Friday, January 30, 2015

In Search of...the Perfect Gut Bug!

Thanks to the Human Genome Project, uBiome, and American Gut we now can see exactly what bacteria call our guts 'home.' A quick Google search will tell us precisely what each microbe does for us and a visit to Amazon will let us purchase the best probiotics available!  But is this the whole story?

Credit: Dana C. Thomas/University of Washington

Here's the headline of a recent paper: "Extensive strain-level variation is detected in the human gut microbiome, with differences in gene copy-number impacting specific adaptive functions and linked to obesity and inflammatory bowel disease."

It's not the species of gut's the strain.

Professor Art Ayers of Cooling Inflammation blog has been hammering this home to us for years. He once compared the colon to a 3-D printer, making a new copy if itself with each meal.  Dr. Ayers once remarked:

Just a thought: I think of the gut, clinging biofilms and churning mixtures of food and bacteria as a 3D nanobioprinter, aka "Lamarck."  Based on a niche description, Lamarck produces complementarily approximate bacteria.

Lamarck, of course, is a reference to the theories of evolution and the adaptations that occur on a very quick timescale in the human gut. To further clarify, Art says:

By providing niches with selective advantage to particular phenotypes among prodigious genomic diversity, the gut establishes genotypes with phenotypes that fit the niches.  There is continuous flow of food and bacteria through the gut, and the only bacterial genotypes to persist are those that increase in numbers relative to others.  At the same time, the genomes are very dynamic, since dozens of replications errors, mutations, occur during each bacterial division and bacteria from unrelated species exchange genes.  So, though this appears to be Lamarckian evolution with the niche defining the adaptations, it is actually just exaggerated selection within outrageous diversity that makes it look like instructions were given to a bioprinter.

A paper released January 29th, 2015 in Cell magazine further explains and clarifies some of the mysteries of the gut biome:

...researchers at the University of Washington show that even when people share microbes in common, the exact strains each carries might be very different.

The implications of this paper are huge, but hardly new to science. Even though we have extensive libraries showing the taxonomic characteristics of our gut flora, and can accurately identify the species occupying the niches we provide and fermenting the food we eat, we cannot really say that X microbe is better than Y. As described by the researchers:

Within each bacterial species, different strains may vary in the set of genes they encode or in the copy number of these genes. Yet, taxonomic characterization of the human microbiota is often limited to the species level or to previously sequenced strains, and accordingly, the prevalence of intra-species variation, its functional role, and its relation to host health remain unclear.

Your Unique Microbes

Cite for Picture

While studying the variations present in normal human commensal bacteria, lots of variability was seen in genes encoding for movement. Bacteria need to move, usually, and have evolved ways of doing so. For instance, in the ever-present Eubacterium rectale, they discovered seven different genes for movement: four for "flagellation," two for "chemotaxis," and one for 'twitching.' Depending on which genes are 'turned-on' the bacteria can act in radically different way.  While E. rectale is a normally harmless bacteria, the implication of these different modes of movement in a species like E. coli can make a world of difference in the outcome of an infection.  But not only is "movement" variable, similar genetics determine the food they use.

Similar differences in genes are seen in bacteria that ferment galactose, starch, sucrose, fructose and mannose, as well as other sugars. So the appearance of key microbes on a stool test only tell part of the story. And bacteria that are thought to produce butyrate may actually be manufacturing a wide variety of compounds depending on their individual genes.  Again, Dr. Ayers was being very insightful when he quipped:

People are sick because of life style corruption of their gut printer.  They literally make themselves sick and print pathogens that are selected for their ability to spread.  The larger the population of ebola infected people, for example, the greater the chance it will spread by casual contact, since the Ebola virus mutates a thousand times faster than bacteria and selection for aerial transmission is very high.

Each microbe we harbor can vary greatly in its genes...the genes they have, the genes they use, and the number of each gene they possess.  Just like humans, there may be blue-eyed Bifidobacterium breve, brown-eyed, or green!

Same Microbes, Different Personalities

These genetic differences within a species have a major impact on that microbes capabilities.  Its drug resistance, virulence, the food it desires, and the chemicals (or smells) it produces can all be different depending on "how it was born." These differences, as the authors explain:

These different capabilities among strains can obviously affect the microbe's lifestyle, yet many may also translate to consequences for the health of the human host.

This research is vital to our understanding of the gut microbiome and why it's important that people partake in uBiome and American Gut.  This is all a numbers game!  The more data available, the better our understanding becomes.  Already they've identified "over 5,000 genes in dozens of species" with significant genetic differences, and that some individual microbes have variations in almost 25% of their genes.


Does this mean we throw our hands in the air and stop worrying about our microbiome?  Not really.  But it should give us pause when self-proclaimed "gut gurus" tell us they know exactly what a healthy microbiome looks like, especially when they then offer to sell us all we need to test for and grow these magical microbes.

In the end, our microbiome is going to do what it has done for billions of years...adapt to our food source and try to keep us healthy.  If a microbe could "want" something, it would probably be that its host remains healthy, happy, and horny.  Individual variations in your own genetics as well as the genetics of the microbiome ensure that each persons "perfect blend" of gut bugs will be vastly different.

The perfect microbiome, though different for each person, will undoubtedly come about from eating a wide variety of plant fibers, fermented foods, and avoiding inflammatory modern foods along with a good routine involving sleep, exercise, sun exposure and a low-stress life.

[Hattip Gemma and Dr. Ayers]


  1. I thought Dr. Ayers was against eating a wide variety of plant fibers as your gut flora cannot adjust to too much change?

    1. I think you will find that Dr. Ayers is against plant toxins, not fibers. From his latest blog post:

      Processing Removes Prebiotic Fiber from Food and Starves Gut Microbiota

      "Diverse and complex plant polysaccharides, e.g. pectin, arabinogalactan, various glucans and fructans, are systematically digested by hundreds of different bacterial enzymes of the healthy gut microbiota. The sugars that result are eventually converted into short chain fatty acids, such as butyrate, that feed the cells lining the colon. The plant polysaccharides that feed gut bacteria are called prebiotics. Unfortunately, prebiotics are removed during food processing to enhance ease of preparation and palatability. The result of decreased dietary prebiotics is selective starvation and removal of bacterial species needed for the development of the immune system, and autoimmune diseases."

    2. Great - modern food processing not only denatures food so much that huge amounts of nutrients are stripped out...but also fermented fibers. What's left? Damn!

      Post-industrial foods - double whammy nutritional disaster.

    3. But what is ironic is that the food industry has figured out that putting inulin, FOS, PHGG, and other really great prebiotics back in lead to a better eating experience and they can then advertise as 'low in sugar, high in fiber!'

      The problem is, they put these prebiotics in the worst foods imaginable (snack cakes, cookies, shakes) and make people think that the 1-2g of fiber turns their crap into healthy food.

  2. I thought that too Marybeth.That quote was from his recent post Tim,but reading way back.he did say there was too much diversity and we should narrow that down to stop our gut population changing so much with every meal.At least that was how it read to me.
    I think that was before he really delved into RS.

  3. I think Marybeth might be right - quite sure I read that on his site - any chance of getting a direct answer from him and posting it here? I tried to go over his old posts, but couldn't find that specific sentence.

  4. This came from Dr. Ayers post on Gut Flora Risk and Repair (January 24, 2014)

    "Variety in Foods Leads to Loss of Diversity in Gut Flora
    It may be more entertaining to eat a new cuisine at each meal, but it confuses your gut flora. Your gut is a river that endlessly moves food from mouth portal to pottie. Bacteria divide and eddies cast some of the bacteria back to mix with food upstream before inevitably moving with the masses down and out. Bacteria that don’t multiply as quickly as others eventually become extinct. Bacteria that grow well on broccoli may wither with onions. If you continue to eat some broccoli and some onions, then your gut flora will adapt, but if the type of polysaccharides, the soluble fiber, changes continuously, then you will end up with the stunted gut flora of Americans. Diversity of gut flora is reduced by too much variety in food."

    1. I shall see if I can summons the good doctor for comment!

      We may be reading something into that quote that is not there. It also may be a really good clue as to how we should eat, and why people like me have seen such good results with long-term supplementation of potato starch.


    2. I've tried reading his stuff, and I just can't. Assertions like the above confuse me.

      Why would bacteria that don't multiply as quickly as others become extinct? This makes no sense.

      Broccoli and onions are bags of polysaccharides, some more prominent than others. Both feed many types of bacteria. This might mean that the gut might look different eating broccoli or to eating onions, but that is the hallmark of a diverse microbiome. Flexibility.

      But to have extinction because I skipped broccoli one day?

    3. Agreed Wilbur - I can't wrap my head around that one. Between varied diets and intermittent fasting, you'd think we'd me making things worse - and yet we're all healthier. Something doesn't quite track - I'll be very curious to hear what he has to say if he makes his way over here.

      There is something to be said for keeping food variety low *per meal* for those with poor digestion, that makes sense to me. Limiting the number of enzymes required and having a better chance of approximately equal digestion times - those things make my digestion much better. And paleo man probably ate a meal of what he found, rather than assembling a varied 'meal' of 10 different items. But I wouldn't expect this to be nearly as much of a problem for those with better guts.

      But gut-farming only a limited variety to create a gut with just a few 'strong' bugs would seem to lead to an inflexible digestion, agreed. And I don't see how that's a strong adaptation.

    4. Tim - interesting thought. I add my question - is it that using potato starch as a primary starch is 'limiting variety' of fermentable fibers --> stronger gut - or is it that potato starch is such a specific targeter of that strain that Heisenbug writes about - the Clostridium cluster XIVa?

      "These are the butyrate producers, and have been shown in study after study to be some of the most consequential bacteria for gut health. Cluster XIVa alone accounts for up to 60% of mucosal bacteria in the gut. And we now have proof that when you bulletproof your gut with fermentable fiber, as Jeff Leach has, it is these groups that are doing the bulletproofing. "

      (from: )

    5. (oh, and now I see that Dr. Ayers did comment - apparently I should read the whole thread before I comment :D Thank you for inviting him, Tim!)

    6. I think that what you guys are quickly learning is that there are two sides to this puzzle...the science side and the practical side. I think it's great we all try to learn as much of the science we can, but then have to put it all into practical terms.

      I try hard to present the science in a way that everyone can relate to. Sometimes I miss important things, or leave them out because they defy a practical explanation.

      In the end, it's all so personal and individual that the science presented may not seem applicable to you. That's where self-experimentation and further reading on your part come in.

    7. @Terra,

      I'm not convinced we can say, conclusively, that we are all healthier.

      Although it's clear some are reporting significant improvements, I believe it's important to acknowledge that not everyone is having the health improvements they'd hoped for.

      My conclusion? It's complicated. We talk about it in simpler terms to make the conversations manageable, but surely there's more to it.

    8. @Jin - agreed, not everyone is getting all the benefits, not everyone is getting the benefits they most desire and a few are getting serious health down-turns. It's impressive though that as many people here and over at freetheanimal are reporting significant improvements.

      Apologies for generalizing - it's my hyperbolic brain :)

    9. @Tim - yup :) And with the microbiome as uniquely specialized to each person/each diet...there's nothing for it but to self experiment until things work. Cause no prescription/protocol could possibly cover everyone :)

  5. I'm curious about whether it's something everyone can fix, by supplementing fermentable fibers, eating fermented foods, and sticking with real food.

    That's another way of me asking, am I too broken already to fix?


  6. I feel similarly, Michelle. I've "fixed" myself a great deal, but seem to be stuck at mild constipation. I'm grateful - compared to what was, this is wonderful. But I wish I could know if there was something I could consume to get everything really good. My diet isn't varied, but its pretty good: some protein, healthy fats, vegetables, fermented vegetables, some potato, PS, some banana flour. I guess I'll just keep doing what I'm doing. One bad thing I eat: half & half in my coffee. I'm pretty sure I'm "sensitive" to it, as it causes instant bloating. It's the one vice I'm not willing to forego. Thanks, Tim!

  7. Note the post was meant to discuss the interspecies variability of gut flora, depending on the environment. "Your E. coli is not the same as my E. coli".

    But it seems Dr. Ayers is needed to explain some of his other statements...

    We keep goats, and they are known to need and eat about 400 plants species to thrive and be healthy. 401, I thought, when they finally found and ate my geraniums, 402 with begonia gone from the window sill :-(

    If you observe animals, you know that any change in their food must be gradual (at least in herbivores), like you cannot suddenly feed a lot of fresh green grass to a horse that was fed with dry hay only before. Too fast a change can cause colic, their gut flora must adapt slowly.

    So he might mean something along this line, hopefully he will show up to comment.

    1. I can see that. I have the same issue if I don't eat beans for a while. The first day back, I get gas. 150 g/day of fiber, and I get gas eating beans! But that's day one only. The next day my gut adapts, and I am fine.

      But did my bean esters go extinct? Nah. They just became less populous, which is tantamount to growing more slowly. When I ate the beans, they grew faster to handle the next day's beans. Diversity and flexibility.

  8. Yes, I hope he does chime in. I do remember him saying something like that awhile back and asked for clarification which never came. I do read his blog, but can follow only bits and pieces of what he says, so am very grateful to have Tim deconstruct some of it for us.

  9. I think that all gut microbiota can be fully repaired and that is just hampered by not having good methods to simply introduce gut bacteria, e.g. by capsules of freeze bacteria/fecal transplants.

    All of the genes needed are present in a spoon full of common soils (though not recommended.) That just shows that gut bacteria are not unique or coevolved or susceptible to extinction in anyway other than in an individual.

    A problem with gut microbiota on a whole food diet with prebiotics is usually a result of not eating the missing bacteria. Commercial probiotics contain few that are useful, since most of the species present are just those that are commercially available for some other purpose.

    Individual gut microbiota consist of populations of a couple of hundred different bacterial species. The populations change in size with each meal. The greater the difference in the prebiotic composition of each meal, the greater the change in populations. The total of all of the populations stays about the same, so an increase in one species population is at the expense of others.

    Seasonal changes in diet would be easiest for a gut microbiota to track. Rapid changes between different prebiotics just selects for less diverse generalist microbiota that are not as versatile as more diverse. Plant cell walls are the major prebiotics in leafy vegetable and consist of dozens of different polysaccharides that can be digested by a hundred different bacterial enzymes. Storage polysaccharides in seeds and roots are much simpler in structure and require fewer enzymes for digestion. RS is the simplest.

    Absence of a prebiotic needed for a species population could leave that population at the brink of extinction. Diets with little or no prebiotics would result in expected immune problems, such as autoimmune diseases and cancer. Food processing systematically eliminates prebiotics and is a substantial threat to health of gut microbiota. Whole foods, but not whole grains, are much safer. Plant polyphenolics, especially lignin, e.g. grain bran, are not nutrients for the microbiota.

    In most cases, small residual populations persist, probably because they are maintained in a archive form in a structure such as the appendix, which would also provide protection against antibiotics and diarrhea.

    Carbohydrates and phytochemicals are not typically studied by researchers in biomedical fields or molecular biology. The central dogma of information flow in molecular biology is DNA (genes) to RNA to proteins (enzymes) and most people ignore that many of those enzyme are used to make or digest polysaccharides/oligosaccharides such as those of plant prebiotics. Two hundred of those enzymes are coded by genes in the gut microbiota. A bacterium has about a thousand total genes and humans have only 23,000 with about a thousand on each chromosome.

    I hope this is helpful. Sorry if it remains cryptic.

    1. Thank you Dr. Ayers. I found this explanation clear and even optimistic. If it's more about gene transfer than living bacteria, I guess my fears over not getting anaerobic material seeded would be unfounded. It seems as the technology to profile DNA continues to advance and become cheaper, maybe we won't have to wait on big pharma to "save us". As you said, they have not done much with the commercial products currently available and I hope that their efforts in FMT will not follow a similar path.


    2. I'm sorry, but it leaves me just as confused. MaryBeth's pasted paragraph is condensed now into a single sentence "Rapid changes between different prebiotics just selects for a less diverse generalist microbiota that are not as versatile as more diverse." I can't get cut and paste to work, so I hope I got it right. I Have trouble figuring out what this means, but it would be nice to see studies.

      The new paragraph also backs away from outright extinction to the "brink of extinction" and small residual populations. This is key in my mind. Bacteria grow so very rapidly that a small residual population can become significant in hours, if not minutes. They can also switch food supplies. I think this is a lot more complicated, and I am unwilling at this point to accept that switching among prebiotics has any significant effect.

    3. To clarify, I meant any significant effect as stated in the quoted sentence. I do agree that it will change relative populations.

    4. Thanks, Art! The science behind all of this is confusing for sure and not always intuitive.

    5. Wilbur,
      I am sorry that you are so confused. I am just trying to explain my thoughts on how to help people with their health issues. Some people benefit. Apparently they don't help you. I will keep trying.

      People eating processed foods or a typical American Diet have a microbiota with reduced diversity. That reduced diversity may result from fewer prebiotics, but I just bring up the additional possibility that continual dramatic shifts between different prebiotics, paleo to vegan, may reduce species diversity. Less extreme diet changes may be all that is necessary. Some personal microbiota may be more susceptible to species loss by particular diets.

      The gut is like a continuous flow fermentation system with a mixture of 200 different populations of different species of bacteria. Food is occasionally going in one side and bacteria are exiting the other. Antibiotics occasionally wipe out the populations of a quarter of the different species and diversity drops. If the prebiotics present feed only half the species, then diversity drops. Commercial probiotics just pass through without enough reproduction to compensate for dilution as the food passes through. Processed food starves out microbiota diversity by lack of probiotics.

      The model lacks many aspects of a human system. In the human, there is transfer of genes between species 1, 2 and 3, so new hybrid species would be present every day. There is also the possibility of introducing new species. Most people add dairy probiotics or fermented food probiotics, but these lactobacilli just pass through without substantial reproduction, since they are not adapted to the gut environment. These probiotics can provide some of the functions of normal gut flora and aid immune system development, but since they don't reproduce effectively, they may not provide enough bacterial volume to even eliminate constipation, because they can't convert prebiotics into substantial amounts of new bacteria.

      Bacteria under perfect conditions only divide every 20 minutes. The gut is not perfect conditions, so most of the time the rate is probably closer to an hour. Also, the food is moving and the vast majority of bacteria depart as the bulk of feces. Bacteria are very limited in the kinds of polysaccharides that they can digest, since different enzymes are needed for each of hundreds of different polysaccharide components. Most typical probiotics can't digest any polysaccharides.

      Bacteria of course don't become extinct in a day, but we are talking about years of diets without prebiotics, e.g. a very low carb diet that confuses carbs for body vs. microbiota. Some people never adapt to RS, because the appropriate gut bacteria are absent/extinct. I think that the needed bacteria are sensitive to common antibiotics/drugs or the prebiotics needed to maintain the population are removed by food processing.

      The discussion is designed to explain why modern diets and lifestyle produce modern diseases. I think that food processing that limits prebiotic amounts and diversity, extreme shifts between prebiotics, antibiotics/medications and excess hygiene, account for gut dysbiosis and immune dysfunction of modern diseases. I don't know what the alternative model is. Medicine makes no attempt to explain the initial cause of disease and individual genetics makes only a minor contribution.

      Hope that is helpful.

    6. Yes, it does! I agree wholeheartedly with everything you've said here. It just seemed very strange to me to need to worry about extinction on a daily basis, which you state here is not the case.

      I have no scientific basis for it, but I try to keep most of my plant species rotating about every week or maybe two. I have no diet dogma - I just eat what interests me.

    7. It clears it up for me too. thank you Art.

    8. Dr. Ayers,
      Thank you for taking the time to comment here, you are busy with your own blog, but know that people read widely, and chances are those who are here are also reading your site, so you're helping the same bunch!
      If you would indulge another question? - re your comment - "...dairy probiotics or fermented food probiotics, but these lactobacilli just pass through without substantial reproduction"
      Would you please elaborate on your dramatic (IMHO) change of position on fermented veggies - what made you change your thoughts that these SBOs are transient rather than repopulating the gut as you have previously said so many times on your site. In particular, in your post - you draw distinction between dairy probiotics which will not repopulate the gut vs fermented veggie lactobacilli which will.
      " Bacteria that grow on dairy cannot survive in the gut."
      "New bacteria must be eaten, and I think that the cure, short of the real deal fecal transplant, is still available in the original, paleo form of naturally fermented, live foods....Fermented Vegetables"

      Are there new publications which inspired this reevaluation? If so, would you be so kind as to link to them?

    9. Newbie,
      I was making a refinement and apparently just added confusion instead.

      From my perspective, the bacteria that are missing in autoimmune diseases are those that ferment prebiotics, e.g. Clostridia. Fermented veggies have grown lactic acid bacteria on the sugars, acidified the brine and left the prebiotics behind in the crisp veggies. The lactic acid bacteria are related to the bacteria growing in the gut of babies fed breast milk, i.e. lactobacilli and bifidobacteria. Thus, the unique gut microbiota of babes is "dairy probiotics" that provide all of the function of an adult gut flora in developing the aggressive and suppressive parts of the immune system.

      To a limited extent, the lactic acid bacteria in fermented veggies can also support full development of the immune system, but that stops quickly after you stop eating the fermented veggies, because the lactic acid bacteria don't grow well in the gut. The adult gut needs a microbiota of bacteria that grow on prebiotics, e.g. diverse plant polysaccharides.

      Homemade fermented veggies also grow some bacteria on their prebiotics and it is those contaminants that may softened the veggies a little, which are potential candidates to repair damaged gut microbiota.

      So, I am making a distinction between commercial krauts that are usually made from pure cultures of lactobacilli (not SBOs) and homemade krauts that contain other bacteria that may digest prebiotics and fix your flora.

      So my position hasn't changed, but it is difficult for me to provide all of the implications at once. I still think that homemade krauts have a major role to play in repair of gut microbiota.

      It is helpful to me that you persist in your questions, so keep asking until it its clear to you. Thanks.

    10. Dr. Ayers, that was a very clear answer - thank you.
      You say that the LABs on fermented veggies leave behind the prebiotics, but I thought that is what they are eating to make lactic acid to acidify the liquid.
      With fermented dairy, the LABs eat the lactose.
      Which carbs are the LABs on veggies eating and what are they leaving behind as prebiotics? Thank you for your patience.
      ps - I do eat my homemade kraut daily because of your recommendation. You are NOT wasting your efforts to make us healthier.

    11. Art, you mentioned the somewhat softened homemade fermented veggies as being having potential to repair the gut. Would you say then that. "The mushier, the better"? Or is just slightly soft good enough?

      Also, you use the word potential. Are you saying that it might, IF it were contaminated by the right bacteria? And therefor there is no guarantee that mushy is better?

      I make my ferments using an airlock because I enjoy the crunchy, crisp results.

    12. Dr. Art,
      So the main reason for fermenting veggies before consuming them is to reduce the substances they produce to defend themselves in a hostile world ? And if you make the ferments mushy you'll get a paltry few of the bacteria that are able to proliferate in a human gut.
      But if you really want to consume a good dose of probiotics you can spend a lot of money on a pill containing only a few strains, or do what any species on this planet has been doing for millenia , not just hominids, and eat dirt.
      Every time I watch a youtube depicting ancestral living humans- like the Hadza- having a meal, I'm struck by how much common ole garden dirt is routinely consumed. Because it's simply impossible to keep dirt out of your food if you don't have plates and tables ....and wet ones etc My dogs are exactly the same. Try gnawing on a bone in any backyard in the world without also ingesting copious amounts of dirt.
      Not rhizoplane or rhizosphere or any other kind of 'special' dirt. Just the stuff under your feet.
      What on earth is the point of 'doing a Wilbur' with diverse plant polysaccharides, if you aren't also doing it with the bugs which can actually use those fermentable fibers to have lots of kids?
      We have this crippling, cultural aversion to dirt. Put a few 'select' strains in a pill and charge vast amounts for them and they're 'SBO probiotics'
      But if it's dirt's dirty.
      Sure the dirt contains more than a few pathogenic strains. But that's the point. If we routinely consume the local dirt,our immune systems have seen it all before.
      We let our dogs lick our faces, and feel proud of NOT rushing to the bathroom to scrub off the slobber. But it's such a baby step.
      Just sayin.

  10. Hi folks
    Does anyone know if raw honey's antibacterial properties interferes with probiotics? That is, I have a shake with PS and other fibers and chase down some probiotics (3 recommended on FTA) with said shake - if there's honey in the shake will it kill all the bacteria I'm ingesting from the probiotics? Should the honey be taken separately a few hours apart from the probiotics or will they act synergistically?

    Thanks to Tim and everyone who comments/contributes to this blog, it's a great resource and very supportive atmosphere!


    1. @Josh

      "Should the honey be taken separately a few hours apart from the probiotics or will they act synergistically? "

      Most probably it would be better to separate, by a few hours.

      Though, who knows, would some bacteria be protected by honey polyphenols, resulting in synergy?

      Bacteria coated by polyphenols acquire potent oxidant-scavenging capacities (2009)

      "Several microbial species, including probiotic lactic acid bacteria, have the ability to irreversibly bind a large variety of polyphenols (flavonoids) and anthocyanidins found in many colored fruits and vegetables and to enhance their total oxidant-scavenging capacities (TOSC).

      The possibility is considered that clinically, microbial cells in the oral cavity and in the gastro intestinal tract, complexed with antioxidant polyphenols from nutrients and with cationic ligands, might increase the protection of mammalian cells against damage induced by excessive generation of reactive oxygen species during infections and inflammation."

    2. I'm thinking that if my great grand mother and ancient greeks were often eating authentic greek strained yoghourt (usually fermented by 5 probiotics) with thyme honey, they probably were into something already back then...

    3. Thanks for the food for thought, Gemma & Space!

      I guess with all of this, there's no one-size-fits-all black and white answer!


  11. "Diets with little or no prebiotics would result in expected immune problems, such as autoimmune and cancer." The prebiotics being vegetables (fresh and fermented) and other whole foods?

    If that's the case, my gut flora must be so screwed up because I have always cooked with whole foods and now even more so (a year with fermented and 3 years of my own kefir). I continue with RA flares. I get so confused sometimes. Am I doing too much, not enough. I don't experience any food intolerance and TMI is good. I was using PS but then became confused (by reading Animal Pharm) if it was good for me or not.

    This whole process to help myself can get overwhelming at times!

    1. It does get confusing!

      It need not be overwhelming, though. Make minor tweaks based on what makes sense at the time. Maybe try ramping up the raw veggies, maybe try adding some honey, you know, just small changes at a time and see how you feel after a few weeks.

      You say you have RA, I doubt that there will be any quick fixes from dietary interventions, but if you keep trying, sharing, and reading you may come up with a really good plan for yourself that may help others. That's all we can really do at this point, ya know?

    2. @navillus

      We can compare RA notes as time goes by. I recently went off low dose intermittent Doxy which seemed to be keeping my RA in remission. I want to see if my infection load is low enough that my own immune system can keep it in check. My joints still ache off & on. My primary complaints remain life-Interferring low mood, manageable lowish energy, and recent cyclic acne. The acne started with the introduction of fermentable fibers.


    3. @Michelle
      Navillus and Marybeth are of the same��. My last post was posted before I realized I had not changed.
      I too did the antibiotic protocol with minocyline pulsing. It worked well and during the protocol I was doing probiotics etc. I quit the protocol a year+ ago.
      I mostly get flares in my wrists. This present flare, I am having a hard time shaking. It doesn't really keep me from doing much. The only thing i did differently was during the holidays and I was away from home so the fermented foods took a hiatus. Other than that not much different as I don't indulge.
      I do do what Tim said by tweaking and try by adding. Lately it's a teaspoon of local honey. I exercise 5x a week and am in no need of losing weight. Energy is good and mood would be better if it weren't for the winter!�� I pretty much keep to a schedule as far as what I eat and do. Bone broth w/ veggies, turmeric, sauerkraut or kimchi,kefir, oatmeal w/coconut milk and oil and dinner is protein and veggies some times cold potatoes reheated or black rice. Can't forget a cup of coffee w/ coconut milk in the AM!
      Yes, I am very interested in keeping up with you and comparing notes!

    4. @navillus
      Diet is not enough for health. A gut microbiota adapted to your diet is needed, so as you point out, your autoimmune symptoms point to missing species of gut bacteria. Eating veggies with new bacteria is part of the cure, but have you considered the antibiotics that you are still taking? Many common medications have antibiotic activities that damage gut microbiota. Your medications may be the culprit. Vitamin D deficiencies are a symptom of chronic inflammation, e.g. RA, and most people with deficiencies remain deficient after supplementation. Dental infections may also provide enough inflammation for RA.

      Antibiotics decrease immune system function by killing gut microbiota and by damaging the immune system they reduce the symptoms of immune attack in RA. If the antibiotics are stopped, the immune system will start to function again with renewed RA symptoms. Further repair of the gut microbiota would permit development of the damaged tolerance part of the immune system and lead to a cure of the RA.

    5. The reasoning, as I understand it, behind low dose intermittent minocycline or doxycycline for rheumatoid disease (all connective tissue disease, not just RA) is there is an infectious etiology.

      Cell wall deficient L-forms of mycoplasma(s) strep, chlamydia(s), and others(?) have an affinity for the joints and the antigen provokes a bacterial allergy in the body.


    6. Dr. Ayers,
      I have not been on antibiotics for over a year. I was having my vitamin d levels checked and they were good. I was also and still am supplementing with vitamin d. Also was supplementing with fish oil capsules. I ran out and have not reordered (do I need to?). I do not take any medication except for vitamin d, C and fish oil. I had so many kefir grains, that I have been consuming some now for a week.

      I am having all my silver fillings removed next week. I floss every day and oil pull with coconut oil.

      Could it be that it is taking my system longer to repair itself?
      Thanks for the help!

    7. Doesn't low dose minocycline and doxycycline also act as anti-inflammatory? They use them for acne as well. It's not a therapeutic dose for bacterial infection.

    8. If any nerds are interested in reading a bit about the antibiotic protocol, there is a "short version" at Roadback at the following link:

      If for some reason that link doesn't work, it's ---> STUDIES ---> PROTOCOLS ---> HISTORICAL PROTOCOL.

      Also from the link:

      "...This protocol views inflammatory forms of arthritis as a persistent cell-mediated hypersensitivity created by long exposure to antigen derived from a hidden or invisible microbial source (i.e. mycoplasma or closely related bacterial L forms).

      It appears that mycoplasma produce their pathogenic effect in man, not by the classical method of invasion and rapid tissue destruction as in lower animals, but by creating a cell-mediated response resulting from long-standing cellular parasitism with gradual sensitization of the host through intermittent antigen release from the cells.

      Rheumatoid disease progression to its most advanced stage is the over-reactivity of the host tissues with the development of the hyperimmune or autoimmune state, probably through cell or molecular mimicry. This phase of the disease, characterized by the production of cell- mediated antibodies, macroglobulins and the rheumatoid factor appears to be an expression of a second line of defense in the immune system, logically deterring the spread of microbial precursors. The therapeutic focus must be on eliminating mycoplasma as the key antigenic source...."

      And, "...The fundamental treatment goal in the induction of a sustained remission is to control and suppress antigen production. The final objective has been the ultimate elimination of the microbial antecedent.

      In the primary objective, the suppression of antigen production, dosage needs to be tailored to the individual patient to avoid the sudden release of excess antigen and delayed drug sensitivity by over-medication. The degree of anti-mycoplasmal medication may need to be reduced to the minimum, such as minocycline, 50 mg. once or twice a week, gradually increasing according to patient tolerance in these individuals.

      An important guideline in successful treatment has been the avoidance of over-medication with paradoxical worsening. Too much medication can cause a delayed hypersensitive reaction to the drug itself and induce a flare of the arthritis with the development of symptoms closely mimicking the disease (Herxheimer Reaction). A therapeutic balance can be readily reestablished by the temporary interruption of the treatment for a week and then restarting at the same low dose...."


    9. Michelle and Gabriella,
      I know that the rationale for antibiotics is explained by rheumatologists is related to joint infections, but I think that the data are weak. I also don't buy into the bacterial antigen mimicry. They just have a system that reduces symptoms and it doesn't matter if it causes additional damage to the immune system, because they are not measuring immune function. They also use potent immunosuppressants that are antibodies that silence parts of the inflammatory system that provide protection against infections.

      I taught immunology for many years and find many of the practices of medical immunology puzzling at best.

      The antibiotics act on the gut not at the site of inflammation and that is why the dose is said to not be therapeutic for infections. In the gut, where the pills dissolve, the dose is very effective at killing the target, gut bacteria that are involved in development of the part of the immune system that results in the attack on joints. That is why the antibiotics as said to be anti-inflammatory.

    10. @Navillus

      Re: winter & mood. I'm in the Chicago area. A few years ago I purchased a light box. I got the model recommended by CET. I use it from about the end of September until March, in the morning.

      It helps me feel more alert during the day instead of dragging/sleepy all morning and into the afternoon. Plus, I feel ready for sleeping at bedtime instead of tired + wired.

      I still struggle with low level depression, but believe it would be worse without my light box.


  12. Wow, Michelle! Somebody has been reading!

    "Cell wall deficient L-forms of mycoplasma(s) strep, chlamydia(s), and others(?) have an affinity for the joints and the antigen provokes a bacterial allergy in the body. "

    Crazy, no? And antibiotics and antifungals just exacerbate the problems.

    1. @Tim
      I am not sure why I developed RA. Maybe it was an unhealthy Microbiota to begin with, but antibiotics got me to remission. I wouldn't hesitate to go back on Doxy if I could not control my disease.

      There are people with scleroderma who have gotten to remission and reversed the progression of the disease with as little as 200 mg minocycline daily. Usually, people with scleroderma are given little to no hope.

      If antibiotics are part of the original big picture problem, sure, I get that, but I would not want to scare anyone off of trying the low dose protocol on Roadback.

      Way too many success stories to dismiss!


    2. Michelle - you are seeing the 'science vs. practicality' well. Antibiotics are a fact of modern life. I wouldn't hesitate to use them in case of massive infection, but at least I am starting with a good gut flora and have a good idea how to quickly rebuild.

      The real problem with antibiotics is their over-prescription and even wrongly prescribed (ie for viral infection) nature. And giving them to babies at the drop of a hat.

    3. Tim,
      And don't forget that all categories of common medicines have been tested for their antibiotic activity and it is substantial. Common drugs kill bacteria. So the real problem is over-prescription of drugs in general, and that is also the source of selection for multiple drug resistant superbugs.

  13. Dr. Ayers (& Tim) - when making homemade fermented kraut do you use a starter, and if so, which one? Or do you just make them with some salt? I'm not that clear on the difference between homemade and "commercially" bought, if the store-bought are actually fermented? Thanks - even though most of this is beyond me. Just trying to eat and stay well. I opted for a dental bridge as opposed to an implant because the surgeon insisted on an antibiotic. I said no way. He thought I was nuts.

    1. I make sauerkraut from cabbage and salt. About 1/4 cup salt to 15 pounds of cabbage. Then mash it all into a big crock until its swimming in its own juices, weight down with a set of crock weights and cover.

      Since I purchased a nice crock, weights and cover my kraut turns out much better than earlier attempts using a plastic container and a dinner plate with a rock on top.

      Initial investment for a 3 gal crock kit is about $150, but well worth it. You can make kraut much cheaper, but might as well get the right equipment, it should last forever. Any health food store will have it and help you out.

      I've never used a starter.

      Did you see the blog post here from last summer on kvass? Pictures and lots of comments!

      Also a good post on making vinegar in here somewhere, too.

    2. Anonymous,

      I believe in his blog Dr Ayers has advocated for making vegetable ferments without a starter, because using one would cut down on the microbial diversity. Most store bought sauerkraut is not fermented, but a vinegar product. Bubbies is a fermented brand available at places like whole foods. I live in a large metropolitan area and smaller local boutique brands are available as well. Dr Ayers claims commercial fermented vegetables use a starter for consistency, and hence is less diverse and valuable than a homemade ferment.

      I have a big Harsch crock which does work very well. However, I have found it easier to make smaller batches in a half gallon wide mouth jar using an airlock and glass weights you can buy on amazon. You don't need any special equipment, but if you use one of these systems, you never get mold on the top.

  14. @ Kate and @ Tim
    I too make my own kraut - I use the Bubbie's jars from when I was buying it - I too make 1 cabbage at a time, 2 jars worth - never moulds. Nothing fancy. No air locks. ust one big leaf topped with cut up center stalk to weigh it all down,
    @ Tim - I tried not cooking the steel cut oats at all - in the fridge with 1.5 times water overnight - they were softer by morning - added my usual fruit and walnuts with cinnamon - quite tasty - only issue, it's all RS2, no RS3 - and I probably need more of the latter, cuz get RS2 with PS. So rethinking it - any thoughts??
    Also, Tim, do you know which CHOs the bugs are eating on the kraut and what they are leaving behind for other bugs in the LI. Thoughts on soft kraut vs crunchy, in reference to Dr. Arts's comment?

    1. It's fun to play with fermenting foods, eh? Once you get brave enough to actually try eating what you made it's really fun.

      Don't overthink the RS2/3 issue. Just eat. You are making wise food choices, no sense turning it into another worry in your life.

      This whole soft vs crunchy thing is a new concept to me. No idea.

      I know my kraut seems to go through phases of crunchiness as it ferments. The best batch I made was this fall, I just left it in the crock and ate the entire 3 gallons over a 4 month period. It was fun noting the subtle differences as the weeks wore on.

      I also made a batch just prior to that one and froze it, I'm eating some of that now. It's also nicely crunchy, and was frozen after only about 3-4 weeks of fermenting.

      So possibly 'crunchy' refers to less time in the crock.

      I wouldn't worry about it. If you are making your own fermented veggies and eating them regularly, you get an "A" from me!

    2. Hey Tim,

      Have you ever tried fermenting those mushrooms?


    3. Here's one way that I think about ferments relative to the gut. In the crock, the lactic acid bacteria are on the surface and are rubbed around the veggies in the salt and a brine forms with water drawn out of the veggies. Sugars and small molecules from the veggies are fermented by the bacteria and lactic acid is produced. The veggies are crunchy, because they are still made of the plant cell walls that are made of complex polysaccharides, prebiotic fiber that the lactobacilli can't digest. The kraut juice contains the lactobacilli that are like dairy probiotics. If less salt is used, then other bacteria grow that are more similar to colon bacteria, and they digest some of the prebiotics and soften the veggies. I don't know where the limit of salt for growing additional bacteria besides lactobacilli is vs. some baddies. Taste and texture probably tell the story. If it tastes foul, then perhaps it should be avoided. (Although there are plenty of desirable, foul tasting ferments that are quite healthy.) So kraut has probiotic juice and prebiotic fiber.

      Food introduced into your stomach has the proteins, fats, sugars and starch digested and absorbed via stomach and small intestines. All that remains is prebiotic fiber that goes into the colon where it is mixed with anaerobic bacteria that grow on the fiber and produce SCFAs, e.g. butyrate that feed the colon cells. These colon bacteria are essential for development of the immune system. SCFAs are also used to produce more gut bacteria to form hydrated stools. Absence of sufficient gut flora diversity to digest fiber causes constipation and SCFAs are converted into body fat (obesity.) Ferments produce prebiotics like passage through the first half of the GI tract.

    4. A couple things . . .
      I've been using an airlock system and salt brine for a few years now, for my fermented vegetables. They usually have a good "crunch" to them. Previously, when I didn't use an airlock, the ferments tasted great (and were usually softer) but my stools also felt like they were burning me (they felt hot, painful and itchy). That symptom ended as soon as I started the airlock method. I suspect there was something oxygen-loving that was upsetting my system.

      Recently, when I upped my fermentable fiber intake, with both food and from-a-bottle sources, plus the addition of SBOs and FloraMend, I gained ~10 pounds in six weeks and my OCD tendencies recurred. However, I had a bunch of things improve – more regular BMs, better sleep, better energy, better skin. I backed off the fiber and probiotics, and the weight is slowly starting to come off again. My guess is that I need to ramp up more slowly, get back on the wagon with home ferments (I've been lazy in the last six months), and may add AOR's Probioic-3. Thoughts?


    5. @Cheryl,
      Ten pounds of bacteria, or your clothes are tighter?

    6. My clothes are tighter, as in "I have to go shopping for new pants" tighter. It's interesting, because the extra weight felt healing to me in some way, but also incredibly annoying . . . annoying physically because I can't move/exercise as easily. I was already above ideal weight, so to gain felt frustrating.


    7. Cheryl - which probiotics were you taking? Our family (3 of 4 with mental health issues) did great on Probiotic 3 - reduction in all kinds of things, including mental health symptoms. Then, for some variety, we switched to Prescript Assist - anxiety and irritability spiked all over the place. We're going back to Probiotic 3. Someone else reported increased irritability with PA. Seems likely to me there some strain of gut bug that's just not agreeing with the environment of some people, yk?

      Since the real issue is *feeding* the bugs properly, once replacement bugs have been seeded into the gut, continuing to take them seems redundant to me. So hopefully Prescript Assist's 29 bugs have gotten a foothold *snort* because we need to back off that particular combo.

      File this under FWIW and N=3 :D But know that mental health effects from changing the microbiome happen to other people, too.

    8. @Terra

      I was taking Prescript Assist and FloraMend. I started with PA, before I increased any fermentable fibers. I took it for 1-2 weeks, once per day (more than that gave me a crushing headache), and didn't have any issues. But when I added the fibers on top of that, and then sometimes took FM instead of PA, things went haywire. I just don't know what did what. I want to try Probiotic-3 next. I called them today, to see how much lactose is in each capsule, since I'm super sensitive to dairy (there's 5mg in one capsule, or is it 3mg? . . . eek, my brain!).

      For the last week, I've taken zero probiotics, and have cut my fermentable fiber intake by ~2/3. I also forgot to say that I started taking milk thistle in the past week, and I think it's helping to calm things down.

      Yeah, I definitely don't think it's a coincidence that the OCD tendencies (which thankfully are only mildly annoying) increased with all this experimentation. My mood, in general, is meeeelloooooow. My husband was amazed how calmly I dealt with his screaming match with the new dishwasher he had to install (a quick project turned into a 1.5 day project).


    9. Very interesting! Thank you for laying out the path of effects there - it's really helpful to have several people reporting on this mental-effects stuff :)

      I, too, have been atypically robust dealing with stressors (screaming match with new dishwasher ROFL - but, yes, stressors like that used to tail-spin me, and now they just....don't, even with the added anxiety of PA). Even the anxiety itself will surge...and then retreat (which it never did before). Same with irritability.

      Here's a thought - could the increased activation be due to increased serotonin production? We know that the gut should be producing a certain percentage of the serotonin we need - well if dysbiosis had screwed up that process and reseeding the gut is restarting it, it seems reasonable to assume that for a while there would be too much serotonin in the system, yes?

      Excess serotonin would certainly account for the mild activation symptoms I'm seeing in my little family self-experimentors group. Would serotonin affect your OCD in this manner?

      (incidentally, I'm also using a liver smoothing herbal combo to chill out this issue - interesting, eh? :)

    10. On average, I'm a calm person, and can handle stressors like the Dishwasher Debacle . . . but they're still emotionally taxing. I was so mellow that I wasn't even emotionally taxed by it. It was quite an amazing feeling.

      I'm not sure what to think about the whole thing. I'm reviewing the different pathways for detoxification (phase 1 & 2), as well as serotonin production, dopamine production, and so on . . . my intuition says there's some sort of connection there (as it relates to my situation, and perhaps others too). A quick google search shows that it still looks like serotonin deficiency is linked to OCD, though it's not yet definitive regarding whether it's a cause or effect of OCD.

      I'll post an update after I experiment again with increasing fermentable fibers and adding in the Probiotic-3. In the meantime, we can keep sleuthing!


    11. @Cheryl - a small update on PA effects :) The other day I got what appeared to be a case of food poisoning. I was quite ill for about 24 hours. I piled on the kefir, doubled my PA *and* added an equal dose of Probiotic 3. Thankfully, this combo kicked the food poisoning to the curb. FAST.

      In the aftermath though, I decided to see what using both Probiotic 3 and PA might give me in terms of easing the anxiety/irritability. And it's working! I'm very excited. I'm not as chill as I was without PA, but I'm willing to keep experimenting, because my gut flora were really whacked (everything from food allergies to hormone issues to digestion issues to candida to autoimmune issues). I strongly suspect I *need* everything in the PA, so I'm eager to try this combination.

      Just to keep track, I'm also taking 8 TBS potato starch, some banana & some larch currently. I'm still rotating the secondary starches around, trying to suss out which ones are more challenging for my system. When I get a notable reaction to one of them, I take note, back off to PS only for a time, and then keep experimenting at a lower dose.

    12. @Terra - Thanks for the update! Sorry to hear your gut was nailed, though it's encouraging that you were able to deal with it so quickly. I also feel like PA is beneficial for me, but I also feel like I need something else in addition to it. I ordered the Probiotic-3 and am eager to try it. I'm still being cautious about which and how much of the RPS/et cetera to take. One day at a time! I upped my RPS again last night (I'd been taking very little for 2-3 weeks) and had some bizarre dreams, but I know that will calm down after a week or so.

      I first experienced OCD-like symptoms started sometime around age 10-12, after I had several amalgams put in. After getting mononucleosis in high school, I was given antibiotics for a secondary infection . . . nothing was the same after that. Endometriosis, food intolerances, acne and boils. I'm so much better now, but the food intolerances, BM issues, blood iron anemia, and mild anxiety/OCD-ish/insomnia issues are still lingering. Currently, it's the food intolerances that are the most annoying. However, I now have more hope for figuring out all of this than I've had in a long time. This blog has been a blessing!


  15. I have made sauerkraut with a Fido airlock jar and now with a polish crock with ceramic weights. I had one batch of sauerkraut, using an airlock, come out mushy and awful tasting. I believe I played around with the salt and did not use the enough. I make kimchi too and love it more than the sauerkraut. For my kvass I use the same airlock jar. Caraway seeds are excellent in sauerkraut!

    I cook my steel cut oats with coconut milk and coconut oil , some cocao nibs and cinnamon. So I guess I am losing the RS? But then I put green banana in my kefir shake (homemade). So do I get a pass? :)

    1. You get a pass...just this once!

      Your food choices look really good!

    2. If it helps, I use 3 Tbsp salt per 5 pound cabbage - ORGANIC ONLY (IMHO)
      If extra liquid needed as it dries - 1 tsp salt/1 cup water, and I pour it in. I put the jar into the fridge by day 4 or 5 - is that what the rest of you of are doing? I assume the lower temp stops ongoing fermentation, so the kraut is crunchy.

    3. I let some of mine go several weeks (6-8) on the counter. Still crunchy. Nice and sour.

      Refrigeration does not stop fermentation. It slows it down quite a bit.

      My biggie is fermented hot sauce. I found about a lb of super duper hot Carolina Reapers that I mixed with habaneros, Cayenne, garlic, tomatoes, etc. when I open it, you can smell the heat from across the room. That sits on my basement counter about a month.

      I made a fermented portabella mushroom ketchup (no tomatoes). It was fantastic.

      Equally fantastic was a fermented habanero mustard.

      Guests went wild over both, but too often over indulged on the mustard. It was fun to see red, sweaty faces.

    4. I have not tried fermenting mushrooms (yet). One of my favorite condiments is fermented black bean paste. I developed a taste for it when I lived in Korea. I buy it at the local Asian supermarket. It stinks really bad! A little goes a long way. It's great mixed in with rice.

    5. Tim, this is off topic...did you like living in Korea? My son leaves for Korea in April, helicopter pilot with the Army.

    6. Strange, this comment went into the spam folder. Oh well.

      Yes, I loved Korea! He will probably be at Camp Humphreys, that's where i was, too. Home of the original MASH 4077th.

      I can only imagine the cool stuff he will get to see from a helicopter, the country is just beautiful. Hopefully he has a curiosity for the local food, there is some truly unique cuisine to be had there.

    7. @newbie, in my Fermented Vegetables book, it says not to add salted water to sauerkraut. They say it can cause discoloration and possibly a mushy kraut. It says to add other veggies that are known to give off liquid. Turnips being one of them or sliced onions, grated carrots or beets. There are a few other options too. Most recipes say to leave kraut fermenting for 4 weeks.

      @Tim, my son is looking forward to his tour. One thing we taught our kids, was how to eat ethnic. Plus that's how I cook having grown up over seas.

    8. Wow, that's news to me - been doing it for quite a while, never had issues. So what do you do as the liquid level drops and some of the kraut is now exposed without liquid?? I find that happens after a week or 2 in the fridge.You can't just put raw veggies in at that point, can you?

    9. This is an excerpt from Sandor Katz, the fermentation guru, from his site ..
      "Check the kraut every day or two. The volume reduces as the fermentation proceeds. "
      "Sometimes brine evaporates, so if the kraut is not submerged below brine just add salted water as necessary."

    10. I got to spend some time in Korea too as the guest of locals. It was a fantastic experience! Thankfully my hosts were dedicated to showing me authentic Korea, not some American version.

      I learned to ask what my food was after I had eaten it. I was there in summer, and there was very little cooking. My favorite dish was a bowl of what I thought were clear noodles and something called "mountain vegetables." After my second bowl, I noticed uniformly placed black dots on the noodles. They turned out to be eyes! I was eating whole fish, not noodles. I had other interesting stuff, like raw sting ray. The kimchi got me though, and I suffering in a few hours before and during the 16-hour flight.

      The people of Korea were wonderful. It was a great experience.

    11. I want to go visit Wilbur! Those ferments sound amazing! I thought I was thinking out of the box when I fermented rhubarb...

    12. @Newbie, in Sandor Katz's, The Art of Fermentation, he says "if at any point it seems that water has been lost (in an open crock due to evaporation), simply add a little dechlorinated water.

      I am with you, I think I would go with Sandor's recommendations. Although once it's refrigerated does it necessarily have to always be submerged?

    13. Thanks for that tip - I supposed once the LABs have established dominance and reduced the pH, there's no need for the salt. I'll go with his book information I think.
      I've always thought that in the fridge it does still need to be submerged cuz, as Wilbur noted, bacterial growth is reduced, it is not zero.

    14. For submersion, I think that it depends. My sauerkraut is never fully submerged. I am lazy now and buy several types of raw sauerkraut, and there's not even enough liquid. Fermented okra, however, gets yucky in color and soft if not fully submerged. I've gotten mold, even in the fridge. But I think submersion is generally less urgent.

  16. I'm not sure where to ask this question but... In the American Gut blog "3-day Cleanse", Luke Thompson mentions that the three participants took VSL #3 probiotics. I'm wondering if those bacteria were identified or compared? I've heard that VSL #3 is one probiotic that remains in the gut long term, so I'm wondering if they tracked them. I didn't see them in the detailed chart (the last one) in the blog, and there's no way to comment there.

    1. Wow, dnvrdave, that was a great article! First I've seen it.

      My impression reading the article is that "cleanses" don't really do much to the gut microbiota in the long-term. I would have liked to seen all of the reports they collected, I don;t think they did a great job with the ones they did use. Then again, there are probably not that many gut geeks like us.

      The study I'm involved with now is using PEG for a colon cleanse and they are tracking gut microbes for 3 months before and 6 months after a total colon cleanse as done for colonoscopies. I think this will prove to be a bit more drastic than a juice cleanse!

      I think the takeaway from that article is that we should be normally consuming lots of healthy plants and fruits and ditch the SAD diet completely!

      Also, their "touching a cotton swab to some “used” toilet paper" method of sample collection leaves a bit to be desired, but I think they had a big enough sampling that their results are meaningful.

    2. Tim, Have you seen this study? It was linked in the above article (but required a subscription to read). It's closer to the meat/dairy vs vegan one I'm doing.
      I'm still trying to digest it (ha ha), as it has a lot more wonderful detail. What's your opinion? I haven't started paying any attention to fermentation yet, since neither diet seems to have any notable effect on my health.

    3. Dave, that's a great paper comparing a total vegan diet with a ketogenic diet, you'll notice in Fig 3 that the butyrate and acetate SCFAs are cut in half on the keto diet, and the isobutyrate and isovalerate levels are doubled.

      I'm not sure the implications of the raised "iso's" but the lowered butyrate is concerning to me. I wish they would have checked the pH of these samples as well.

      What this study was designed to show is the rapid-response of shifting microbes to different eating patterns, and it demonstrates that very well. I think the researchers concluded that the vegan diet looked better in terms of a health biome.

      "Finally, we found that microbiota changes on the animal-based diet could be linked to altered fecal bile acid profiles and the potential for human enteric disease. Recent mouse experiments have shown high-fat diets lead to increased enteric deoxycholic concentrations (DCA); this secondary bile acid is the product of microbial metabolism and promotes liver cancer26. In our study, the animal-based diet significantly increased the levels of fecal DCA."

      But what I found really interesting, was a link to this paper referencing the study: The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes

      I especially liked this line from the abstract:

      " By out-sourcing this aspect of digestive physiology to our gut microbes, we maximize our ability to adapt to different carbohydrate nutrients on timescales as short as several hours due to the ability of the gut microbial community to rapidly alter its physiology from meal to meal. Because of their ability to pick up new traits by lateral gene transfer, our gut microbes also enable adaption over time periods as long as centuries and millennia by adjusting their gene content to reflect cultural dietary trends."

      It's becoming apparent to me that as we gather vast piles of gut microbe data, we're seeing that it may not be the exact collection of bacteria one has, but more the byproducts and effects that the collective flora has on the individual.

    4. Tim -

      That looks like a great paper (Devil). I'm going to sit down with a Friday beer and enjoy both!

      I personally believe that, for me, there is no special diet. People I talk to want to know if I'm paleo or some other label. I don't think it matters because the bugs change and seemingly keep me in line by making me prefer certain foods.

      The only thing they can't adapt to is death by starvation, antibiotics, and possibly certain food additives, water additives, and possibly some meds.


    1. LOL. Scare tactics? Imagine the opposite - new weight loss therapy.

    2. yeah, kind of a strange way to report this:

      "Importantly, the FMT was not the only possible cause of the woman's weight gain. In addition to treatment for C. difficile, she had also been treated with several antibiotics for Helicobacter pylori infection. Other possible contributing factors in the woman's weight gain include the resolution of her C. difficile infection, genetic factors, aging, and stress related to illness. However, as noted above, she had never been overweight before."

      It's possible, though.

      But, from what I've been hearing, the FMTs are good at getting rid of C. diff infections, but the new gut flora doesn't persist very long.

      Still, an exciting therapy. It will be cool to see where this goes over the next 10-20 years.

    3. I would guess that the woman had a damaged gut flora and constipation. In other words, she was not digesting prebiotic fiber in her diet. FMT bacteria are not necessarily stable, because they are shoved out by the replenishment of the original. In this case the woman was lacking most of her gut bacteria, Her daughter's bacteria, considering her obesity, could digest prebiotics, but lacked bacteria to metabolize short chain fatty acids to make stool bacteria, with the result that the colon was saturated and passed the SCFs on to the blood and body for storage as fat. Hence the daughter donor's obesity and her subsequent weight gain. She was eating the same, before and after the FMT, but after she could digest prebiotics to fat instead of passing them in stools.

      Genetics is seldom a major factor in disease, but gut bacteria are familial.

  18. sorry, my network connection died just as I was about to post a comment to go with the link - Just curious as to Tim's thoughts on this article. thanks

  19. Tim, you mentioned the total colon cleanout with PEG for colonoscopies. I have a screening colonoscopy coming up in a couple of weeks, and I'm getting depressed and anxious thinking about it. I've spent the last year and a half diligently tending my gut flora with prebiotics, probiotics, healthy diet, etc.; and the fruits of that effort are literally going to be flushed down the drain.

    So I'm starting to strategize the "rebuild" of gut flora afterwards. Do you (or others) have any thoughts on what the best first steps would be?

    1. Excellent! I think you will do fine. These PEG cleanouts are probably 50/50 hurtful or helpful to the general population that's eating a SAD diet.

      If one has a bad microbial population, the PEG could give you a fresh start. If you have a good gut flora, the PEG will wipe it out.

      In your case, it won't just be a matter of luck. Presuming you have an appendix, you won't be wiped completely clean.

      In the future, I could see people having fecal samples frozen and saved for occasions like this, but for now, you'll just have to do your best to eat as good as you possibly can leading up to and then immediately afterwards.

      So, maybe, make your first post colonoscopy food a nice smoothie with some fruits and veggies and some extra added prebiotic powders (ie. pull a 'Wilbur'), then go light on the meat for a few days and eat lots of starchy veggies, yogurt, sauerkraut, nuts, honey, garlic, onions, oatmeal, and drink lots of tea.

      Get those starch and fiber eaters really built up fast, pumping out butyrate and whatever else they do, so the bad guys don't stand a chance.

      I dread the day I have to do something like that! But it's not the end of the world.

    2. So, would you have a colonoscopy? We're supposed to have one every 5 - 10 years if you're considered healthy - more frequently if there are issues. My grandfather died of colon cancer, and I have a history of constipation, so.... I haven't had one in years though, and am also dreading the day.

      Also - I read somewhere it takes 2 - 3 years for the gut to recover after antibiotic use. Is that true?

    3. Thank you for the suggestions, and for the words of encouragement! I do still have my appendix; in fact, I've seen it (kind of)! When I had my first colonoscopy 12 years ago, I requested that the procedure be done with no/minimal sedation, since I have odd reactions to some meds. So I got to observe the whole thing on the video screen. When the doc reached the end of the colon, I asked about the appendix, and he pointed out the area on the screen. I can't say that I could distinguish much, but the idea was kind of cool.

      And, heh, I think that I've been reading too much gut stuff, because I've already started freezing some poop samples (double-bagged in the chest freezer in the garage), just in case there's some real problem afterwards. I know that a home freezer isn't cold enough to really do a good job, but it might be better than nothing. But, hopefully, I'll be able to get those good guys built up fast, and it won't be an issue.

    4. "So, would you have a colonoscopy?"

      Nope. Not unless there was a compelling medical reason, like a familial history of colon cancer or I start bleeding out of my butt.

      I can't wait to tell the next doctor I see that I am not planning on getting one, as I turn 50 this year. Actually, I wouldn't mind getting a sigmoidoscopy, where they only go in a foot or so, and see what they see.

      I'm not a fan of them clipping out every polyp they see and then claiming they just saved your life when there is no evidence that all polyps turn cancerous. Also not a fan of the PEG clean-outs.

      I'll take my chances, but would never try to discourage others from making up their own mind.

    5. Yeah, I've been telling doctors for years I'm not having mammograms anymore. Every article I read - in mainstream media no less - ends up telling us lives haven't been saved by mammograms, numerous false positives lead to numerous unnecessary biopsies, and more. It's probably worse than the colonoscopy in terms of the responses you get. And then of course I'm not a million percent sure I'm making the right decision... Oh, and then there's the statin they keep trying to prescribe. It's exhausting nicely explaining you'd just rather not.

      But back to Art and this gut healing conversation. If one is lacking the necessary bacteria, where are we supposed to get it? Just keep woofing down the fermented veggies? Try some of the SBO probiotics? Any thoughts on this Tim?

      By the way, you've inspired me to stop using a piece of paper towel to close the door of public bathrooms. I'm forcing myself.

    6. It would be ingenuous of me to pretend I knew the right answer, but if I were to take a stab...

      I think the important thing is to avoid antibiotics and excessive sterilization in our normal course of life. If you absolutely must take antibiotics, you can recover from it.

      Aside from that, it's important to eat the foods that we know build a good microbiome: fruits, veggies, fermented foods, starchy foods, and eat as much of the stem/skin/seed/roots as possible, not just the sweet flesh.

      Lots of people have phased fibrous plants out of their diets for the most part, especially low-carb paleo type diets. And the SAD is not known for much fiber to begin with.

      I personally don't take any probiotics or SBOs, but I think they are great for people to try when getting over symptoms of a dysbiotic gut. They have a proven immune system stimulating effect, and that's what this whole thing is really about.

      Also, don't overlook the non-food related parts of your life: sleep, exercise, stress...all well-known gut killers!

      I think you will know you are "there" when you find you don't get the seasonal illnesses everyone else gets, you sleep good, you have great digestion and you can do whatever you want.

    7. Tim -

      Check this out about gut microbiome analysis and detecting colorectal cancer

      I come of age in just a couple of years, and I'm not sure. I know of somebody who got perforated. And I'm hesitant to blush my shiny, new microbiome that has been very good to me!

    8. Anon -

      Funny, I use a paper towel in a restroom. I don't want to use their antibiotic soaps. People are disgusting in bathrooms. I figure if I can get in and out only touching me, I'm good.

      I'm perfectly fine eating with my hands just after petting the dogs, though. Dogs are not as disgusting as people.

    9. Interesting! One day we will look at our love affair with the colonoscopy and laugh. I have heard all kinds of horror stories about colonoscopies.

      If I need one, I'll get one, but just to look around? No thanks. If you have a family or personal history with colon cancer, or are unhealthy, overweight, and eat the typical SAD diet and take the typical bag of pills, then maybe would be great. They will find and remove some polyps and get you on a recurring schedule. What a business model!

    10. @Wilbur - ha! My strategy as well :D

    11. That gets into who is "at risk" enough to warrant a colonoscopy regularly. Yeah, my grandfather died of colon cancer at 84. And I wouldn't say my digestion is stellar - but it's not horrible. I feel great physically - mentally, is another story. I think I'm going to opt out of the colonoscopy and pretty much everything else.

  20. A lot of interesting discussions on this blog the last few days. I thought I would chime in with my results to date in case they are helpful to anyone. I’m the gal with the chronic headaches and migraines experimenting with “doing a Wilbur” to see if it helps my head.

    After Christmas I ramped up my RS/fiber intake, pretty quickly reaching 80 grams per day. My original goal was 100, and I occasionally get there, but the gag factor is keeping me pretty steady at about 80. My original recipe had 2 raw potatoes per day, but I eventually realized they were giving my strong sinus pressure which went away when I switched to potato starch. (Cooked potatoes are no problem)

    Re Headaches: I think my number of headache free days has gone up. However, the change is not substantial enough for me to be sure the fiber is helping.

    Re the discussion on hormones: I am a post menopausal 56. The frequency of my hot flashes has gone up this last month. However, as before they are brief and don’t bother me much. I think my overall temperature is warmer. It is winter here and the cold is not bothering me nearly as much as it usually would.

    Re the discussion of probiotics: I have a number of probiotics on hand and I usually take one or two. I have B infantis, a Jarrow bifidum blend, L GG, L plantarum, Primal Defense, and Prescript Assist. I have noticed nothing with any of these. I had thought last fall that maybe the Prescript Assist was helping my head a bit. Started taking 5 per day. Nothing. No mood changes for me either. Calmness attained with the fibers remains unabated though and I love it.

  21. Continued…
    Re fermented foods: I’ve been following the discussion of crunchy vs. Soft etc with some interest. I love fermented foods but they don’t always love me back. I couple years ago I provoked a massive migraine with about a tablespoon of Miso. A glass of beet kvass with 2 T of Great Lakes gelatin mixed in had the same effects. Needless to say both are off the menu LOL. My experiments with kombucha and kefir were not encouraging. I do tolerate small amounts of veggie ferments. I can’t find the paper, but I read once that the level of histamine in sauerkraut peaks early in the fermentation process and then eventually goes way down. I suspect that might apply to me but who knows? This week I have been having a couple spoonfuls/per day of the brine from the fermented okra I made last summer. I’ll have to say it tastes absolutely delicious to me. So far so good. I also recently made Gemma’s goulash with the sauerkraut I put up a couple months ago. Absolutely delicious and no ill effects. Yeah!

    Re weight: No change for me. I’m 5’8” and have been about 125 pounds since forever (save two pregnancies). Initially, my appetite was suppressed but it rebounded in about a week. I was taking my fiber “shakes” a couple hours before breakfast and dinner, but now I usually have them right before the meal or even with it. I found Dr. Ayer’s comments about familial bugs and the case of the lady who gained after fecal transplant interesting. My own siblings have all struggled with their weight most of their adult lives, as have my parents. Don’t know how I was spared.

    Re dogs: I adopted Wilbur and Stuart’s recipes for my two recently adopted dogs. Just checked their rear molars, and the substantial tarter they had back there is gone! Might be the rawhide et al I have been giving them though. When we got them the female was urinating frequently, including many in house accidents. I suspected a mild uti. Whatever it was, it has totally resolved. Perhaps the fiber was helpful with this.

    1. @Kate
      What fibers are you giving your doggies?

      Re: headaches. I have a lot of trouble remembering my symptoms or what I'm taking day to day, so I made a quick and dirty spreadsheet I keep in my iPad.

      I'm tracking which supplemental fibers I'm taking and how much. I'm also marking whether I'm taking them with breakfast or before bed.

      I have a column for supplemental probiotics. Cycle day. Comments on sleep, mood, hunger, and energy. Poop. And, unfortunately, a column for the condition of my chin (major break-outs since starting to supplement with fiber powders). Really, the chart is more simple than it might sound. It helps me "see" what's going on.

      I backed down on my initial enthusiastic intake of fermentable fibers after having some days where the bloating and gas was too much to function comfortably at work. With my schedule, taking my 2T. total of PS, Inulin, and FOS at bedtime instead of at breakfast seems to working out better.


    2. The doggies get PS, Larch whatever its called, and psyllium. And usually a smidgen of something else. Mixed in canned pumpkin. You are smart to keep records. I probably should do the same. Actually, your comment jogged my memory. My intial mix was potato, inulin, and a couple others. I really turned the corner on my over full, bloated, feeling when I added psyllium. Tastes like straw, but seems to be a major player for me.

    3. Soon "Doing a Wilbur" will be replaced with the 'Kate App'.

      I think it's great what you are doing. Not blindly following any particular suggestions, but tracking your own health markers and trying different approaches.

  22. And a couple more thoughts:
    Re colonoscopies: Wish I knew what I know now back when I had my colonoscopy. I remember how great my head felt when I was completely empty. My diet back then was pretty low fiber. Headache came right back with the reintroduction of food.

    Miscellaneous: Senses of taste and smell still more acute. I also have had mildly elevated blood pressure for the last decade—the only conventional measure that is out of whack for me. Seems to have gone down some but not quite fully “normal”.

    Re constipation: I have rarely been constipated in my life, except sometimes when travelling. One thing I noticed on the fiber regimen that I never noticed before. Certain OTC drugs are constipating! Not seriously, but enough to be annoying. I occasionally take a Benadryl. I now realize they are constipating. I also took an Ibuprofen for a muscle strain and bingo, same effect. I’ll be thinking twice before I pop one of these again.

    1. "Certain OTC drugs are constipating! Not seriously, but enough to be annoying. I occasionally take a Benadryl. I now realize they are constipating. I also took an Ibuprofen for a muscle strain and bingo, same effect. I’ll be thinking twice before I pop one of these again. "

      This is exactly what Art Ayers has been saying. Some of the mysterious effects of medications come from quickly altering our gut flora. Scary!

    2. Isn't the sense of smell/taste thing odd! We've been noticing not only increased sense of smell and taste, but strong repulsion by things that were previously enjoyed. Foods that used to be delicious or interesting (but usually not that healthy :P) now taste tasteless or just...wrong. Foods that are healthful have this huge increase in complexity of flavors. We sound like wine testers when we eat now, "Did you notice a smooth fruity finish? wow!" LOL

      Smells have been profoundly effected - we went shopping for some essential oils for a diffuser the other day and an hour later we decided it was hopeless. EVERYTHING we smelled was 'wrong'. I suspect the strong imbalance of concentrated smells was the overall wrongness factor - food & plants would never smell like clearly they were 'wrong'.

    3. @Kate I had prehypertension when I started this. Now I'm rock-solid 115/70. But it was the very last thing to come into line. There are so many things I've considered. One is that it takes time for blood vessels to become more supple and relaxed, and so it just took time. Also, I read a study of reversed Alheimers which had a list of things the participants did - I was ready doing all (of the practical) ones but one, so I tried that - co-q10 supplements. Also, there are suggestions that a lot of people have magnesium deficiency. A good gut helps. I've been eating a ton of dried figs lately. They make me very happy. All of these are linked to BP.

      @Terra on smell: Yes!!!! I've had that experience for many months! People ask me how I can resist "delicious" things, but I hate to say because it smells awful. I can often smell the dirty burned oil in fried foods. The smell of refined sugar is strong and turns me off. All brown rice smells rancid to me. On my walks, I feel like a dog. I can smell the rotting leaves. I smell turned earth before I see it. I once smelled a natural gas leak only to finally come upon a dropped egg on the sidewalk. It's crazy. I was not like this before. Of course, I mentioned that there is scientific basis since sense of smell is influenced by the immune system.

    4. I'm cracking up reading your smell descriptions :D YES - anything even remotely rancid makes me physically step back! And that covers a huge amount of packaged or restaurant cooked food, and definitely in any oily seeds, nuts or whole grains, since oils actually go rancid very quickly. Most people have no idea how much rancid oil they eat every day. I've always reacted when I eat it, but I've never had this much refinement in identifying it before! Of course, one effect of this is I have zero fat in the food-portion of my diet. So I'm staying with my grass-fed butter + coconut oil in my coffee every morning, because I need fats from *somewhere* :P

      One weird inversion that's happened since I started PA is I'm suddenly craving sugar. I can't stand it in low-quality foods, but I want it! I feel certain the PA is starving out something bad (candida, whatever) and it's clamoring for sugar to sustain it. Ha. The PA is going to win, oh sugar-craving bug! :D

      Similarly, fasting got really tough for me when I started PA. It wasn't before *at all* - fasting was super easy for the past few months (I use a 2x a week, 24-36 hour approach). Again, I'm sure something in the biome is being wiped out and it's not happy about the lack of nutrients. I do use my potato starch during fasts, so the *good* gut bugs are just fine.

    5. @ Wilbur, thanks for the info about your blood pressure. That's very encouraging. Mine was typically 130 something over 80 something. Now I am edging under 130 and occasionally seeing the upper 70s. I'd like to be where you are! I do take Magnesium (commonly recommended for migraines) and have tried co q 10 (also recommended for migraines). Maybe I'll try the latter again. Maybe I will see something with it now that my baseline is better.

    6. @Kate

      It's funny, I have a science background, yet I approach things like this unscientifically. I don't record the things I do, and I do several things at once, making it impossible to discern any possible causes and effects. Somewhere I hit on something or somethings that work. I've read that race car drivers often wear the same underwear during races, believing that the underwear caused them to win races. I often feel like that! (As a child, I had a pair of brown shorts that caused me to crash my bicycle. I blamed my parents one day for making me wear them after a particularly memorable crash.).

      Anyway, here is a description of the study on Alzheimers I mentioned.

      I forgot that I became interested in calesthenics-type exercise at the same time. It feels really good. I Don't know much about yoga, but there are probably similarities. Calisthenics are supposed to help with circulation and BP. So, at about the the time my BP decreased, I had focused on the gut, co-q10, magnesium, and calesthenics/yoga. Which, if any, helped I do not know.

      Also, I had a volatile period in which my BP would be 130/80 ish, but would then drop to 90/60 ish. Can't explain. Now it is always 115/70. But I have learned to not measure after a fiber feeding. The fiber is hard to digest and increases BP.

      I am always super-nervous at doc visits. My wife laughs at my hyper animation. But this last time, even feeling my own nervousness, and being cold and naked, I registered 120/80 in the office. A lot better than the 150/100+ that caused considerable concern before.

    7. @Wilbur

      Ha, ha, I hear you. Lots of science and engineering in my background, so I should know better, but I am always running multiple experiments with plenty of potential confounders. And I'm totally with the race car drivers. Bit of a golf obsession here and golfers are all about such fetishes.

      That being said, I think I've always had the exercise recommendation pretty much dialed in, and in the course of my headache reduction quest, I have tried most of the supplements recommended to lower blood pressure. So my suspicion is the favorable turn in my blood pressure is due to the fiber. Last night was 120/72, hooray!

      I guess it was about 10 years ago, when both my husband and I were getting dirty looks from the docs for our elevated blood pressure, that my husband downloaded some treatise from one of the medical associations. One thing that has always stuck in my mind are the recommendations for taking your blood pressure. Wait at least 30 minutes after eating or drinking. Don't have any coffee. Make sure you don't need to go to the bathroom. Rest quietly for about 5 minutes. LOL, I try to have all those things in line at the doctor's office so my reading is not too elevated!

  23. So i was reading The Art of Fermentation today and came across fermenting urine for nitrogen living plants. You ferment for 28 days and dilute it 1:1 with water. Any gardeners ever tried this?

    1. Funny you should ask. When there aren't enough fish in a planted aquarium, a little human pee will help make the plants grow. Not too much though.

      When my kids were going to camp, the plants growing on the bottom of the lake in the swim area were very lush and green. Then the camp director showed all the kids a big oil drum and told them that the amount they are peeing in the water is equivalent to the volume of the drum. The kids were told they need to get out of the water and use the latrines referred to as Pooh Corner. The plants all disappeared! LOL! Seriously. At the time I was breeding tropical fish at home in many planted tanks, some of them CO2 injected so my kids were very aware of the effect of various 'fertilizers' on aquatic plants.

    2. @Gabriella, I read your response to my husband as we used to have a couple of tropical fish tanks. I am going to try this spring/summer with the urine fermentation on the garden for shits and grins! I will report back with my yields!­čśÇ

    3. navillus,
      It you just ferment fresh urine for 28 days most of the nitrogen will just gas off as ammonia - which is a much more potent greenhouse gas even than methane. And even methane is considerably worse than carbon dioxide.
      Ammonia is also deadly to fish and a big problem in fish tanks because the fish excreta will readily turn to ammonia if it's not converted into nitrates by denitrifying bacteria. That's why Gabriella mentioned that you shouldn't add much urine to a fish tank. The fish already provide more than enough nitrogen in their own excreta to grow an aquarium plant jungle. But the biological filter (the denitrifying bacteria) needs to be 'on song' or you'll just kill all your fish with ammonia.
      This 'far far too much of a good thing' effect is very well illustrated by the sea bed under fish farm offshore enclosures, which is a dead zone from the ;'too many kids peeing in the water' effect. If the enclosures are moved every couple of days, it doesn't happen. But it's an expensive exercise moving such a huge net, so they don't bother. And the industry isn't well enough regulated to force them to, so they're just happy to create a moonscape, and move on. And business is competitive, so it needs to be regulated, or the bean counters just say 'too bad, future generations, our shareholders want the profits now.
      One way to make sure the denitrifying bacteria get the nitrogen before fermentation transforms it to ammonia is to just apply the fresh raw urine to a different plant or patch of soil every day. There are literally billions of denitrifying bacteria in every square foot of soil on planet earth. And they all just love eating the nitrites in fresh urine and turning it into nitrates- which plants use to grow.
      Remember the SBO's I talked about, not in an SBO pill, but actually in real dinky di dirt. Well dirt is also teeming with denitrifying bacteria.
      For the last couple of decades I've been doing this in another more roundabout way by just pouring the fresh urine when anyone goes to the toilet through a 2.5 metre high 400mm wide column of woodchips. By the time the fresh urine gets to the bottom (it takes about two days) the denitrifying bacteria on the surfaces of the woodchips have converted all the nitrogen to nitrates and it can be applied to plants whenever - even years later.
      Fresh urine is also a potent antibacterial medicine . It can be used both topically and systemically. But don' ferment it first. It will taste disgusting, and probably make you very sick. And if you eat a high salt diet, even fresh urine is just too salty.

    4. Very True Stuart. All of it. Dog piss on lawns is the thing that anyone can identify. The centre of the area is dead and the grass on the outer portions is super healthy. So there's a 'sweet spot' for using urine as a fertilizer.

      I only put a couple of tablespoons into a 30 gallon aquarium and it turned the water green. Which was really excellent given I was at that time, in that tank, breeding white cloud mountain fish. My other tanks had South American Dwarf cichlids, so they were all doing fine given there were many other fish in those tanks.

      The green water effect was quite impressive. I could see the green swirl around because of the filtration system. The fish loved the conditions because the fry had lots of micro-organisms and protozoans to eat. The tank was also heavily planted. Of course green water tanks are not much to look at unless you are a biologist. Then they are absolutely fascinating.

    5. Gabriella
      Anyone who can keep cichlids happy and healthy has my profound respect.
      Such beautiful fish. And they have a gracefulness which has always fascinated me.
      The biological filter factor in keeping aquarium fish is critical isn't it? It's a constant reminder of the delicate balance all organisms (including humans) need to thrive.

      My Orafti HP finally arrived. I started using it yesterday. One thing I did notice immediately was that there was no increase in flatulence whatsoever. Usually when you introduce a new fiber, particularly a highly fermentable one like inulin, there's more gas, for a few days at least. But with the Orafti HP, nothing. Apart from that, I haven't noticed anything spectacular. Only that the longer consume fermentable fiber the better I feel.
      My father had prostate cancer for the last 20 years of his life. He still lived to 86, but for the last few decades he experienced worsening urinary urgency/hesitancy. He always urged me to get my prostate checked regularly. And for about the last 15 years I've noticed a gradually diminishing lag between the urge to pee and the need to pee. And my prostate has been getting slowly bigger. PSA testing revealed that I don't yet have prostate cancer, but probably would eventually. In any case, saw palmetto supplements were so effective at resolving the urinary hesitancy that I wasn't too concerned. But a month ago I noticed that I was experiencing neither urinary urgency or hesitancy, and I haven't used saw palmetto for a couple of months.
      Also, I listened to a Chis Kresser podcast yesterday on functional medicine approaches to treating/preventing Alzheimer's disease during which he stressed the importance of the gut/brain axis. It occurs to me that gut health seems to be the long overlooked precondition to all health markers. So the gut/brain axis is but one.
      So to you all, and particularly Tim, without whose efforts we'd all still be clueless and struggling with such a huge range of health issues, a heartfelt thanks.

      I actually don't rotate fibers like you Wilbur. So my smoothies are now even more Wilburesque than Wilbur's

    6. Gabriella,
      I forgot to mention that you talking about the dog pee burn marks on lawns reminded me that before I built the woodchip urine compost tower, we used to put neat fresh urine on the lawn. But we'd pour the container of urine through a funnel placed on the ground so that the urine got straight into the soil under the grass. Even neat, the fresh urine would never burn plants (even at the point of entry of the urine, as long as it went straight onto the soil without touching the plant.
      Those SBO's, how I love them.

    7. Stuart -

      I do not have prostate issues, but I too have noticed changes in urination urgency. Sort of like the hunger urgency. I feel the need to urinate, but I can wait if doing so is inconvenient.

      With the HP, I've found that it seems to produce gas lower in the intestines. I don't know how to explain it. Rather than it starting in the middle of my gut, it seems to start in my butt? It's not a bloating gas, yet I am surprised by its quantity. If my gut is really talking to me, and I believe it is, then it really seems to like the HP. I've cut back on regular inulin.

      Ha! You're trying to out-Wilbur me! I use a large plastic cup of water to mix my fibers. I've recently had to reduce the amount of water in the mixing because the quantity of added fiber causes it to overflow. But, yes, I get a feeling of contentment after my fiber drink.

      My latest adds are grape seed flour and (soon) ground dried dandelion root.

      I am also buying in to your idea of eating dirt. Not actually eating dirt, but not washing my hands after playing with the dogs, even when I eat. Hard to describe. Just being natural. I haven't soaped my hair in weeks, and I only soap my armpits and nether regions when I bathe. At first it was uncomfortable, but now it's fine. My skin and hair feel better, I think.

    8. Wilbur,
      We are so conditioned to be clean aren't we? And yet when you think of all the effort people go to to eat paleo, the one simple thing that ALL ancestral hominids (not to mention most life forms which can move in the history of planet earth) did routinely was to consume copious quantities of dirt of no particular distinction, root zone or any other zone. And yet because our cultural heritage is so powerful, we just find it too difficult.
      And we have plates, so we can avoid eating dirt.
      I've honestly never seen a Hadza or Australian Aborigine wash anything.
      In a smoothie, I really don't even notice the taste of the dirt juice.Maybe a hint of earthiness which I now quite like.

      The dandelion root powder would be high in inulin wouldn't it? What else?
      And what about the grape seed flour, apart from the procyanidins? What spurred you to add them to the line up?

    9. Stuart

      Over the summer, we visited a farm. One of the farm kids was about 2, still in diapers. The parents were working nearby, but it was clear that it was the responsibility of a farm dog to keep him out of trouble. The kid was muddy from head to toe, as was the dog. In one of his hands, he had a chicken leg that he and the dog were sharing. It was a beautiful sight. And everybody was commenting on how wonderful the parents were to let the boy live, as well as how healthy the boy must be. I was surprised at the reaction of those around me - I would have guessed that someone would have been negative.

      Ashwin Patel got me thinking about seeds. Grape seeds were a natural part. It's impossible to find grapes with seeds, and even then the grapes are giant balls of sugar.

      I like to try to get my fibers from natural sources if I can. I had never even considered the possibility of dandelion root powder, but yes it exists. Just gonna try it and see if I like it.

    10. "Ashwin Patel got me thinking about seeds. Grape seeds were a natural part. It's impossible to find grapes with seeds, and even then the grapes are giant balls of sugar. "

      I once watched a very pretty blonde lady eating grapes from a vine. I said, "Wow! You grow seedless grapes!" She said, "No, they all have seeds."

      First time I'd ever seen anyone eating seeded grapes and not spit out the seeds!

      Also, when I lived in Korea, the locals all ate the entire apple, core, seeds, stem and all. I try doing both now. Even eating watermelon seeds despite my mother's warning that they will lodge in my appendix and start growing!

      I also use whole flax seeds in my Wilbur-esque concoctions. I'm sure gut bugs love eating at the hard shells.

    11. Hi Tim,
      You might be interested....apples seeds and cyanide - although the dose per apple is small ......

    12. I accidentally swallowed not one, but two small olive pits this past summer. I try not to think about it.

      One of my daughters-in-law is half Ukranian/half Lebanese, and grew up going back and forth between the two. She laughs about all the apple worms she has eaten, saying "how bad can they be, all they've ever eaten is apples. Have you ever seen what a chicken will eat?"


    13. Hey "C"! Yes, I have seen what chickens will eat! My chickens go crazy when they see me turning the compost pile because it means a shovelful of squirmy maggots.

      Apple worms, lol. People fight over the worm in a bottle of tequila! When I pick raspberries, I never look too closely at them before I plop them in my mouth. Aphids, spiders, bird's all good!

    14. Newbie - That's interesting about the cyanide, but maybe that's exactly WHY why should eat apple seeds. Microdoses of most poisons like that actually have a beneficial effect on the body. Homeopathy relies on it.

      My whole life I had been taught to never, ever eat the kernal found inside an apricot pit...a fair warning because we had an apricot tree and in the oldest, sweetest apricots the pit would sometimes split in two and you'd find an almond looking nut in the middle. Pure poison, they all said.

      Imagine my surprise when I was eating in a restaurant in Afghanistan, and there on the menu in broken English was 'Apricot nuts'. I thought for sure they were trying to poison us, so I ordered them. They tasted good, like nutty almonds.

      I looked it up on the internet and lo and behold there is a whole 'thing' to apricot nuts, and a huge conspiracy theory group saying that apricot nuts can cure cancer but the 'Guvermint" doesn't want us to know.

      Lots and lots is written about the cancer-fighting compounds in apricot seeds, and most end up mentioning the cyanide.

      Please don't run out and start eating apricot nuts, but there is lots of magic left in this world and some of it is undoubtedly in the seeds we discard.

    15. Re: watermelon seeds, my grandfather (who grew up on a Greek island) told me to always eat all the watermelon seeds. He said back home they told you eating watermelon seeds would ensure you didn't get worms!

      And re: apple seeds, my husband (and now son) have always, instinctively eaten the entire thing, core, seeds and all. I've seen no harm come to either as a result - and perhaps a lot of benefit!

    16. The cyanide content in apple seeds has always fascinated me. I've heard that there is enough cyanide in the seeds from ten apples to kill you and FURTHERMORE (lol) about ten (more lafs) people die every year worldwide from eating too many apple seeds. I've always wondered whether it would be a quick clean way to euthanize goats when necessary. No idea whether any of the above has a shred of truth to it.
      And as always the principle of hormesis is ready to through a spanner in the works of credulous alarmism like 'apple seeds are poisonous'

      Do you know how much fermentable fiber is in the grape seed and/or dandelion root flour. They're both clearly pretty potent for other reasons, but I'm just curious about the fiber factor. Seeds are usually high in glycans anyway , and tubers in resistant starch aren't they? I can get both quite cheaply here.
      Loved the image of the filthy toddler and his dog sharing a chicken leg

      Anyone know how damaging pharmaceutical anti parasitics are to gut flora? Or a good 'natural' antiparasitic. I want the microbiome benefits of dirt, but not the parasites.
      Maybe apple seeds?.

    17. Lauren,
      Oops, you'd already answered my question. Watermelon seeds. Probably Neem too. Are you reading this Ashwin? You'd know.

    18. I looked into the inulin content of dandelion a while back. For some reason, 20% of the weight is in my head. I might be wrong. I'm pretty sure the leaves are 12%, and the roots should be higher.

      The total fiber content for grape seeds seems to range from 25% for white grapes and 50% for red. I don't know how much is soluble though. I don't make it a significant part, about a tsp per day.

    19. Wilbur,
      Thanks. Grape seed 'extract' for the procyanidins is such a huge market. There's probably so much grape seed residue from that just wasted. And of course grape seed oil. I've started scavenging unsold seeded grapes from the local fruit store, juicing them, feeding the juice (as you mention pretty well pure sugar) to my garden, and eating the skin/seed residue. I've got so much of it now, even in two days. I'm going to try sun drying it so I can keep it.
      I found that the cheapest way to buy the dandelion root is from a horse feed supplier. Apparently it's very good for horses It's about AU $20 /kg that way, and both the root and leave/flowers are available. . How much did you pay?

    20. That an interesting way to approach the grape seeds. I think the stuff I bought are leftovers from wine making. The thing is that nobody around me sells grapes with seeds (I think seeded grapes have no seeds, like skinned fish has no skin - it's terribly confusing) on a regular basis. My kid would probably enjoy the grape juice.

      I paid about twice that for the dandelion root powder. I can get dried chopped roots for about the price you pay. I'm not sure if I want to go the horse feed route - I'm not sure how well they clean it for dirt and dung. I know you'd pay extra for that, but I'm still squeamish.

      I put some dried dandelion root in my tea today. Man, it gives me gas. Just like chicory root and sunchokes. I'm going to keep pushing it though.

    21. Wilbur,
      That's really interesting about the dandelion root causing gas. I've noticed that some things will cause gas withing seconds of eating them. And some actually seem to need to reach the colon first -so about 4 hrs. No idea what's going on with the first type of gas. Maybe some weird signaling pathway. The reason I know I'm not just imagining it is that it happens with those foods regardless of what I've eaten the previous few days. So it has no connection with what's actually in my colon at the time.

    22. Stuart,

      I can eat onions, garlic, and leeks by the truckload with no gas. But dandelions, chicory, and sunchoke give me bloating gas. Yacon can give me very loose stools. As much as I can recall, those are the only foods that really do much to me. I think maybe it is the short chain inulin.

      I can't think of anything that gives me immediate gas. But, hey, each of us is unique! I wouldnt doubt some sort of signaling.

    23. You know, this immediate gas thing is interesting. There must be a mechanism our body uses to 'fast-track' certain foods.

      Used to be, I'd eat Thai food, and within 20-30 minutes I was urgently voiding the contents of that meal, still identifiable. As the bowels control the amount of water contained within, it's probably a way to move threatening foods through expeditiously.

      So, maybe if you eat something that doesn't agree with you, your stomach and small intestine go into overdrive to get the offending food to your large intestine where it is quickly fermented by gut bacteria resulting in lightning-quick gas.

      When you read up on transit time, it supposedly takes 4 hours to get food from stomach to large intestine, but I am living proof that there are exceptions to that rule!

      Do you guys pick your own dandelions? I love the greens first thing in the spring before the flowers even appear. Also at that time, the roots are very sweet. As summer wears on, the roots and leaves get very bitter. As soon as I can spot dandelions in the spring, I dig up a few roots and start making dandelion green salads for the few weeks they are still good tasting.

    24. Tim,

      I was reading today that fall and Winter dandelions have the most inulin because they are storing energy. Spring less because they are growing. I've actually acquired a taste for the bitter.

      Someone somewhere mentioned that the contents of the intestine can flip-flop, so that what comes out might be in a different order than it went in. Unscientifically, I believe I have experienced this. And I've also had very quick transit times on stuff that did not agree with me.

      But, in recent times, things are terribly boring. No identifiers. Uniform Bristol type 4. I have no idea what corresponds to what, except this gas which is finally dissipating.

    25. @Stuart

      I don't know where you are in Aus, but at my local farmers market (Gold Coast) I have been able to get tree grapes (jaboticaba) which have very thick skins and massive seeds, as well as banyan tree nuts. Both are amazing.

    26. Lauren,
      G'day, I'm in Brisbane (Ipswich actually). And I have a young jaboticaba tree in my garden. I didn't actually know that it would eventually have tree grape fruit. It has lovely glossy leaves, and I really enjoy saying the word 'jaboticaba; - I call it my Star Wars tree.
      I''ve heard of fhe Banyan tree nuts, but never tried them.
      This is great. Andrea in Melbourne and now you on the Gold Coast. Soon we will be a critical mass of fiber ( or to you i should say 'fibre') hounds and we can split large bags of difficult to find in smaller quantity fibres lke Orafti HP , ;PHGG, and Actistar (85% RS3)

      Calling all Australian microbiome carers!

    27. Jaboticaba tree is wonderful, I have seen it in Brazil (where its origins are, I guess).
      Stuart I hope you pronounce it in Portuguese. Why Star Wars, anyway?

    28. Tim ,
      I've read quite a bit over the years about laetrile - the patented form of amygdalin, which is found in high amounts in apricot seeds.
      Here's an interesting piece about 'the rise and fall of laetrile':

      '.. Its place in history is assured, however, as a focus of political activities intended to abolish the laws protecting Americans from quackery.'

      The article also points out that laetrile has been carefully tested to see if it has any anticancer effect.
      But then, who can you trust?
      Maybe it's better to look after your microbiome and lessen your chances of getting cancer in the first place.

    29. Gemma,
      Jaba the Hutt. Tenuous I know. Do you speak Portuguese? Care to try to phonetically describe its Portuguese pronunciation? I can't wait to impress people with my worldliness.Portuguese sounds so exotic.

      Now I'll take even more care of my grape tree.

    30. @Stuart

      Only some Spanish, not Portuguese.

      jaba the hutt what?

      You can play and listen to the pronunciation here

    31. Okay, if the ground thaws out I'm going to dig up some dandelion roots for taste testing. @Tim, it is interesting about rapid transit times. I used to occasionally go to lunch with a Korean friend at a Korean deli, which according to my friend specialized in home style comfort food. One day a year or two ago, I was really hungry, and instead of my usual giant sushi type rolls I ordered the bimibop (however that is spelled). In fact we both did. I barely made it home, and was pretty well emptied out in a couple hours. Next time I saw her i asked if she was similarly affected, and she said no. It tasted very oily--not a good taste if you are used to paleo fats. Next time I was there I noticed the industrial size soybean oil containers on the way to the bathroom. I'm guessing that was the culprit but who knows. Another item that has done that to me in recent years was yucca (cassava). For a while we were making it for breakfast on the weekends. Took me a while to connect the dots on that one. Not quite as violent as the Korean episode, but bad enough. Maybe my haphazard cooking hadn't sufficiently neutralized the cyanide compounds. All this was before the introduction of all these extra fermentable substrates. It might be interesting to see if I would react the same way.

    32. Kate, how were you cooking the yucca? As I am sure you are well aware that you need to boil it even before you fry it or bake it.

    33. Gemma,
      Jabba (not my incorrect spelling) the Hutt was a huge fat thing in one of the early Star Wars films. It was actually a real puppet, not some creation of special effects wizardry like is used these days. There's photos on the Wiki entry.

    34. @Stuart

      A-ha, that lovely one... wiki says: "His appearance has been described by film critic Roger Ebert as a cross between a toad and the Cheshire Cat."

    35. So many wonderful creations. What an extraordinary imagination George Lucas has. Jabba's appearance really suited his thoroughly unpleasant off world feudal overlord status.

      What do you do with your goats apart from enjoy their company?

    36. Hi Stuart, just seen this:
      "Soon we will be a critical mass of fiber ( or to you i should say 'fibre') hounds and we can split large bags of difficult to find in smaller quantity fibres lke Orafti HP , ;PHGG, and Actistar (85% RS3)"
      Thant would be great!
      ... though even then oz is just so darn big.
      Wish we had out own version of iherb. Maybe it's a business idea. Set up a website selling powders for those in this part of the world.

      Anyway, I've actually had to scale back at the moment as some of the fibres seem to be giving me a candida flare. Weird.
      Got some PHGG on the way, plus some saccharomyces boulardii.
      Might stop the bee pollen in honey for a bit and just take the pollen.

    37. @Stuart Mather, That RS3 sure is difficult to source. I think it might be easier to figure out how to convert RS2 myself. There seem to be people focusing on combination products, but I prefer the single sources. I love the idea of individual buyers coming together to purchase these products. Run it like a crowd-funding operation (i.e. Kickstarter) and if the minimum price required by the manufacturer is met, dole out the fiber to all the people who contributed. Could start with a sample of the product, run it through adequate testing, then if it passes, offer it to interested buyers. Now if we only knew a potato obsessed student farmer from a far northern climate who has all the connections and knowledge to pull this off ...


    38. B,
      I think the biochemists at Cargill spent a lot of time working that one out. It's probably a lot more complicated than just heating and cooling the tapioca starch multiple times. Even if you retrograded it thousands of times you'd never get the RS 3 past about 40% . Actistar is 85% RS3, which as far as I know is the highest RS3 you can get.
      Penfibe RS is still manufactured in the U.S.(it is made from potatoes)
      But unless you can wrangle a sample out of them, you'll have to buy 25 kg.
      I think Richard Nickoley is doing his 'fart powder' all wrong. If he's buying all the powders in bulk, it would appeal to a considerably wider market if he just sold each fiber in minimum amounts, say 2kg. Anyone who is serious about their microbiome will use that amount of many fibers in a couple of years.
      But mixing it all up into one formula is, I think, a fool's errand. One formula will suit no one. I hope he makes a go of it though.
      But there is a HUGE market, right now, for fermentable fibers in bulk, but less than 25 kg lots. All somebody needs is a set of scales and a website.

    39. Andrea,
      Why do you think it's the fiber giving you the candida flare? I can still give myself candida flares by eating sugar of any type, even honey. And even with all the fiber I pamper my microbiome with, sugar will set me back in the Candida Wars immediately. That's why I don't even eat fruit. Maybe in a few years time I'll be able to eat sugar in small amounts. I've read so much and heard so much from Gemma here, that honey is different. But over the years I've proved to myself beyond all shadow of a doubt that as far as Candida Albicans is concerned, honey is first and foremost a license to run any other sugar.
      I'm even a bit careful with food fiber sources like baobab because they're relatively high in sugar.
      That's why I'm so impressed with PHGG, Orafti HP and Actistar, because they don't have any free sugars. There are many others of course like the gums mucilages agar, glucomannan etc. It really is very easy to pamper your microbiome and still completely avoid sugar. Which in my experience is the only way you will ever beat Candida. And the other important thing is that even that won't work in months, it really does take years. If you slip up, even briefly the Candida seems to emerge from wherever it's been hiding maybe biofilms, then when you stop slipping up, it just goes back into hiding How long can the malevolent form of Candida hide before it really does revert to the benign form Duck Dodgers talks about? I don't think anybody knows. But I do aim to find out. Ask me in a few years.

    40. @Andrea

      What fibers? I had Candida flares with spirulina, roasted chicory root, chaga and mushrooms. PS used to be a problem, but now it’s ok. Chocolate, fruits and occasional fruit juices are ok. Even sugar is fine in small amounts.

    41. B said: "Now if we only knew a potato obsessed student farmer from a far northern climate who has all the connections and knowledge to pull this off ..."

      Yeah, yeah...I'm working on it!

      On the Candida issue: It seems to me that the only real way to deal with Candida is to focus on your immune system, and not so much what is causing the flare-ups. Sure, avoid things that cause the flares, in the short-term, but it will be your own immune system that conquers the beast...not just starving it. Trust me, Candida is very patient, it can go much longer than us without food. And you really don't want to make it mad!

      It reminds me of a house with cockroaches. Clean up all the food crumbs and they will have to search for new foods...and soon they are everywhere in the house, not just the kitchen.

    42. @Tim - oh good lord yes! Candida=the great sleeper disease. You can kill it, but you cannot out wait it!

      You know, every time I've dealt with *any* kind of fungal infection I've been impressed at how damn hard it is to eradicate! On my roses? I had to be brutal with anti-fungals. When I first got my horse she had a terrible case of a skin fungal infection, and I had to disinfect EVERY stitch that touched her EVERY day, plus douse her in anti-fungal medication - for about 2 months. If I backed off even a little bit, the stuff came roaring back. (hilariously, once she was cured, I couldn't tell because her skin was still flaking, so I called the vet. He came out and laughed and said, "How did you kill it so fast? This horse doesn't have fungus anymore, she has the worst case of dandruff I've ever seen, from the drug drying her skin! Good job - you did it!")

      @Andrea - Tim's cockroach metaphor cracks me up, but it does remind me to ask - are you sure you're seeing a flare? or could it be the die-off effect of yeast dying as better bugs take hold? I know that whenever I do something that improves my health and the remaining yeast I cope with die off a bit, I get symptoms *of having* yeast - I mean, that's what symptoms amount to :P You're dealing with their daily life cycle in whatever part of your body they live.

      The other reason I ask, is that another aspect of that process (the process of winning over the little bastards, that is) is that they move from a central set of symptoms (gut) to a more peripheral set (vaginal yeast flare, athletes foot flare, skin flare). It's as if when you start conquering their stronghold in the body, satellite areas freak out and flare up. I can think of several reasons why this might be, but whatever the causal chain, it's very consistent in my body.

      Obviously some of the RS can/do feed candida and those of us struggling with candida should avoid them! But I'm definitely seeing straight up die-off effects from improving gut flora with nothing but good-bug-feeding RS & probiotics. I cheer every time a symptom appears & then fades - ha! Rooting you out even more, ya little bastards!

      I wish you luck in the struggle my sister! *salute of the kill-the-candida corps!*

    43. @ Andrea - I'm also giving saccharomyces boulardii a go, and so far really liking the effects. The nicest one so far would seem to be almost eliminating the die-off symptoms from all this good bug>bad bug. Since it tightens up the leaky gut (bad kind! we're calling this bad :D), this makes sense - the toxic crap isn't crossing over into the body. It's allowing me to be aggressive in continuing the good-bug restoration process, which suits me just fine. My boys (who have both dealt with candida at different times and both have food allergies galore) are also doing well with it. My husband is *really* liking that it's eliminated most of the edgy cranky feeling he'd been having (he's never had yeast issues or allergy issues, but remodeling the gut biome was definitely giving him some 'I feel toxic and cranky!' effects).

      Damn stuff is expensive for something that will not re-seed indefinitely though, grr. I really value that Prescript Assist & Probiotic 3 are establishing themselves - makes the $$ feel worth it, since I won't need to take them forever. But so far it's well worth taking for my little N=4 :) Looking forward to your report on the stuff!

    44. Tim,
      What do you think of Duck Dodgers observations that Candida albicans has a benign (and necessary) form and a malevolent form. Maybe killing all the ├žockroaches is the last thing you want to do. Because they''re not actually cockroaches at all. They behave like cockroaches in the malevolent form, but like angels in the benign form.
      Maybe thinking about Candida Albicans as cockroaches is oversimplifying it?
      Just eliminating it all may only create other problems.It's why I have always distrusted the whole idea of ''ántifungals' natural or pharmaceutical. They just seem to be addressing the issue simplistically.
      It's also why correcting gut dysbiosis immediately made sense to me (and I saw the effects immediately too) If your gut is on song,antifungals are kind of irrelevant. And if you don't get your gut on song, any number of antifungals will be unable to ever really solve the problem. Sure they might give you relief for a while. But your 'great business model' idea springs to mind when thinking about antifungals. .

    45. Stuart - I'm also very interested in this conversation and these possible re-definitions. Having gone the extermination route with nominal success (I exterminated EVERYTHING and destroyed my digestion....but by god the malevolent candida was gone *snort*), I'm *very* interested in the idea of creating such robustness and balance in the gut that it's ready for just about anything.


    46. Duck, Gemma, and I have been trading papers back and forth for nearly a year now, mostly on what makes yeast "tick." This needs to be a whole blog post, or a whole blog, dedicated to yeast, but let me just make a few points without any links to papers or any really big words. You can google anything I say here easily.

      1. Yeast is everywhere. Probably every breath you breathe in contains yeast in some form. If not yeast, then some form of fungus (and also bacteria and viruses).

      2. Your body has evolved alongside yeast, and normally it is no threat or problem. It lives commensally (is that a word?) inside and on you. It forms a part of you, known as your "mycobiome" and is just as important as your microbiome, or the bacteria in your gut. Yeast is somewhat of a guard-dog, possessing the ability to suppress bacteria and and other yeasts from turning pathogenic.

      3. When you die, the 'fungus among us' will turn your corpse into dirt. The once commensal yeast will transition into a new form, eat you and spread its spores when you are about gone.

      4. This same fungus sees a weakened immune system as a cue to prepare to turn you to dirt. Proof in this is seen by every doctor who cares for patients in an ICU. Invasive Fungal Infections are the #1 killer of ICU patients (OK, I made the #1 up, but it's pretty high, maybe #1). Generally, ICU patients are given antifungals in preparation for the fungal infections that are sure to come.

      5. You've heard of antibiotics resistance? Fungus (yeast is a fungus) also quickly becomes resistant to anti-fungals.

      6. We looked at a paper that showed that after a round of antifungals that cleared up a fungal infection, there were still living fungi hiding in organs, the pancreas was a stronghold, I believe.

      7. Yeast/fungal infections are very in tune with pH. When the pH of the body (or cavity) is correct, yeast just hangs out and does no harm...when the pH gets too high or too low, the yeast/fungi turn pathogenic and cause infections.

      8. Candida, and probably every yeast, has 4 or 5 (or more) different forms it can take, from a harmless single cell to a hairy monster (hyphal form). It can also lie dormant, but peek its head out occasionally, it can form a biofilm that is nearly impossible to eradicate.

      9. Candida and all yeast can breed in 4 or 5 different ways. It can (and I'm NOT making these words up) bud, bleb, and schmoo. It can reproduce sexually and asexually. It can split into two and cast off extra chromosomes that would kill any other creature.

      10. OK, here's the scary one...a yeast cell can mate with an animal cell and turn it into something that we all fear more than anything: cancer.

      So, what to do? Damned if I know. All we can do is not resemble a dying creature. No immunologically healthy person or animal has problems with yeast or fungus, only those displaying some type of weakness, and maybe you aren't even aware of the weakness.

      So, while the best defense is a good offense against yeast, what everyone really cares about is "How do I get this crap outta me?"

      I wish I knew. But I think we are getting close here. It has to start with boosting your immune system, which can be hard because the things we need to eat to boost our immunity, also causes flares of yeast.

      You can't starve it or kill it, we must have to trick it. Once it thinks you aren't dying, it will leave you alone, and probably even start helping you again.

    47. But if I were going to link a bunch of papers, I'd start with this one.

      Does the Immune System Naturally Protect Against Cancer?

      And I'd point out that boosting the immune system is the single most important piece in this crazy puzzle!

    48. Tim - FANTASTIC list of info! Very much corroborates the bits and pieces I've learned or discovered over the years - but so much more.

      For me the management strategy that has worked best over the years (during complete candida invasion *and* during post-destruction of all bugs with regular candida flares) has been pH management. My stomach acid is low (would love to see how that figures into the cause/effect of dysbiosis, actually), so for a long time I took HCL to correct it. That worked great, but obviously wasn't self maintaining.

      Using potato starch seems to have made my biome pH self-correcting - one less thing I have to worry about :)

    49. (the amount of information the 3 of you have been compiling & comparing amongst yourselves is amazing!)

    50. Tim,
      That''s intriguing, thanks. Looking back, I've had terrible teeth for most of my adult life from being absolutely addicted to eating masses of homemade acid yoghurt, making smoothies with also acid fruit- pineapple grapefruit (human taste buds seem to love acid, isn't it why food acid is added to just about everything?) So my teeth were literally awash with a sweet acid medium for decades.And although I was scary obsessive about brushing and flossing, the low grade inflammation created by that loss of enamel was something no amount of dental hygiene would ever contend with. And I inherited weak teeth from my father. I think my parents were also both in the grip of candida - very weird neurological /behavioural stuff, and constant thrush/ urinary tract infections, And none of my family has ever eaten enough fermentable fiber. So no wonder the candida thought I was dying.
      It probably still does, but now my microbiome is in much better shape, and the oil pulling is amazing.

    51. My Candida loves dairy and lactobacilli. When i stopped them things got really really better without antifungals and probiotics. My mistake with ps was to take it with milk and yogurts. Maybe it's hormones in my case... Fruits and honey don't give me problems.

    52. @Stuart - oh man, what a rough start for your gut biome (not to mention your kid-hood), if both parents were were so out of balance that they were both living with candida overgrowth! Pretty amazing that you're able to correct your flora even now :)

      WRT to your teeth, have you looked into the information on Vitamin K on freetheanimal? My husband has terrible teeth & gums (multiple root canals, threatened gum surgery etc.). He's seen improvements with Green Pasture butter/cod liver supplement in just a couple months of use.

      Among the many health issues my kids have, they have no teeth issues - they both have fantastic teeth. By the route of paleo diet sans allergens, it turns out they've booth had a high vitamin K diet....and there's no other explanation for their fantastic dental health, cause genetics & oral hygiene certainly can't be credited!

      It's certainly worth looking into as a way to help restore your dental health :)

    53. @Tim

      Nice paper, with a lovely quote: "Thus, it appears that our immune system does not only naturally protect us against infectious non-self (pathogens) but also against malignant self (cancer)."

      If they only started to think a bit, finally.

    54. Terra,
      I''ve never taken K supplements, but I've always eaten a lot of ghee and taken fish oil. I really like the idea of a restored microbiome becoming an onboard vitamin factory. I was interested to read Art Ayers cautioning against taking vitamin supplements (even D3) - that it slows down the healing process once you start the process of resurrecting your microbiome. Making your own vitamin K seems like a pretty good idea.
      The increased mineral absorption from a healthy colon is the other side of that vitamin factory coin. I suffered from night time leg cramps for ever (so do my two brothers) I took a lot of supplemental magnesium to try to address this, without any noticeable benefits. I did discover that topical diet tonic water (the quinine) stopped them immediately, but they were still very painful while I was reaching for the tonic water. But one of the most wonderful wins from the fermentable fiber is that the cramps have gradually become less severe and frequent I haven't had any for a few weeks.
      And I think my teeth are stabilizing. When you floss as deeply and thoroughly as I do, you can tell if your gums are inflamed deep down. And mine are starting to feel pretty good, even the dodgy interdental junctions.
      I'm sure it's the oil pulling as well as the fiber/vitamin k production.
      And my scalp, which has been flaky for as long as I can remember (since about age 3) hasn't flaked or itched for about a month. Amazing.really.
      When my father died, one of the things I couldn't help noticing was that his completely bald head was a mass of little flakes For about the last 2 years of his life, all he wanted to eat was jam and white bread. For some people the sugar/candida connection is very very powerful. He was a really skinny guy (like me) but he had a real sweet tooth. Never got diabetes though. And although I've been hypoglycemic my whole life until I started eating fermentable fiber, my pancreas has always been up to the job.

    55. "it lives as a commensal" - what a great post Tim, hats off to you! Your summary is inspiring, getting all of that information in a reasonable list.

    56. I second that, Tim. This should be a main blog post, not buried in the comments! I'd love to see more on this subject, if nothing else than for morbid curiosity. The main reason I am trying to turn my diet completely around is to boost my immune system and hopefully never get cancer.

      Until I started reading here, all I knew about immune boosters were probiotics, yogurt, and 'superfoods.' Nothing made any changes no matter how much or how long I took them. 2 months of potato starch daily has completely changed my health outlook. Getting more into fermented foods and other fibers now, also. I think potato starch is always going to be my go-to fiber, though. I must say I'm not loving inulin (or it's not loving me, lol).

      Good job on this blog, really fun to read and easy to understand without coming across like the know-alls on most other blogs. And no ads? Pretty cool.

    57. Tim,
      That study you linked to was great.. Not much joy there for big pharma though. Very dangerous thinking, this 'healthy human bodies are perfectly designed to recognize and prevent malignant tumors. What will our shareholders think if the anticancer pill just aint going to happen.
      ' ... In fact, a recent study suggested that autoimmune disease may occur as a result of an inaccurate antitumor immune response (103)"

      When you think that medical science is still very much in the infancy of understanding how gut health fits into all this, it makes for a very interesting next few years of research.

  24. Stuart, thanks so much for the information and all very interesting! So glad you were around to set me straight.

  25. Kate and other users of psyllium. Is it the whole seed I want or the whole husks? Thanks. SL

    1. I use mostly husk powder for convenience. I do have the whole seeds, and they have great taste. I'll grind some and put on food. Or I put the whole seeds in the blender when making my kid's smoothies.

    2. I've been using the husk powder, although I'd like to try the seeds.

    3. @ Stuart
      I would classify January as a good month. Fewer headaches and no big ones. I feel fairly certain the fiber is helping, but it is clearly not going to be a quick fix. Continuing is a no brainer however, since I feel so great otherwise.

    4. @ Wilbur and Stuart
      One of the things I noticed with even just potato starch, and it certainly continues with mega doses of fiber, is I never have to get up in the middle of the night to pee. I wonderful benefit IMO. Re eating soil, not ready to go their either, LOL. I have in the back of my mind the series Paul Jaminet did on cholesterol levels of Hunter Gatherers. I don't want to duplicate the high parasite load, although maybe I need a few parasites ha, ha. With regard to bathing, I used to be a shower every day type of person--really liked that squeaky clean feeling. That has been changing the last few months. Unconscious really. Seems like the more fiber I have the less I feel like showering. I'm down to once or twice a week. Not washing my dog covered hands that often either.

    5. Kate,
      It's great that the headaches are moderating I think the parasite apprehension is probably the main historical reason for our hygiene obsession. But I do think you are more likely to get parasites from your pets than from soil.
      I've wondered for a long time whether pharmaceutical anti parasitics - like the anti worm compounds we take and give to our pets - damage the gut microbiota like antibiotics. Does anyone know?

    6. How funny, I wrote a big long reply yesterday, but it seems that it never made it permanently onto the blog.

      I wanted to say thanks for all the replies and comments re candida. I have no idea what caused the flare, or even if it actually was candida, though I do think that it is actually working its way out of my body - which is good! Re-starting some of the probiotics and remembering to take apple cider vinegar in water has helped.
      I have scaled back to just acacia and mung bean at the moment. No real idea whether they ideal, just going on what I am reaching for.

      Probiotics do seem to help me a lot. I had die off every time I started a new one. But the again, my gut was a total car crash!

      So.... the million dollar question is.... how exactly does one boost one's immune system?

      Re teeth, I have horrible teeth too. I finally realised that I may have a low level infection in one of them which has probably been there for quite some time - not always so quick on the uptake over here! Anyway, I found that a good way to remineralise them is eggshells and comfrey. I've started on the eggshells, and waiting for a tea with comfrey in it to arrive.
      For those who may be interested, the tea is by Dr Christopher's and is called 'Calc Tea'. I'd never heard of him but he seems to have been an amazing herbalist. The Calc tea provides the body with absorbable calcium, and some have reported that their teeth remineralised so much that old filings fell out.
      Will definitely let you all know if that happens.

      Stuart, I think 2kg bags of each starch would be ideal. You can mix and match every day depending on what the bugs are saying.
      Who's gonna start a website???? :-)

  26. more on this from Chris Kresser:

  27. Wilbur, I was not following when you posted your information/lists/experiences. Would you please direct me to your posts from the beginning.

    1. That's hard to find! I did not find a search function for this blog, so I had to do a site-limited Google search. Luckily, I knew some terms that would narrow it down. Here is the post my comment appeared in

      Then if you do a page search on "amla" it should get you there quickly.

  28. I would agree with Tim on using the immune system to handle yeast. Plants have a hard time with fungal infections (think potato late blight or the French wine industry), but people only have a problems with yeast, if their immune system, the aggressive half, is underdeveloped. Since immune system development is dependent on specific gut bacteria, repair of the gut microbiota, i.e. both new bacteria and appropriate prebiotics, is the whole issue in fixing the immune system. Elimination of: yeast, food intolerances and autoimmune diseases, are all measures of gut microbiota repair.

    1. Thanks for adding your voice, Dr. Ayers - every bit of validation on this subject is welcome, because picking an approach to the issue is such a murky business :)

      Continuing with gut repair is about my only hope for healing chronic fatigue & food intolerances, so here's hoping I'm on the right path.

  29. Interesting... :-)

    Mapping the gut microbiome to better understand its role in obesity

    Several recent science studies have claimed that the gut microbiome—the diverse array of bacteria that live in the stomach and intestines—may be to blame for obesity. But Katherine Pollard, PhD, a senior investigator at the Gladstone Institutes, says it is not that simple.

    Dr. Pollard presented at the Obesity and Microbiome symposium at the AAAS Annual Meeting in San Jose, CA on Friday, February 13, 2015.

    Using powerful computational tools, Dr. Pollard and her team have reanalyzed several previous studies and revealed that there is no significant relationship between body mass index (BMI) and the types of microbes in one's gut. In fact, her lab found that there was greater variability in gut bacteria between the different studies than between the lean and obese individuals within each study.

    Instead, Dr. Pollard thinks that it is the genetic make-up of the different strains of bacteria that is most important. This is because the DNA in bacteria can vary wildly. For example, while the genomes of two humans may only differ by 0.1%, two strains of the same bacteria can vary by to 30%—similar to the variation between human and mice genomes! What's more, the differences in the bacterial genomes are often important pieces that are involved in metabolism or the processing of sugar and fat.

    Besides reflecting important functional changes in bacterial genomes, losses and gains of genes also affect genome size. When microbiomes are studied using metagenomics—sequencing their total DNA—differences in bacterial genome size can bias the estimation of the proportion of each gene in the sample. By developing a computational shortcut to rapidly estimate genome size using statistical modeling, Dr. Pollard's team has been able to improve the accuracy of microbiome studies.

    "It's not enough to say what type of bacterial species are present, because that doesn't tell you what they're doing," explains Dr. Pollard. "Since two strains of the same species can have such different genomes, you really need to know what genes are there and what role they play in order to link someone's gut microbiota to BMI or disease."

    1. Gemma, thanks for posting this. I'm trying to work through what it means for how I do things, assuming what I'm doing is correct (for me, at least). Maybe diversity of fiber leads to diversity of DNA, and so whatever DNA is needed by the body for health or repair is present and available for service. I've been thing diversity of species, but this (and Dr. Art) strongly suggest something deeper.

  30. @Stuart

    I was looking for info about the fiber content and traditional use of mesquite powder when I found this and thought of you. I suppose it might have been clay though.

    Cabeza de Vaca, traveling through either southern Texas or northern Mexico in the 1520's, is the first European to note details regarding the use of mesquite by Native Americans. While living among the Cuchendados, he observed the use of mesquite pods for food. A pit was filled with pods, which were pounded with a large wooden pestle the thickness of a man’s thigh. The pod meal was then consumed raw, along with handfuls of earth that had been mixed with the meal.

    1. Kate,

      That is fascinating! Have you tried mesquite? It has a fantastic taste. Half a teaspoon "covers up" a lot of the bad tasting stuff. My kid loves it in her fart milks.

    2. I've had some for awhile but I've hardly touched it. For some reason the taste doesn't appeal to me. I suspect it is one of those things I might grow to like. Right now I rely on baobop and a little maca to make my fiber cocktail palatable.

    3. @Kate

      Mesquite. Another useful legume (from Fabaceae)?