlic taken in this way would provide the needed "weeding" without causing excessive harm to the good flora? Then I could try to hit the prebiotic fibers hard without fear of feeding the bad guys. My first foray into potato starch brought some unpleasant reactions. I assumed that the feeding of those bad guys might have been the reason for the problem. I don't seem to have problems with potatoes when eaten. Thanks again for any insight you guys could offer.

    2. @Anon - The smallest thing that should go in your ear or your anus is your elbow (old country doctor saying).

    3. Good Lord! I cannot imagine the burn I get on the topside being put directly into the bottom side! Let us know how it goes, but you're alone on this.

    4. Plus, I think a lot of what happens in the gut needs to start in the cecum, this is the stomach-like pouch at the very start of the large intestine. The fermentation and species present here set up a chain reaction for the rest of the large intestine.

      I would not think that introducing a powerful plant chemical in the distal colon would have an overall systemic effect, but I could be wrong.

      I will also pass on the experiment, but it is a fascinating thought!

    5. If you rub a cut clove of garlic on the sole of your foot, you can taste it in your mouth within minutes. Perhaps doing that would have a systemic antibiotic effect?

    6. Wlbur, maybe garlic paste would result in burn.

      Cukey, get someone else to apply garlic paste to the sole of the foot and find out if there's taste in the mouth. Otherwise there can be cross contamination.

    7. @ Gabi - I should have said that, yes.

  23. Would blueberry concentrate be a good source of polyphenols? Are polyphenols heat stable?