Anti-Inflammatory Diet

All health care starts with diet. My recommendations for a healthy diet are here:
Anti-Inflammatory Diet and Lifestyle.
There are over 190 articles on diet, inflammation and disease on this blog
(find topics using search [upper left] or index [lower right]), and
more articles by Prof. Ayers on Suite101 .

Sunday, October 5, 2014

Celiac, Gluten and Trypsin Inhibitor


Forget the gluten.  Celiac is caused by trypsin inhibitors (ATI) that were increased in wheat fifty years ago to combat pests.  Immune response to ATI spreads to include gluten and transglutaminase that perpetuates the disease.  Celiac is an unexpected consequence of traditional plant breeding that could be fixed with GMO approaches.

Plants Protect Themselves with Antibiotics, Pesticides and Trypsin Inhibitors.
Plants respond to pathogens and pests by making themselves toxic.  Thus, plants produce natural antibiotics, phytoalexins, a.k.a. phytochemicals, polyphenolics or antioxidants, to kill bacteria and fungi.  They also produce chemical pesticides and proteins, e.g. trypsin inhibitor, that block the digestion and utilization of plant proteins by insects.  One of these trypsin inhibitors makes ground soybeans inedible until it is removed in water rinses during the production of tofu.  Another of these trypsin inhibitors, in wheat, is the cause of celiac.

Plants Target the Nerves, Immune Cells and Intestines
Plants have evolved chemicals and proteins that attack and punish plant-eating animals.  A single molecule of caster bean toxin protein, for example, can kill a human cell.  Plants produce some of the most toxic molecules on earth.  The nervous system of insects and other herbivores is typically targeted by plants.  Many recreational drugs, e.g. opioids, THC, nicotine, caffeine, etc., for example, are made by plants in self defense.  Human nerves respond to these natural pesticides and the bitter taste and the vomit reflex help us to detect and avoid toxic phytochemicals.  Gluten proteins contain polyglutamine stretches of amino acids that resist digestion and bind to intestinal cells.  Seed lectins bind to the glycoproteins on the surface of the intestines and inhibit digestion.  Wheat seeds also contain an inhibitor of starch and protein digestion, the amylase/trypsin inhibitor, ATI.  ATI binds to the receptors on immune cells that trigger general inflammatory responses to pathogens, e.g. TLR4.  It is the ATI in wheat that starts an immune response to gluten and celiac.
Wheat trypsin inhibitor causes celiac and autoimmunity

ATI Increased to Make Wheat Resistant to Pests
More than fifty years ago, plant breeders began to screen wheat varieties for resistance to pests.  Breeding ultimately resulted in enhanced pest resistance that resulted from increased production of ATI in wheat kernels.  Modern wheat flour contains modest changes in gluten and other components over the last century with the singular exception of ATI, which has increased about 50 fold.  It is also interesting that ATI is a major wheat allergen.  This suggests that celiac starts as an allergy to ATI present in wheat flour.

Celiac Results from Superfine Milling of High-ATI Wheat
Wheat has been milled more and more finely to improve the shelf-life of bread flour.  The inedible bran and the germ are first removed from the wheat kernels and then the endosperm is ground so finely that the starch granules are broken.  Even "whole wheat flour" is ground in the same way and the bran and germ are simply added back to make it “whole.”  The important point here is that superfine milling results in starch that is readily digested by amylase in the small intestines, instead of acting as soluble fiber to feed gut flora.  The result of eating bread from superfine flour is that gut flora are starved for soluble fiber and the immune system is depleted of Tregs that would otherwise suppress allergy and autoimmunity.  Superfine milling of high-ATI wheat presents ATI to an immune system that is primed for allergy.

ATI is a Good Immunogen
Allergy development requires 1) inflammation, 2) an appropriate immunogen and 3) lack of Tregs (immune system cells that develop in the lining of the intestines and block allergies and autoimmunity.)  The modern milling of wheat flour eliminates a major source of soluble fiber, starves gut flora and reduces Tregs, but allergy development still requires inflammation and an appropriate immunogen.  An immunogen is a protein that will interact with cells of the immune system to produce antibodies and activate aggressive attacks.  I have found that all proteins of food or the environment, i.e. allergens, or of the body, i.e. autoantigens, that act as immunogens to initiate allergies or autoimmunity have the same sequence of three amino acids, a "basic triplet."  ATI has a characteristic basic triplet in its protein amino acid sequence and that is why it is a good immunogen to initiate allergies.

Allergy to ATI is Aggrevated by TLR Recognition of ATI
ATI enriched, superfine flour Is a powerful initiator of allergies, because it starves gut flora to block Treg production and is a good immunogen, but the immune system will still ignore ATI in the gut, unless inflammation is also activated.  Unfortunately, ATI actively stimulates inflammation of the intestines by specifically binding to TLR4, which is the receptor that also binds/recognizes the LPS of bacteria.  Thus, ATI is a way for the wheat plant to defend its seeds by triggering excessive Intestinal inflammation.  Inflammation, immunogen and Treg insufficiency is the ATI allergy trifecta.

Wheat ATI Allergy Leads to Celiac
First exposure to ATI and development of an allergy will make subsequent expose to wheat proteins more immunologically intense.  I discussed the response of the intestinal lining to gluten in previous posts.  Wheat gluten proteins are adapted to provide nutrients for growing wheat embryos and to provide defense against pathogens and herbivores.  Gluten proteins contain long stretches of amino acid glutamine, which is poorly digested by gut enzymes.  The glutamine is also converted into glutamate by the gut enzyme, transglutaminase, tTG.  Unfortunately, during the process, the enzyme is covalently connected to the undigested gluten fragments.  The allergic ATI reaction combined with gluten/tTG conjugates, leads to presentation of the gluten/tTG to the immune system and antibody production agains both gluten and tTG.  Subsequent exposure to gluten results in the autoimmune disease of celiac.

Celiac is Self-Perpetuating
The aggressive immune attack on the intestines in response to eating gluten-containing grains, is bad in itself, but it also causes a series of related autoimmune diseases.  Attack on the intestines also disrupts the development of the lining of the intestines, which in turn disrupts the community of bacteria and fungi, gut flora, that are essential for digestion of plant polysaccharides, soluble fiber, and the development of the immune system.  Gut flora dysfunction results in vitamin deficiencies, food intolerances and autoimmunity.  Thus, celiac is self-perpetuating, because it causes inflammation, immunogen presentation and Treg deficiency.

Celiac Causes Numerous Autoimmune Diseases
Celiac is often associated with other autoimmune diseases, because it causes them.  Antibodies to tTG are diagnostic for celiac and the autoimmune attack on the intestines is mediated by anti-tTG antibodies.  But anti-tTG antibodies of celiac don’t just attack the intestines, they attack any other tissues that have tTG, such as the thyroid gland and hair follicles.  Thus, it should not be a surprise that celiacs are at high risk for autoimmune disease, e.g. Hashimoto’s thyroiditis, of the thyroid gland, including both hypothyroid and hyperthyroid diseases, depending on which region of the thyroid is attacked.  Some forms of hair loss, alopecia, are also initiated by autoimmune attack on the tTG in hair follicles.  Persistent exposure of celiacs to gluten will result in a cascade of autoimmune diseases as other body antigens are presented to the immune system and tissues with those antigens are targeted and attacked to produce arthritis, vitiligo, etc.

Pest Resistance, Plant Breeding and GMO Solutions
Genetic modification of plants occurs every time seeds are planted.  Traditional plant breeding by selecting desirable individual plants grown from crosses of selected parents is one form of genetic modification.  Specifically introducing desired genes using recombinant DNA techniques is another, more controlled method.  Traditional plant breeding has systematically destroyed the diversity of crop plants by loss of genes that are not selected, but even the traits, such as pest resistance, that provide benefit, have also brought unintended consequences.  We now have grains with many desirable features of high yield and disease resistance, but they also provide increased risk of celiac, gluten intolerance and associated autoimmune diseases.  Maybe it is time to consider GM techniques as a safer alternative to fix modern wheat and to examine milling approaches to save our gut flora.

Cure for Celiac and Autoimmunity

Celiac and other autoimmune diseases are perpetuated by the presence of the corresponding autoantigen/allergen, in this case tTG and gluten proteins, and a deficiency of Tregs.  Oddly enough, some pathogens (Helicobacter pylori) and parasites (Helminth worms) stimulate Treg development in the lining of the intestines, in addition to normal gut flora, Clostridium spp.  It may be the relative absence of pathogens and parasites in affluent societies that reduces Tregs and enhances the incidence of allergies and autoimmunity.  Antibiotics and the antibiotic activity of pharmaceuticals in general may also contribute to Treg deficiencies by damage to gut flora.  Clearly, the repair of gut flora and reestablishment of the associated immune system will go a long way toward curing autoimmune diseases such as celiac.  Celiac, however, provides the added complexity that it damages the ability of the intestines to maintain a functional gut flora.  Thus, the cure for celiac would require simultaneous repair of both the gut and its flora, e.g. by a  fecal transplant and supportive diet containing numerous soluble fibers to which the donor flora have been previously adapted, i.e. lacking antigenic triggers.


Anonymous said...

Wasn't celiac disease known prior to 50 years ago? I always thought the connection with bread/gluten was discovered in the Netherlands during WWII.

Would older, less modified forms of wheat such as spelt contain less ATI?

Raj said...
This comment has been removed by the author.
Anonymous said...

Eggs are nutritious after unraveling the protease inhibitors by cooking. Soy can be consumed when processed to remove trypsin inhibitors. Lectins in beans can be heated and eaten. What about wheat?

Tucker Goodrich said...

Color me skeptical...

"Wheat amylase trypsin inhibitors drive intestinal inflammation via activation of toll-like receptor 4"

Submitted: 22 December 2010 by Detlef Schuppan.

Patent: "Methods and compositions for treating celiac disease; US 20130266584 A1"

Priority Date: Apr 29, 2010

Same authors as article above...

Anonymous said...

Dr Art
What would be your take on Wheat Grass shots, similar scenario, already have the bad ingredients but in a higher concentration .

Many Thanks for your commitment to real health

Smith Jones

Dr. Art Ayers said...

Celiac is old, but it was previously much less common. I am trying to figure out why wheat is becoming less healthy. Gluten hasn't changed much, but amylase/tryspin inhibitor, milling and bread production/processing have changed a lot. Antibiotics, food processing and diets have also changed. So the major factors in increased celiac seem to be ATI, milling/processing of wheat and damaged gut flora/inflammation.

The fix for celiac/gluten intolerance is more difficult than for other autoimmune diseases, but is still repair of diet, gut flora and wheat/processing.

Older wheat has less ATI, so won't initiate celiac as intensely, but the remaining gluten will still maintain celiac.

Thanks for your comments/questions.

Dr. Art Ayers said...

Hi Raj,
I am amazed that every time there is a new plague that the medical industry persists in only developing patent medicines. What dietary and life style adjustments provide protection? Were all smokers resistant to flu? Will a nicotine patch prevent ebola? Are all paleo people spared?

It seems to me that there is a real need for crowd sourcing and health hacking to find real solutions to health risks, since medicine is unconcerned with the cause and cure of diseases.

It should be obvious whether heparin (or aspirin or nicotine, etc.) has an impact on ebola, but I could only speculate. Do people with high chronic inflammation have an increased risk? We could ask the same questions about food poisoning or each years' flu. Doctors are simply not looking at patients or their health histories, except to match them with drugs. They have stopped giving diet advice, but if asked they wouldn't have current info. The studies show that doctors are out of date.

What's not to like about tiger nuts?

Thanks for your comments.

Dr. Art Ayers said...

Processing of wheat can't make it safe, because the major toxic component is the gluten proteins themselves. They are plant proteins from seeds and there is adaptive advantage to plants to make their seed proteins dangerous for seed eaters. Plants are not naturally safe to eat and people are fecund, because they develop methods to detoxify plants.

Wheat may have been successful, because it provided the chronic inflammation needed for people to survive the diseases that would otherwise rapidly spread and wipe out large groups.

Thanks for the question.

Dr. Art Ayers said...

Thanks for stopping by.

I think that the patent is kind of silly, because it is designed to block ATI initiation of celiac, but the cure for celiac requires blocking the response to gluten and autoantigen, tTG. After celiac is established, ATI is not important and anti-ATI antibodies don't matter. Gluten proteins are much better at jamming digestion than commercial Abs would be at blocking seed proteins.

Thanks for providing the references, even though it colors me a little casual and retired.

Dr. Art Ayers said...

Smith Jones,
I don't see any benefit to grass shots, but if you enjoy them, then I assume that your gut flora will adapt to tolerate them. I evaluate food on the basis of nutrients for me (fat, protein, modest starch), soluble fiber to feed my gut flora and avoidance of phytochemicals. All the rest is the pleasure of preparing and eating the meal. The last meal that I had was a grilled, thick, grass fed steak with melted blue cheese, yams, kale chips and wine. I enhanced the browning of the rare steak by leaving on all of the fat and brushing it with honey and soy sauce. I don't see where grass shots would fit.

Thanks for you question.

yulotid said...

I was tested for anti-ttg a few years ago and came back positive in the 50s (<20 is normal). However, my biopsy was normal and I don't have any of the autoimmune diseases that you mentioned. What do you make of that? I've been avoiding gluten ever since just in case and I don't think that makes me a quack!

You might also find it interesting to note the following other tests were positive: anti-VGKC, anti-SSB, and anti-GAD65. They all disappeared after going gluten free/paleo and starting CPAP.

Raj said...
This comment has been removed by the author.
Tim Steele said...

I'm going to be in NCBI all week, does your theory on basic triplets apply to wheat proteins?

Got a list of suspects you want me to frisk for triplets?

Mike said...

In regards to autoimmunity, you mentioned a fecal transplant as silver bullet. The idea intrigues me as a person who has been given numerous courses and antibiotics and has some lingering issues from having taken them. I don't have any hangups about it and can see where in theory the results would be remarkable. From what I understand the regulation behind them is so strict you can only have done in you have a c. difficile infection...and even then many doctors are unwilling to go that route. Seeing then as it's unlikely, what is the alternative for someone short of a fecal transplant? Is there really any hope?

Thanks, Mike

chasbari said...

Is any part of the mechanism for celiac related to increased glyphosate residue on processed/milled wheat and the potential disruption it may evoke on gut flora? I know that when I was working on restoring gut flora post DX for celiac that I could not tolerate antibiotics in any form whereas when I was still eating wheat products pre DX there were times when a course of antibiotics would settle things down for a short time even when it was triggering much more in the way of other autoimmune complications like RA flares.

Dr. Art Ayers said...

I was just watching a Nova program on Ebola. They used antibodies against the Ebola spike proteins to treat the patients in the US and UK that recovered.

You should check the spike protein for basic triplet or two basic pairs in proximity, since those structures would make the proteins interact with the heparan sulfate circulation system and explain how Ebola gets into cells. It might also indicate if some heparin treatments might work against Ebola.

That fact that it was easy to raise antibodies against the spike proteins also suggests that they were presented to the immune system via a basic triplet.

Have fun with bioinformatics.

ME said...

Dr. Ayers,

On 6 October you said this: "Wheat may have been successful, because it provided the chronic inflammation needed for people to survive the diseases that would otherwise rapidly spread and wipe out large groups."

Could I get a better explanation of this statement? Are you saying wheat was a successful food crop (i.e. didn't kill off wheat dependent societies) because the allergic reaction (chronic inflammation) in the wheat-eaters kept infectious diseases at bay, allowing them to reproduce more successfully?

If this is the case, how does it not contradict thinking within this branch of the health community that chronic inflammation makes you more susceptible to disease?

Also, if the above "keeping at bay" model is the case, what is the mechanism through which this happens?


Dr. Art Ayers said...

I conveniently divide the immune system into aggressive and suppressive halves. The aggressive half is needed for control of pathogens and the suppressive half prevents attack on self and food. Wheat enhances the aggressive and provides protection against infectious diseases, whereas the suppressive half is needed to prevent autoimmune disease and allergies. Inflammation stops infection, but promotes modern autoimmune diseases and allergies. Eating wheat does the same thing.

Inflammation enhances all of the defenses, e.g. reactive oxygen species, offloading of lymphocytes at infections, activation of neutrophils, antibody production (the inflammation transcription factor is NFkB, nuclear factor for B cell production of the light, k, chain of antibodies.)

Inflammation requires a lot of energy expenditure, but wheat provides a lot of starch/glucose.

Thanks for the question.

Dr. Art Ayers said...

I don't buy into glyphosate as a practical problem. I doubt that there is much around wheat, since it isn't yet a GMO plant.

I think that the natural toxicity of plant phytoalexins as antibiotics is more significant than herbicides/pesticides, so I never worry about glyphosate in food or even GMOs. Trans fats, vegetable oils and processing to remove soluble fiber are much more serious.

The antibiotic activity of common drugs, e.g. statins, acid lowering, antidepressants, etc., is much more harmful to gut flora and is the actual cause of multiple drug resistant superbugs.

So don't worry about glyphosate. Worry about wheat and any drugs/supplements that you take.

Thanks for the questions.

Dr. Art Ayers said...

Repair of gut flora is, in my opinion, the most important public health issue in medicine today. Unfortunately, no one has found a way to make money using freeze dried feces to cure disease. It is literally possible to replace a million dollars in medical treatment with a hundred dollars worth of poo pill. The medical industry essentially refuses to study it and without study there is no regulatory approval.

In the mean time, I think that we have to get beyond the pill and start thinking again about the normal course of gut flora acquisition. Normally we get a starter set of "dairy" probiotics with mother's milk and when we have teeth, we start to eat crushed veggies. Many mothers continue the time honored practice of premasticating food for toddlers. That chewing transfers the mothers gut flora to the kid with the result that a new adult gut flora gradually takes over.

Starting as an adult with damaged gut flora, it is harder to fix. It is just as difficult starting with formula, which systematically produces an inflammatory gut flora. Fixing requires continual exposure to new bacteria that can take up residence in the gut. Most of the bacteria that grow on simple sugars, e.g. lactic acid bacteria, that are present in fermented foods, can provide some of the benefits of a healthy gut flora, but the desirable bacteria are those that grown on soluble fiber. So what is needed are the bacteria that would digest the soluble fiber of fermented vegetables into mush. So we need some fermented food recipes that are therapeutic for gut flora.

See my other posts for more ideas on repairing gut flora. There are also links for DIY fecal transplants.

Thanks for the questions

Mike said...


Thank you for the response it was much appreciated. I am in total agreement- the practicality and convenience of the poop pill make it a very attractive treatment- for that reason it's why I see it largely remaining "underground". It is sad to know that something which could revolutionize and do so much good for people suffering is kept from them, at least in a clinical setting. As you had mentioned, it would be cheap to administer and would massively cut into the millions of dollars of profit to be made by keeping people sick. That in itself, is the issue that I see and have come to realize as I've gotten older.

One thing I'd like to ask about is the diverse range of bacteria that is contained within a healthy person's gut. Do you feel the individual is more or less born with that diverse range or they simply acquire it? I've heard different opinions with some saying it is acquired as the baby grows and is exposed to different sources (people, playing in the dirt, etc.) while others say when the baby is born it is transfered from the mother (vaginal birth). Not every child is born vaginally and grows up to be fine. In either case, it requires a long time for the childs immune system to evolve so I see improving one's gut flora as a constant, daily endeavor.

I've begun incorporating some of your principles- I do have my own small plot of land where I grow some different types of vegetables ilke carrots- I've been uprooting them and eating them dirty. I've also been incorporating different types of fiber/starches and using probiotics supplements like prescript assist and aor probiotics 3. I'm not sure what other good one's there are but I'm going to use these for a while while incorporating a lot more dirty vegetables. The soil is very diverse- I often wonder how much of the bacteria found in soil resembles the species found in the gut? If the bacteria found in the soil is not transient and can permanently colonize this could be a big help. I've also been playing around with the idea of a fecal transplant- seems like that would be the effective, short term solution.


Dr. Art Ayers said...

You bring up a lot of important points.

Gut flora in a newborn is derived from placenta, vagina and breast milk. Normally the new gut flora is related to the mother's mouth flora via ? The breast milk quickly converts the baby's gut flora to milk-selected bacteria that provide most of the bacteria to gut communication for development of the baby's immune system. The milk flora is related to typical dairy probiotics for obvious reasons. Adult gut flora bacteria do not survive in the milk dominated baby gut.

Formula or solid food provides an advantage for adult gut flora to grow. A single bottle of formula is enough to convert milk flora to adult gut flora and those adult gut flora quickly inactivate many of the benefits of breast milk. There is a big difference between exclusively breastfed gut flora and exclusive + one bottle of formula. The only reason that babies can survive on formula is because formula gut flora are inflammatory. (See my discussion of wheat and cities.)

The rapid shift from milk-flora to adult gut flora after a baby's addition of solid food. Clearly, these new bacteria did not come from the baby's prior history and were derived from the environment. That's why everyone kisses babies, including the dog and the floor, to provide needed gut flora diversity.

It is silly to think that vaginal, breastfed babies and Caesarian, formulafed babies are the same or fine. They are quickly normalized by exposure to antibiotics and processed foods that harm the gut flora, but they are not the same.

Dairy probiotics are expected to be transient, but other probiotics, soil bacteria (modified in gut) and fecal transplants are as permanent as gut flora can be. In many cases gut flora are seen to be temporary, because diets were not altered along with the new gut flora. Also transplant recipients fail to understand that most pharmaceuticals have profound impact and act through changes in gut flora, since they have profound antibiotic activities.

Thanks for the thoughtful questions. (Many of the subjects are also covered in my other 200 blog posts.)

Sabrina said...

Dr. Ayers,
I have been reading your blog for years, and have a great deal of admiration and respect for you and your work. Thank you for all the valuable research and information that you have provided to your readers.

I have a story to share. I am a 38 year old mother of three who was diagnosed with Celiac 6 years ago just after my third pregnancy. I have been on a strictly gluten free diet since my diagnosis, and was on the SCD and GAPS diet for three years. While my symptoms improved somewhat, I still had frequent bouts of diarrhea, and what I now recognize as mild anxiety. My stomach always felt terrible in spite of all the probiotics and supplements that I tried. I started to read about fecal transplants and made a mental note to try one at some point.

In April of this year, after experimenting with some dairy, I ended up in hospital for a week with severe inflammation of the colon. My physicians said that I had C difficile and pumped me up with three different types of antibiotics as well as heavy doses of steroids. I had read that C difficile was almost impossible to eracdicate once and for all with antibiotic treatment. I talked to a GI specialist who promised to help me do a fecal transplant since it is approved by the FDA for C difficile. After 4 days they repeated the C difficile test (this time a more sophisticated kind) and said that they could find no evidence that I had ever had the infection.

I was devastated because this meant that I had received all those gut flora disrupting antibiotics for no reason, and that I would no longer be eligible for a fecal transplant.

When I was discharged from hospital, I was very depressed and still very, very ill. I had lost 20 pounds, had severe diarrhea and was so weak that I kept falling when I tried to walk. I was desperate to get back to caring for my children. I told my husband that it was time to try a DIY fecal transplant. I had hit rock bottom and things could only improve or stay the same.

We did a fecal transplant that night following instructions from the Power of Poop website. My wonderfully supportive husband was the donor. I retained the transplant for 6 hours overnight. Within 18 hours, I felt that my digestive system had been transformed. I had NONE of my previous symptoms. Three weeks after the transplant, we went on vacation to Boston and NYC, where I walked for miles each day, and ate out at all kinds of restaurants regularly.

It has now been 6 months, and I am still symptom free. I only wish that I had done the fecal transplant years earlier. It has changed my life.

Kiran said...

I thought you might be interested in this..

yulotid said...

Is a fecal transplant really necessary? The problem with pills is that it's hard to get enough bacteria in number to displace the indigenous strains. A long fast should solve this problem, preferably followed by a good set of pre and probiotics for some time. I would think that intermittent fasting would be a great way to keep pathogenic bacteria in check on a routine basis as well, just as it keeps cancer and cariogenic cells in check. It's pretty amazing but the vast majority of humans on this planet haven't gone more than 1 meal without eating in decades! Not just that but those meals are also typically high in refined carbs.

Jana Snyder said...

I just discovered your website, and I'm encouraged by the science and sense I find here! I'm wondering, though: is there one post that summarizes your approach to diet? It's pretty easy to pick up on what you're against, but it seems like it could take hours to sift through all these thorough posts to piece together what your affirmative recommendations would boil down to.

Dr. Art Ayers said...

The standard, non-mobile, version of my blog has a link to my Anti-Inflammatory Diet, which is just an outline of one easy approach. It is just a typical paleo diet of meat/fish/eggs and vegetables. Since most people who search for control of inflammation and associated diseases will also be deficient in vitamin D, because inflammation blocks solar production, I also recommend getting your vitamin D serum level measured and check to see if supplementation actually works by remeasuring.

The major point of the diet is to eliminate grains, vegetable oils and processed foods that don't provide soluble fiber to feed gut flora. Paleo is the easiest approach, but other diets will work if the appropriate gut flora are also established. There is no point to a new diet, if corresponding new bacteria are not added to the gut for adaptation.

Most people also need to repair their gut flora to suppress autoimmune diseases, and I have several posts on gut flora fixes.

I hope this helps.

Dr. Art Ayers said...

I agree with your perspectives. Most people can completely repair damaged gut flora and reverse inflammation associated diseases, but it takes a lot of persistence. Fecal transplants are remarkably successful for curing a broad spectrum of diseases.

Lamentably fecal transplants are still awkward. Frozen or freeze-dried fecal capsules make it a lot easier, but you are correct that it is difficult to displace a whole existing gut flora. Previous protocols knocked out or destabilized gut flora with antibiotics, but that has obvious disadvantages. Other difficulties were presented by not immediately shifting to a new diet that supported the history of the donor gut flora, or by continuing use of any drugs, since most pharmaceuticals have high antibiotic activity.

It seems to me that using a PEG-based total bowel irrigation would be a good prelude to fecal capsules.

I wouldn't expect routine fasting to be helpful, because recent studies show that changing eating patterns destabilizes gut flora. Fasting would however be useful prior to a shift to new gut flora. Whey protein might also be helpful, because it natural destabilizes adult gut flora in favor of dairy probiotics.

Most probiotics, e.g. dairy probiotics, are not established in the adult gut, even though they may temporarily provide some of the benefits of an authentic gut flora.

I think that it is informative that the medical industry refuses to study ways to repair gut flora with combinations of diet (non-glycemic fiber) and sources of new gut flora, e.g. homemade fermented vegetables. All they recommend after antibiotics is bandaid dairy probiotics that they know fail at repairing gut flora. Clearly, their business model is based on maintaining damaged gut flora, inflammation and vitamin D deficiencies. Fixing gut flora on a large scale would decimate the medical industry.

Thanks for the comments and questions.

Missy said...

Dr Ayers,

First I want to thank you for your valuable time and information you provide.

I am female in my early forties. Last year I started getting some autoimmune sx (arthralgias of my fingers) cold feet and my ana was checked and was nucleolar positive. Further tests turned up positive Scleroderma antibodie(s) (yes 2). However the rheumy said because I have no raynauds or rashes or skin sx that he will wait and see.

Telling me this may never turn into a full autoimmune disease and so I do not have a diagnosis.

I have visited np's as well and they suggested to start on minocycline abx and ldn. I have not done that.

I am trying to head things off at the pass though and turn things around so I am not diagnosed with a full disease.

I eat pretty much in tune with PHD. No gluten. I eat rice and potatoes. I have read voraciously on your diet recommendations and think I would like to add Neem (as touted by the brilliant Ashwin Patel) Probiotic 3 and rs in the form of rs3.

You mentioned adding a soluble fiber as well. Psyllium good? I could add this to my coconut oil smoothies if so.

Anything I'm forgetting?

I do not want to do anything at this point to turn my early sx into a full blown disease and so would LOVE your advice if this is a good way to go about fixing myself.

All the best.


Dr. Art Ayers said...

Health = diet + gut flora adapted to diet + exercise + sleep

You seem to have mentioned diet and probiotics. The diet should include basic macronutrients plus food for your broken gut flora, soluble fiber, aka non-glycemic fiber. RS3 fiber is one type of fiber, but I wouldn't recommend just eating the processed fibers, when you can get them in a better form in fruits and vegetables. All of the polysaccharides in plants are potential fiber for your gut flora.

You mention a couple of probiotics, but those are only temporary fixes. Your symptoms indicate a major loss of species diversity in your gut flora, normally associated with antibiotics, pharmaceuticals, processed foods and constipation. You have to go beyond probiotics and introduce dozens of new species of new bacteria not present in probiotic capsules. I have several posts on the topic.

You are almost certainly deficient in vitamin D with your level of inflammatory symptoms. Test, supplement and retest.

You haven't mentioned omega-3s.

All of the antibody tests just show that you have some inflammatory destruction of connective tissue with presentation of typical nuclear antigens. The problem is ongoing inflammation and a deficiency in Tregs due to your damaged gut flora.

You need to find the source of your inflammation, e.g. diet, dental, infection, etc. If you fix that and repair your gut flora to regain your Tregs, then you should see a decline in nuclear associated antibodies and an elimination of your autoimmune diseases.

Taking antibiotics will block some of your symptoms by ruining the rest of your limping immune system. That doesn't make sense, but it is a typical medical approach to addressing symptoms and making sure you are not cured.

Thanks for your questions. Let me know how you do.

Missy said...

Thanks Dr Ayers,

I am vit D deficient and will start to supplement. Is low vit Da source of inflammation?

I will also implement omega 3's.

You said, "The cure for many allergies and autoimmune diseases is just to eat a couple of tablespoons of resistant starch each day and if needed, supplement with probiotics containing Clostridium butyricum."

So this would be a start but not all that's needed correct?

Also is this what you were talking about when you said I needed to introduce other sources of bacteria?

"Sources of Bacteria to Repair Damaged Gut Flora.

We must eat new bacteria in order to replace bacterial species lost by antibiotics or unhealthy diets.

Probiotics -- specialized bacteria that grow in milk products

Spices and herbs -- plant products abundantly contaminated with bacteria that digest plants

Fresh vegetables -- bacteria are on the surfaces of plants unless the vegetables are cleaned or cooked

Fermented foods -- Bacterial growth leading to acid or alcohol production has been used in the preparation and storage of many foods and provides a rich bacterial resource.

Environment -- Bacteria are transferred to our hands and face from other people, pets and surfaces, unless hands and the body are continually washed. Sanitizers and frequent washing of hands and surfaces eliminate acquisition of environmental bacteria to repair damaged gut flora. Social isolation and hygiene block repair of gut flora.

Replacement -- experimental replacement of damaged with healthy gut flora (fecal transplant) has been very effective in curing many diseases without significant risks, but is restricted by the medical industry."

Am I on the right track now?

Thank you so much.

yulotid said...

Wouldn't supplements have an antibiotic effect on the gut as well?

Vitamin D isn't exactly found in large dense quantities in natural foods and where it appears it tends to come with fiber and other nutrients. If large doses are toxic to complex multi-cellular organisms like us, then I can only imagine how a simple bacteria would respond.

Greg said...

Yulotid, as I understand it vitamin D toxicity in humans is due to the absorption of too much calcium. The problem is hypercalcemia, not direct toxicity of vitamin D. I doubt that will be an issue for the gut flora, so unless vitamin D affects them by some other mechanism, I wouldn't expect supplementation to adversely affect gut flora. Also, Chris Masterjohn has argued that adequate vitamin A and vitamin K2, especially the latter, protect against vitamin D toxicity.

Unknown said...

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raphi said...

Hello Dr.Ayers,

Your ATI initiation hypothesis is interesting. I'd have to think about it more & reconcile it with Fassano's gluten-zonulin-occludens hypothesis that stands stronger every time it is tested. Do you see yours & his as mutually exclusive or complimentary? Or neither maybe...

Concerning glyphosate - sorry to be blunt but I think you are completely mistaken regarding its' purported safety. Please review some of Dr.Seneff's (MIT) articles on the matter here Alternatively, you can find many of her lectures/presentation on YouTube quite easily. Her background in computer science & lack of entrenchment within conventional medicine makes her a fantastic source of scientifically sound information regarding GMOs, vaccines and diet.

Thought provoking post!

Dr. Art Ayers said...

I see my views on celiac to be complementary with the zonulin models. Note that zonulin is a heparin binding protein and deficiency in heparan sulfate proteoglycan results in protein losing enteropathy that is readily treated by heparin therapy. This all fits into a broader vision that includes HSPG circulation and many heparin binding events. Also note that inflammation and its impact on vitamin D are also involved, e.g. the receptor for vitamin D controls intestinal defensin production in villi crypts and of course the antimicrobial peptides contain heparin binding domains.

All of the interrelationships make celiac a complex topic.

I don't find Dr. Seneff's arguments persuasive about GMOs or glyphosate. There is just too little science and too much speculation. After reading hundreds of articles and being knowledgeable about the science, I do not hesitate to feed my family GMOs that have been treated with glyphosate, but I do avoid all pharmaceuticals (most are potent antibiotics), wheat, vegetable oils, trans fats, and processed foods with diminished soluble fiber. Most processed foods are more unhealthy than environmental toxins, so I don't worry about GMOs. Unfortunately, the benefits of organic vegetables are not significant, which confirms that toxins are not a big worry.

The bottom line, is that sticking to a simple paleo diet of meat, fish, eggs and plenty of veggies (not to clean) and saturated fats, instead of vegetable oils, is a simple, healthy diet. All that is needed with that foundation is adapted gut flora, sleep and exercise. Beyond that don't worry, be happy.

raphi said...
This comment has been removed by the author.
raphi said...

Thank you for expanding on other factors contributing to celiac aetiology. I'll take a look at HSPGs - any 1 paper you strongly reccomend?

The GMO topic is so vast that a 'yes' or 'no' position for me is untenable. I would eat some GMO foods, some I wouldn't. It'd also depend in which country I was and on my state of health. Regardless, I believe we should genetically modify organisms to our advantage. Your point about 'oversold organics' is well taken. I do try to eat organic but under no illusions of it being vastly superior. Most for encouraging local farming, non-monocrop practices.
The problem with GMOs I am more confident about is the disastrous farming practices that go hand-in-hand with current application of GMO technologies & mono-crop agriculture. Lets put this aside for a moment though.

I am not sure if the btToxin-plasmid is transmissible via horizontal gene transfer to our eukaryotic cells. I remain unconvinced by the technical arguments on both sides. However, the general precautionary principle (touted by Nassim Taleb) forces me to acknowledge the following:

1) we have recently shown inter-species vector exchanges to occur despite previously thinking this could not happen.
2) 'Maternal & fetal exposure to pesticides associated to genetically modified foods in Eastern Townships of Quebec, Canada' saying "To our knowledge, this is the first study to highlight the presence of pesticides-associated genetically modified foods in maternal, fetal & nonpregnant women's blood. 3-MPPA and Cry1Ab toxin are clearly detectable and appear to cross the placenta to the fetus." Toxicity thresholds weren't explored in this study but this should surely give us pause, don't you think? If not, please explain why - I'd be very curious.
3) Glyphosate is a potent mineral chelator. This is how it kills insects, part of the reason why there are less nutrients the plants can take up & also (potentially) but likely bad for us via the same mechanism (chelation). Substantial concentrations remain on the food from what I understand. If this is the case, what about our bodies would make us able to handle such molecules?

Like you (surely), I am also frustrated by a lot of the anti-GMO rhetoric & poor science brought to the table. I don't think the pro-GMO lobby is any better. It's surely worse, generally.

I'm much less worried about the 'genetics' of it compared to the surfactants, chelators & other compounds used a lot in GMO & also in non-GMO farming to a different extent.

Would you mind picking out a specific mechanism about glyphosate argued by Dr.Seneff that you think I should revisit? Just to give me a more tangible idea of what you disagree with.

As always Dr.Ayers, your views are much appreciated!

Cloudia said...

Dear Dr. Art

Is using boswellia as an anti inflammation herb a problem?
Its been working miracles with my gut.


Dr. Art Ayers said...

Hi Claudia,
Frankincense and Myrrh. How festive.

The active anti-inflammatory chemicals in Boswellia are the large boswellia acids that make frankincense a resin. These are plant chemicals, phytochemical/antioxidants that are natural insecticides, fungicides and antibiotics. The Boswellia essential oils are a different groups of molecules half the size that are steam distilled and have different properties. Like most phytochemicals, the mixture of Boswellia chemicals impact hundreds of human proteins and change the gut flora, i.e. they are just like mixtures of pharmaceuticals with complex benefits and damage. Your liver detox system will gradually eliminate all of the phytochemicals and your gut flora will gradually become resistant.

You will be healthier without phytochemicals, but they may be of temporary benefit.

Health results from diet, adapted gut flora, sleep and exercise. The body needs protein and fat, and gut bacteria need soluble fiber/prebiotics. That's just the paleo meat, fish, eggs, for protein and fat ; and vegetables for soluble fiber to feed gut flora.

Most people forget to feed their gut flora and reintroduce missing bacteria. Remember that low carb diets mean low sugar/starch, but plenty of low glycemic plant polysaccharides to which your gut flora is adapted.

Make your own fermented vegetables!

Thanks for your questions. I will try to write more on Frankincense and plant resins this week.

Unknown said...

Dr. Ayers,
My brain is spinning with all your incredible research information.
My entire family of 4 has a liver defect called 'alpha one anti-trypsin deficiency'. My husband and I are genotype MZ, and unfortunately, our two adult sons are both ZZ.
Is this the same type of 'trypsin' to which you refer. I am beginning to connect the dots.
I found your site via DrBGanimalpharm. And, I also read free the animal, so I'm now convinced to try the potato starch.
Thanks for your dedication!
Debbie Manahan

Unknown said...

Erosive osteoarthritis in hands please comment. Drinking dry white wine and its effects on inflammation. GcMAF Bravo Probiotic yoghurt 100ml daily will this be helpful. Also Behcets lifetime but ulcers not as bad since the arthritis took over my hands !!

Dr. Art Ayers said...

My initial thoughts to explain your symptoms:
Behçet's disease is an autoimmune disease that targets autoantigen annexin 2A ((contains two basic triplets), a calcium binding protein that also binds phospholipids and IP3. Also linked to celiac.

A major point here is that celiac leads to lots of other autoimmune diseases and is probably the source of gut damage and immune system damage that causes all of your other problems. It also leads to chronic inflammation, which blocks vitamin D synthesis in the skin and leads to vitamin D deficiency and related diseases.

Vitamin D deficiency is not usually fixed with casual supplementation, because it is caused by chronic inflammation.

The bottom line is that, if you fix your gut (diet and gut bacteria), you will fix your immune system. If you fix your immune system, you will fix your inflammation. If you fix your inflammation, you will fix your vitamin D deficiency. If you fix these problems, all of your autoimmune symptoms will reverse. If you just treat the symptoms, your diseases will progress.

Start with my Anti-Inflammatory Diet and fix your vitamin D and sleep.

Probiotics are helpful, but are not enough. All that you need to fix yourself are in my ca. 200 posts. Spend a few hours paging through all of the articles. The remedies are cheap and effective, but they require commitment and due diligence. You must participate in your own health.

Reasonable wine consumption is not a problem.

Let me know of your progress.

Anonymous said...

Dr Ayers, what do you think of sequenced amino acid modulator therapy? Also known as peptides/amino acid injections to treat allergies? You said in one of your posts that it is not good to shift from allergy to autoimmune through immuno-modulating therapies. I would love to know what your thoughts are about this therapy.
Thank you

mc said...

Dear all,

In autoimmune thyroiditis patients, two studies showed no deficit in Treg number, but:
“a defect in Treg function in both Hashimoto and Graves, despite the distinct pathophysiology of these diseases”.

So, if numbers are OK, how to normalize Treg function?

Please comment, I found Your advice very useful

Unknown said...

Hi Sabrina
Did the transplant positively effect celiac disease?

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Unknown said...

Bis[4-(dimethylamino)phenyl]-[4-(methylamino)phenyl]methanol is produced from degradation of methyl green. bis[4-(dimethylamino)phenyl]-[4-(methylamino)phenyl]methanol

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