Gut Flora Risk and Repair

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The two most important contributors to health are diet and gut flora.  All of the other contributors, such as exercise, genetics, environmental toxins, hygiene, etc. are of minor importance.  A healthy diet, such as The Anti-Inflammatory Diet that I recommend on this blog, is simple and relatively easy to follow after weaning from the Standard American Diet.  One version of the healthy diet is just eating meat, fish, eggs, dairy and plenty of vegetables, but avoiding vegetable oils and grains.  Most people will be healthy with that general diet, but if and only if, they also have a healthy gut flora that is adapted to the food they eat.

Most people make themselves sick by not matching their gut bacteria to what they eat, so let me repeat the main point of this article:

You will get sick if the bacteria in your colon can’t digest your food.

And sick means allergies, autoimmunity, cancer, etc.

Read and Heed or Dead

What Killed American Gut Flora?

There are hundreds of different species of bacteria growing on partially digested food (soluble fiber) in your colon.  Americans are sick, not because they are too poor to buy food, but because they have the worst, i.e. least diverse, gut flora in the world.

Do:  We pick up, recruit, eat new bacteria and repair our gut flora by:

• touching surfaces, people, pets, etc. and putting our fingers near our mouths,
• eating live fermented food, or semi-clean vegetables,
• not cooking/killing/sanitizing all of the bacteria around us,
• eating probiotics and transferring some of their genes to our gut flora.

Don’t:  We wipe out or reduce the diversity of our gut flora by:

• using inappropriate hygiene that kills the bacteria we need for health,
• taking antibiotics that kill gut flora and compromise our immune system,
• trying to eat a wide variety of foods, which is counterproductive and only permits a few varieties of bacteria to survive.

Hygiene Kills Beneficial Bacteria

Nothing comes from nothing…  For bacteria to come out, bacteria must go in.  You have to eat bacteria to extrude them by the pound.  Each day a single bacterium growing and dividing in your gut once per hour will produce a million daughter bacteria (24 doublings, estimate that doubling two, ten times is about a thousand, and 1000X1000= million.)  So if you mixed a milligram (about the size of the period at the end of this sentence) of gut bacteria with ample food, you would have a kilogram (pounds) of bacteria by the end of the day.  Similarly, it takes about a day for a single bacterium applied to a petri dish of nutrient agar to produce a colony weighing about 10 milligrams.  The point here, is that a single bacterium that makes it through the acid bath of the stomach can be a major player in your colon in a couple of days.  This is a very good thing.  We want to kiss babies, because babies systematically vacuum up bacteria from the darkest  of corners and with shameless generosity present them in an irresistible pucker.  We need those bacteria, and so do the babies.  Hygiene, e.g. antibacterial hand soap, bleaching surfaces or closing toilet lids isolates people from potential sources of beneficial gut bacteria. 

Traditional Food is Fermented (with Live Bacteria)

Shockey

In most cultures, extra food is mixed with something like salt or spices to kill local problem microbes and then bacteria are permitted to grow.  The result is fermentation of the sugars available in the food with production of organic acids, e.g. vinegar, that stop the growth of other bacteria that might grow on protein and cause objectionable flavors.  Homemade fermented veggies contain a wide variety of happenstantial bacteria that can adapt to productive gut growth.

Cooking Kills

We cook to dissolve and soften foods.  Meat can be eaten whole and our stomach enzymes will easily digest the protein and fat to provide all of our nutritional needs.  The only plant material that can be digested by our enzymes is starch.  The rest of the plant requires cooking to make the protein available and the remaining carbohydrates, soluble fiber, require digestion by hundreds of different enzymes produced only by microorganisms.  Cooking will release soluble fiber to feed gut flora, but it also kills bacteria, so some raw foods must be eaten to make sure that the gut is always supplied with fresh bacterial recruits.  Cooked or pasteurized foods do not contain live bacteria and are not useful as sources to repair gut flora.

Probiotics are not Gut Flora

Commercial probiotics are made from bacteria used in dairy products (dairy probiotics) or bacteria used to make enzymes in other products, such as laundry detergents.  

These bacteria can be repackaged and sold as probiotics, because they have already been tested for toxicity.  These bacteria don’t normally grow in the gut and if you swallow them, they just pass through.  These “probiotics” can temporarily provide some of the functions of gut flora, because they are bacteria, but they don’t grow in the gut.

Gut Flora are Bacteria Created in the Gut

Gut bacteria produce chemical signals that coordinate the metabolism of food by hundreds of different species of bacteria.  We call these chemical signals vitamins, because humans extract the vitamins from the bacterial biofilms that always line the gut, so humans don’t need to produce their own vitamins.  Gut flora can produce all of the vitamins that we need, so it is not surprising that multivitamins do not provide any health benefit and concentrated vitamins my be harmful by disrupting normal metabolism of gut flora.  Biofilms also promote the exchange of genes between different species of bacteria, so the concept of species does not actually apply to gut flora, where new species are rapidly being created.  A common example of this process is the curing of lactose intolerance by simply eating small amounts of live yogurt for a couple of weeks.  The cure results from the transfer of a gene that produces an enzyme to digest lactose from the yogurt probiotic bacteria to the regular gut bacteria.  The new species, a natural GMO, continues to grow in the gut, digest lactose, and cure lactose intolerance.  The yogurt probiotics just get flushed away and that is why dairy probiotics must be eaten continuously to provide some of the benefits of healthy gut flora.

Antibiotics Kill Gut Flora, Compromise the Immune System and Cause Disease

Antibiotics are a huge benefit in curing and avoiding infectious disease.  Unfortunately, antibiotics can cause lasting damage by killing beneficial species of bacteria of the gut flora.  Loss of essential bacteria is commonly seen as food intolerances (true food allergies are rare) or constipation.  Since gut flora are needed for development of both the aggressive and suppressive parts of the immune system, which occurs in the lining of the gut, then antibiotics slowly lead to loss of function of the immune system that leads to autoimmunity or allergies.  Probiotics typically administered following antibiotic treatments do not repair the gut flora and leave the immune system damaged and prone to autoimmune diseases and allergies.

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.

Matching Food to Gut Flora Takes Time

All of the gut problems that people complain about, gas, bloating, diarrhea, constipation, food intolerances/allergies (except gluten and a couple of others), etc. are due to a mismatch between food and the digestive enzymes of gut flora.  Modern food processing retains protein, fat and starch and removes the polysaccharides/soluble fiber that reaches the colon, feeds gut bacteria and produces short chain fatty acids (acetic acid, butyric acid, propionic acid) that feed the colon and reduce inflammation.  It takes time for gut bacteria to adapt to new soluble fiber in new foods by recruiting or creating new bacteria, and this is only possible, if inappropriate hygiene is avoided or if homemade fermented foods are eaten.

Dr. Oz’s Pain: Constipation and Bursitis

Dr. Oz has complained several times about his constipation and the pain he feels in his shoulders during surgery.  He has recommended numerous treatments.  Since I feel a friendly affection toward Mehmet after talking/shouting at his image on the screen for hours, I think that I should give him some advice to relieve his pain.

Hot, Cold, Topical Treatments Are Effective, but Don’t Penetrate Themselves

Dr. Oz keeps talking about how various topical applications penetrate the skin.  He has even recommended the use of an electrical system to carry pain relieving steroids into his tissue by what looks to be electrophoresis.  This is dubious.  I would recommend that he stick to the topical chemicals, e.g. capsaicin, menthol, that target the hot and cold sensors of the superficial layers of the skin and result in deep penetrating nerve signals that trigger anti-inflammatory responses in the underlying bursa.

Constipation Is Caused by Damaged Gut Flora or Dysbiosis

Dr. Oz, like most physicians, does not usually explain the causes of diseases, such as bursitis.  Unfortunately, when he tries to explain problems, such as constipation, he overlooks important aspects of the problem for a facile physical model.  In the case of bursitis, it is important to realize that the patient, Dr. Oz, is also constipated.  Constipation can be aggravated by dehydration or “holding it”, but in Dr. Oz’s case, the combination of bursitis, an autoimmune disease, with constipation (and gas) suggests the more complete explanation of dysbiosis or damaged gut flora.  Dysbiosis is what causes constipation, because bowel stools, poop, is mostly packed, hydrated bacteria that grow in the colon by digesting soluble fiber.  If you eat an apple a day, there is enough pectin and other plant polysaccharides, i.e. soluble fiber, to increase the volume of the stools to make one regular.  [Don’t be confused by the misconception promoted by Dr. Oz that the volume of stools results from insoluble fiber, such as in whole grains.  The husk part of whole grains is useless or unhealthy and grains in general are not needed for a healthy diet.]  

Flush Toilet Hero

Dr. Oz’s constipation suggests a damaged gut flora.  Since he is a physician, one would suspect that he has used antibiotics in the past few years and wiped out essential types of gut bacteria.  Dr. Oz probably followed his own advice and attempted to patch up his damaged gut flora with probiotics.  Unfortunately, as I have repeatedly explained, dairy probiotics don’t survive in the gut and cannot repair damaged gut flora.  But Dr. Oz is even harder on his gut flora.  He has recommended the use of colloidal silver throat spray when he has been exposed contagious germs.  Silver, although ineffective for its intended use, is very toxic to gut flora after it is swallowed.  Dr. Oz also subscribes to numerous approaches to house and body hygiene, which are probably occupational hazards for surgeons.  Hygiene is the enemy when it comes to ingesting bacteria lost to antibiotics.  The atomizing flush toilet is my gut flora hero for spreading contagious health.

Damaged Gut Flora = Damaged Immune System

Constipation is bad enough, but damaged gut flora can mean that some of the bacteria needed for the gut-based development of cells regulatory T-cells (Tregs) that keep the immune system under control, are missing.  Constipation can lead to deficient Tregs and that means a major predisposition to autoimmune disease and allergies.  [Fecal transplants cure autoimmune diseases and allergies.]  Antibiotics, silver, hygiene excesses and constipation suggest to me that Dr. Oz has been cruising toward some rude immunological sequelae.

Autoimmunity Results From Antibiotics, Dysbiosis and Compromised Tregs

Autoimmune diseases result when a trifecta of inflammation, compromised Tregs and appropriate antigens occurs.  Normally physical damage, such as abusive shoulder exercise, results in inflammation as the first step in healing.  The inflammation can rev up the immune cells in the local area of tissue damage and some of the proteins, such as lubricin, which lubricates the bursa, may have basic triplet amino acid sequences that lead to presentation to immune system cells.  But no antibodies against self tissues are produced, because the Tregs stop the process.  Healthy gut flora produce healthy Tregs and block autoimmunity.

Dr. Oz abuses his shoulder bursa during surgery, but it can’t heal properly, because he has damaged his gut flora and compromised his Tregs.  The result is the autoimmune bursitis from which he now suffers.  He can reduce the symptoms and inflammation with topical anti-inflammatory natural chemicals, but he needs to repair his gut flora to repair his Tregs and reduce autoimmunity.  In the mean time, he is contaminating his local environment, family and friends with his unhealthy bacteria.  I wonder if Dr. Oz’s friend, Dr. Mike Roizen also suffers from autoimmune diseases?

Prescription to Repair Gut Flora:  Anti-Inflammatory Diet, Soluble Fiber, Fermented Vegetables, Less Hygiene

KEEP YOUR TOOTH BRUSH NEAR THE OPEN TOILET 

Celiac, Gluten and Trypsin Inhibitor

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Wheat

Summary

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.

Health Diagrams II — Curing Autoimmunity and Allergies

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.

Peanut Allergy Cause and Cure

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Summary:  The cure for peanut allergy should follow naturally from knowledge of the cause.  Since most allergies and autoimmune diseases result from the combination of 1) inflammation, 2) breakdown of immunological tolerance and 3) presentation of a primary immunogen, it follows that some types of peanut allergy are based on a continued problem with immune tolerance and fixing that defect should eliminate an allergic response to peanuts.  The current cure to resurrect immune tolerance is by enhancing regulatory T cells (Tregs) in the gut using resistant starch to improve the growth of Clostridia in the gut.

Peanut allergies are dangerous and this post does not advocate any medical treatments, but rather attempts to explain the cause and cures of allergies.

Just Treat the Immunological Tolerance Problem Instead of Mast Cells

Most people in fear of anaphylaxis from peanut dust, just try desperately to avoid peanuts in any guise.  That avoids the problem, but why not cure the allergy?  Recent research shows that peanut allergens can be prevented from establishing an allergic response in mice by addition of Clostridium species of bacteria in the gut flora.  It was shown that the Clostridia increased Tregs (regulatory T cells responsible for immune tolerance) in the lining of the intestines via interleukin 22 production.  So the cure to some peanut allergies may be increasing Tregs and fixing tolerance.

I Said It All Before

It is not a large step to combine my previous posts covering potato resistant starch for treatment of deficiencies of immunological tolerance with my explanation of the cause of allergies and autoimmunity to provide a simple explanation of the cause and cure for some peanut allergies.

Peanut Allergen is a Typical Bean Storage Protein Except for the Basic Triplet

It is not difficult to find out why peanuts are allergenic.  I just went to the National Center for Biotechnology Information (NCBI) web site and queried the protein sequence databases for “peanut allergen.”  Here is the complete amino acid sequence (each of the 20 amino acids of the protein is assigned a letter) of the major peanut [Arachis hypogaea] allergen:

MMVKLSILVALLGALLVVASATRWDPDRGSRGSRWDAPSRGDDQCQRQLQRANLRPCEEHMRRRVEQEQEQEQDEYPYSRRGSRGRQPGESDENQEQRCCNELNRFQNNQRCMCQALQQILQNQSFWVPAGQEPVASDGEGAQELAPELRVQVTKPLRPL

The triplet of basic amino acids (R=arginine, K=lysine), RRR in this case, which is found in all allergens and autoantigens, is highlighted in red.  If you eat peanuts with an inflamed gut and you have wiped out your Clostridia and associated Tegs with antibiotics, you have a good chance of developing autoimmunity, as well as a peanut allergy.  The cause of allergies is that simple and the cure is equally simple.

Shellfish Allergy Shows the Relationship between Allergy and Autoimmunity

I ran across a list of other food allergens when I was checking up on peanuts.  Shellfish was listed as another of the big allergies.  I looked up “shellfish allergen” and ran into thousands of entries.  The first couple of dozen proteins lacked the characteristic basic triplet, so I had to step back and try to guess the most typical shellfish for first exposure, i.e. the primary immunogen.  All of the other shellfish allergens were various versions of the muscle protein, tropomyosin, so I looked up “shrimp allergen.”

MDAIKKKMQAMKLEKDNAMDRADTLEQQNKEANNRAEKSEEEVHNLQKRMQQLENDLDQVQESLLKANIQLVEKDKALSNAEGEVAALNRRIQLLEEDLERSEERLNTATTKLAEASQAADESERMRKVLENRSLSDEERMDALENQLKEARFLAEEADRKYDEVARKLAMVEADLERAEERAETGESKIVELEEELRVVGNNLKSLEVSEEKANQREEAYKEQIKTLTNKLKAAEARAEFAERSVQKLQKEVDRLEDELVNEKEKYKSITDELDQTFSELSGY

Note the predicted basic triplet in red.  Since I was on a roll, I also checked out related tropomyosin sequences in humans:

MDAIKKKMQMLKLDKENALDRAEQAEADKKAAEDRSKQLEDELVSLQKKLKGTEDELDKYSEALKDAQEKLELAEKKATDAEADVASLNRRIQLVEEELDRAQERLATALQKLEEAEKAADESERGMKVIESRAQKDEEKMEIQEIQLKEAKHIAEDADRKYEEVARKLVIIESDLERAEERAELSEGKCAELEEELKTVTNNLKSLEAQAEKYSQKEDRYEEEIKVLSDKLKEAETRAEFAERSVTKLEKSIDDLEDELYAQKLKYKAISEELDHALNDMTSM

Once again the basic triplet indicated that there was a related human tropomyosin that could interact with antibodies to the shellfish allergen or could be an autoantigen participating in autoimmune diseases.  So I checked PubMed for “tropomyosin autoantigen” and quickly found that antibodies to tropomyosin are important in ulcerative colitis (UC).  Thus, shellfish allergy may be an indication of an underlying predisposition to UC.  And, the traditional cure for allergy by injection with small amounts of the allergen to convert from IgE to IgG, would convert a shellfish allergy into UC.

Avoiding Allergens Makes No More Sense Than Trying to Avoid Autoantigens

To fix allergies, it is necessary to eliminate the cause and block perpetuation of the condition.  The cause is based on 1)inflammation, 2) broken immune tolerance and 3) primary immunogen.  Peanuts are the primary immunogen, but that is unimportant if the causing conditions are eliminated and tolerance is reestablished.  Clearly, if immunological tolerance is reestablished, then it's just a matter of time before peanuts are no longer a problem, because increasing Tregs will silence the dramatic immunological response to peanuts.  Tolerance is based on Tregs and Tregs develop in the intestines in response to Clostridia feeding on soluble fiber/resistant starch.

Curing Peanut Allergies is Based on Repairing Gut Flora

There are a couple of hundred different species in the pounds of bacteria in the healthy human gut.  Most of those bacteria require soluble fiber that is systematically removed during food processing.  For most people, the cure for peanut allergies will be resistant starch/Clostridium therapy, followed by further repair with fermented foods that provide the typical lactic acid bacteria and soluble fiber along with companion bacteria that can recolonize the gut.  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.  If there is severe dysbiosis, as indicated by constipation, then fixing the gut flora is a little more difficult, but for most people cures are much cheaper and effective than just treating symptoms.

A guide for the use of resistant starch is provided by Richard Nikoley, et al. at Free the Animal.

Contagious Health

Healthy gut flora: bacteria from family, friends, Fido and food provide the foundation for the complex microbial community of the intestines, which controls the immune system.  Antibiotics and hygiene are detrimental to gut flora and health.

Gut Flora Are Complex

Recent studies of the gut flora, e.g. the human gut biome, show that each individual maintains more than 150 different species of bacteria.  Worldwide, that means that about a thousand different bacterial species are common residents of the human gut and together those gut bacteria use more than 1 million different genes.  Many of those genes code for the enzymes used by gut bacteria to digest plant polysaccharides, i.e. soluble fiber.

Hygiene Isolates People from Healthy Sources of Gut Flora

Every time we speak, we release a mist of bacteria from our lungs, mouth and GI tract.  These bacteria are on our skin, clothes and personal items, and provide a source of the bacteria that make us healthy.  Parents and older siblings pass these bacteria on to younger children.  These donated bacteria are essential for the development of a healthy immune system and children growing up with healthy relatives and exposed to soil bacteria via pets, farm animals, etc. are healthier than children who are more isolated.  

In this sense, hygiene is unhealthy, because an individual is isolated from new sources of bacteria that could replace those lost by limited diets, antibiotics, etc.  Otherwise, health is contagious, since gut bacteria from healthy individuals can spread among the population.  Washing hands and food is unnatural and unhealthy.

Few Bacteria Make You Sick, but Many Are Essential for Good Health

Food intolerance can result from “good” family hygiene, limited diets and exposure to antibiotics.  A common intolerance results from the absence of bacteria that produce an enzyme to digest dairy lactose, i.e. lactose intolerance.  Lactose intolerance can be readily cured by eating a dairy product, such as yogurt, that contains both lactose and live bacteria (probiotics) that can digest the lactose.  Simply eating moderate amounts of live yogurt daily for a couple of weeks resupplies the gut flora with bacteria that can digest lactose, and the intolerance is gone.

Soluble Fibers Are Plant Polysaccharides that Are Digestible by Bacterial Enzymes

Humans only produce enzymes to digest one polysaccharide, starch.  All of the other hundreds of polysaccharides present in plants are only digestible by bacterial (and fungal) enzymes of the gut flora.  If the bacteria and enzymes needed to fully digest a particular food polysaccharide are absent, then digestive problems ensue and the polysaccharide can act as a laxative.  Continual eating of the problem food with a new source of diverse bacteria, e.g. lightly rinsed vegetables right from the garden, then the gut flora will incorporate new bacteria that can digest the problem polysaccharide and the gut is happy.  

Soluble fiber feeds the gut bacteria that convert it into short chain fatty acids that nourish the colon. Constipation results from the absence of the bacteria needed to digest dietary fiber and to produce the large volume of bacteria that make up well hydrated stools. 

Gut Bacteria Are Needed for Healthy Immunity

Cells of the human immune system are stored predominantly in the lining of the intestines.  Intensive study of the interaction of the gut bacteria with the gut has revealed that both the aggressive half of the immune system that attacks pathogens and the suppressive half that protects the body itself from attack, develop in the gut in response to particular types of bacteria.  Thus, the absence of one type of bacteria can cripple responses to infection, while other bacteria are needed to block autoimmune diseases and allergies.  Most diseases are caused by disruption of the normal interactions between gut bacteria and the immune cells developing in the gut.

Antibiotics Lead to Autoimmunity

Antibiotics have dramatic and lasting impact on gut flora.  Cattle treated with antibiotics and a high carbohydrate diet have an altered metabolism (obesity) that leads to rapid fat accumulation in their tissues.  This is good for making tasty beef, but the same approach in people produces the suite of diseases in affluent societies.  

Children treated with an antibiotic for a simple ear infection, are much more likely to return to pediatricians for treatments of subsequent obesity, infections and diseases.  Compromised gut flora can take years to return to normal function after antibiotic treatment.  Loss of the appendix, which is the normal source of bacteria to replenish gut flora after diarrhea, results in an increased risk of abnormal gut flora and numerous autoimmune diseases.  It is likely that most autoimmune diseases are preceded by prior treatment with antibiotics that disrupted normal gut flora and permanently altered the immune system.

Interventions to Treat Disease:  the Anti-Inflammatory Diet and Fecal Transplants

It should be obvious that a disrupted or unhealthy gut flora will compromise the immune system and contribute to disease.  Treatment of diseases is complicated by the use of drugs that also impact the gut flora and produce additional side effects.  An alternative approach would be to support the healthy gut flora and normal development of the gut immune system.  As always, the answer is a supportive diet and a source of gut bacteria.  The diet is obviously the Anti-Inflammatory Diet that provides support for almost anything that ails you.  Probiotics are not retained in the gut, but they can contribute a few of the genes needed for a healthy gut flora. The source of bacteria for a  healthy gut flora may range from minimally washed garden vegetables, to the more aggressive total replacement of gut flora with a fecal transplant from a healthy donor.  

Dr. Oz Five Food Felons

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Biofilms on intestine microvilli

The medical industry is slowly pulling away from diet advice that has contributed significantly to disease in America.  It promoted or at least tolerated, the shift from butter to margarine and polyunsaturated vegetable oils, and from saturated fats in meats to starches and grains.  The medical emissary, Dr. Oz, still supports medical advice that is not based on medical research.

Dr. Oz's Five Food Felons and Why His Choices Are Unhealthy:

"1) Trans fats raise lousy LDL cholesterol and triglyceride levels, lower your healthy HDL cholesterol level and fuel disease-triggering inflammation."  Trans fats are inflammatory and should not be eaten.  New labeling has permitted substantial amounts of trans fats to be added to processed foods and still be labelled "No trans fats."  LDL blood levels reflect inflammation, but artificially lowering the LDL with statins has no impact on heart disease.  Lowering LDL, by lowering inflammation with fish oil and/or repair of gut flora, diet and exercise is effective.

"2) Saturated fat in red meats, poultry skin, full-fat dairy products and palm and coconut oils fuels cancer risk, coronary artery disease, dementia, obesity and diabetes."  Linking saturated fats with heart disease, etc. was never supported by medical research.  Elimination of red meat, removing skin from chicken, avoiding egg yolks, etc. and replacing them with omega-6 polyunsatured vegetable oils has been a major contributor to inflammation and disease.  Full fat milk is the healthful choice, especially for children.  The change was dangerous and is being reversed with new emphasis placed on omega-3 fish oils.

"3) Added sugars and 4) sugar syrups cause the proteins in your body to be less functional and age your immune and cardiovascular systems and your joints. Plus, they disrupt your metabolism and contribute to almost every lifestyle-related malady, including some cancers."  Oz got this right even though they initially promoted high fructose corn syrup (half glucose/oligos) and its evil and even higher fructose sister agave nectar (all fructose/oligos.)  Equally bad, however, are the hyperglycemic starch in breads (including whole grain!) and over cooked pasta.

Gut flora

"5) Refined and processed grains don't contain the fiber or nutrients (contained in 100 percent whole grains) that you need to keep the bacteria in your guts happy, glucose levels regulated, immune system strong and digestion running smoothly."  Dr. Oz and company fail to understand the basics of vitamins, soluble fiber and gut flora.  Grains are not healthy for most people, because of the toxicity of gluten and hyperglycemic starch.  Ultra fine milling and fast commercial bread making eliminate the resistant starch.  "Whole grain" processed foods just add back the insoluble fiber that is considered toxic, because of its phytic acid content.  Grains should just be replaced with whole foods, such as vegetables that contain the soluble fiber that feeds the gut flora that provide all of the needed vitamins and are required for immune system development.

Why Does Dr. Oz Make Health Mistakes?

Dr. Oz has been criticized for promoting foods, supplements, medical treatments, etc. that are not supported by medical research.  While that is true, I think that he is just following the general views of the medical industry and simply doesn't know any better.  Sadly, most doctors don't have the background to read scientific research papers, let alone their own biomedical literature that is rife with scandals of nonreproducibility and inappropriate industry influence.  Doctors find it hard to give valid dietary advice, because nutritionists have false information and celebrity doctors, and their research teams, don't do their homework.  The result is the mix of ancient orthodoxy, industry promotion, alternative medicine and unscientific fads that appears in the media.  Doctors need a scientific background sufficient to answer the essential question posed to health claims, "Does it make sense?"

Health Diagrams II — Curing Autoimmunity and Allergies

---All 200 posts here---

In this second in a series of posts explaining the concepts that I think are central, but misunderstood, about health, I am focusing on how diet and gut flora impact the immune system and cause autoimmunity and allergies.  This cause also suggests a simple cure.

Health in Diagrams I -- Gut Flora and Diet
Health in Diagrams III -- Inflammation from Cell to Tissue

Gut Flora to Tregs to Suppression of Autoimmunity

It is important to understand at the outset that autoimmunity and allergies are caused by a damaged immune system, and repairing the damage cures the diseases.  Damage to the immune system typically represents a break in the continual development of immune cells in the lining of the intestines.  Immune cell development in the gut is dependent on bacteria, the gut flora.  Damage to the gut flora, e.g. by antibiotics, processed foods that lack flora feeding fiber or extreme diets, disrupts development of immune cells.  Typically, loss of the immune cells that keep the aggressiveness of the immune system in check, regulatory T cells or Tregs, results in autoimmunity.  Fix the gut flora and autoimmunity recedes.  

Health Requires Suppression of the Aggressive Immune System

For simplicity, I am focusing on the T cells of the immune system that develop in the intestines and either kill other human cells that are dangerous, e.g. virus-infected or cancer cells, or provide protection by regulating the aggression, Tregs.  Normal functioning of the immune cells permits elimination of damaged or dangerous human cells, while at the same time avoiding rampages of lethally armed T killers.  Examples of untamed T killers in action are degenerative autoimmune diseases, such as arthritis, asthma, prostatitis, celiac, Hashimoto’s thyroiditis, type I diabetes, inflammatory bowel diseases and atherosclerosis. 

Milk Births Baby Immune System

It should not be surprising that the focus of immune system development is the gut.  We start as babies with explicit links between nourishment and immunological protection.  Milk connects the immune systems of mother to baby.  Immune cells from the mother are transferred in milk and colonize the respiratory and digestive system of the baby — the mother’s immune system coats and buffers the baby’s exposure to the world.  Milk hormones close the baby’s gut and milk bacteria are the first probiotics that exploit the milk prebiotics (bifidus factor, human milk oligosaccharides) to produce a gut flora.  [Also note that most commercial probiotics are adapted to grow on cow’s milk and hence these dairy probiotics do not survive in adults.]  The lymphatic system of the breast terminates at the nipple and samples antigens/pathogens from the baby’s mouth, resulting in baby-specific secretory antibodies that return in the milk.  Milk supports a starter set of gut flora, essentially dairy probiotics, that stimulates development of the baby immune system, but inhibits adult gut flora that would digest the protective components of milk.  Formula, on the other hand, is inflammatory to the baby gut, because it supports adult gut flora before the immune system is ready.  Inflammation and stimulation of innate immunity is sufficient, if supported with high levels of sanitation, to permit survival of babies fed formula.  Milk of any type is incompatible with adult gut flora, so breast milk will attack adult gut flora and adult gut flora will digest and inactivate the otherwise beneficial components of the milk.

Milk, Kefir and Gut Flora

Aggressive and Suppressive Cells of Immune System Develop in Intestines

Gut bacteria are required for the development of immune T cells in the lining of the intestines.  Mice grown without gut flora do not have functional immune systems.  In humans, extensive antibiotic treatment produces defective immune systems that are either overly aggressive, i.e. autoimmune, or susceptible to infection and cancer.  They can’t be both.  Aggressive T killers are stimulated to develop by filamentous bacteria and Tregs develop in response to members of the Clostridium family.  In a healthy body, there is a balance between aggression and suppression; there are functional defenses against infection and cancer, while also avoiding autoimmune disease and allergies.

Suppressive Tregs are Deficient in Autoimmunity

Immune cells result from replicative divisions of stem cells.  Antibody producing B cells are produced through a million random rearrangements of antibody genes and those B cells producing antibodies against common self proteins are killed (clonal deletion).  Similarly, T cells are produced by rearrangements of receptors and those that would recognize self are eliminated.  The T cells then migrate to the intestines where they can develop into killer T cells or Tregs, in response to gut flora.  The Tregs act to suppress killer T cells that mistakenly recognize healthy self cells.  Thus, the initial elimination of self-attacking T cells or for B cells that produce antibodies that bind to normal cells, is not perfect and the Tregs are needed to avoid the mistakes.  Tregs are necessary to avoid the immune attack on healthy cells that is the basis of autoimmunity.

Autoimmunity Starts with Inflammation, but Requires Deficient Tregs

Bacterial or viral infections, or physical damage causing inflammation is the first step in autoimmunity.  It is the inflammation that initiates the interactions between proteins, autoantigens, of normal cells and cells of the immune system that bind, internalize, fragment and present the antigen fragments/peptides to activate B or T cells with corresponding receptors.  The activated B cells make antibodies specific for the antigen and the T cells will kill cells displaying the antigen.  It is interesting that most proteins are not autoantigens and are never involved immune reactions.  Only proteins with an unusual triplet of basic amino acids, similar to the quartet of basic amino acids used to transport proteins into the cell nucleus, are candidates to be autoantigens or allergens.  In fact, since nuclear proteins already have a quartet, i.e. the nuclear localization signal, they are common autoantigens.  The last requirement for autoimmunity is a deficiency in Tregs, because if the Tregs are functioning, they will block attack on healthy cells.  Treg deficiency usually results from loss of the type of gut bacteria that stimulate Treg production in the lining of the intestines, i.e. species of Clostridium.

Hospitals are Notorious for Clostridium difficile Infections

Fecal transplants are now recommended as a safe and efficacious treatment for C. diff hospital infections.  That makes sense, because hospitals are where antibiotics are routinely used and C. diff can only infect people missing their healthy species of Clostridium.  Thus, the hospitals wipe out the gut flora with antibiotics and then recolonize them with their own antibiotic resistant C. diff.  More antibiotics can’t fix it, but providing healthy gut flora (transplant) can.

Autoimmune Diseases are Treated/Exacerbated with Antibiotics

Both the aggressive and the suppressive immune cells require gut flora, so after initial antibiotic treatment wipes out bacteria required for suppression and results in autoimmunity, the remaining aggressive half of the immune system can be eliminated by blasting the remaining gut flora with more antibiotics.  Of course this will leave a highly compromised, incompetent immune system that will ultimately yield more extreme symptoms.  This is the typical medical progression for Crohn’s disease, for example.  The alternative is just fixing the gut flora to begin with and curing autoimmunity.

Cure Autoimmunity by Feeding Clostridium Resistant Starch

Autoimmune diseases, by their symptoms, show that sufficient gut flora to stimulate the aggressive half of the immune system is still present.  What is missing are the Clostridium species that convert soluble fiber, such as resistant starch, into short chain fatty acids, e.g. butyrate.  Patients treated with antibiotics usually walk away from the hospital with a suggestion to eat some yogurt to repopulate their missing gut flora.  Unfortunately, dairy probiotics don’t survive in the gut and cannot repair the gut flora and immune system.  The result, after the gut fails to repair and the immune system crashes, is autoimmunity.  There is a more appropriate possibility to avoid or fix autoimmunity.  Some people suffering from autoimmunity (and with remnants of their gut flora intact) have simply fed their gut flora on resistant starch and achieved complete recoveries.  Others fail to respond, because their gut flora is too severely damaged and necessary bacterial species are gone.  Those individuals need to eat the missing species of bacteria and some probiotics (more common in Asia) contain Clostridium species.  Consistent with this use of soluble fiber to feed gut bacteria that produce butyrate and stimulate the suppressive immune system are reports of healing by combining potato starch (RS) and probiotics with Clostridium butyricum (Probiotic-3).  Repair of the suppressive immune system by repair of gut flora (including fecal transplants) and feeding gut flora with appropriate soluble fiber, may be a general approach to the cure of most autoimmune diseases and allergies.

Paleo Gut Flora Repair

200th Post — Diet, Inflammation, Disease & Gut Flora

— all 200 Posts —

I started posting to Cooling Inflammation on 21 Aug, 2008 with How Your Diet Makes You Sick or Healthy.  My impetus for writing was my growing awareness that diet was the major reason why people were sick, and that health myths were preventing people from being healthy.  Inflammation originated by diet-inflicted injury and people attributed their sickness to genetics, environmental toxins and pervasive pathogens. 

My Path to the Obvious

My research background started with plant biochemistry, including carbohydrate structural analysis and polyphenol chemistry.  At that stage I was interested in understanding how plants protected (phytoalexins) themselves from pathogens, and I expected to use this perspective to explore human innate immunity.  From there, I went on to enzymology and protein characterization, biofilm structure, plant genetic engineering and breeding, monoclonal antibody production, mycotoxin detection, stem cell analysis, passive immunity in neonates, computational modeling of collagen and heparin binding, and heparan sulfate proteoglycan inhibition by inflammation.  These were temporary foci and the research imperatives, in retrospect, prevented me from seeing the bigger pictures, although they did leave me with a broad skill set.

Perspective: Water and Surface Tension

When I finally decided to slow down, smell the flowers and start having kids, I switched from research to teaching, from university to small liberal arts college.  For the first time, I actually thought about what I was teaching and my first revelation was that after teaching biochemistry for twenty years, I didn’t understand water and surface tension.  I could provide the platitudes from the Molecular Biology of the Cell, but I couldn’t do it mechanistically with colliding, sticky, energetic water molecules in my mind or at the blackboard.  I had to develop functional explanations of hydrogen bonds, entropy and thermal energy, that translated into the structuring of a layer of water molecules responsible for hydrophobic interactions and surface tension.  I extended that to include an explanation of the two layers of water holding together cytoplasmic membranes, the tube of structured water that holds together the cylinder of stacked bases in DNA or the shrink wrapping water layer surrounding proteins.

Perspective: Heparin Binding and Amphipathy of Sugars and Basic Amino Acids

As the kids got older, I started to dabble in research again and my expertise in carbohydrate chemistry led me into cartilage (mostly the glycosaminoglycan, GAG, chondroitin sulfate) synthesis and ultimately another GAG, heparan sulfate proteoglycans (HSPGs).  I was attracted to the dynamic HSPGs, that recycled with a half-life of six hours and formed layers around chondrocytes that secreted cartilage as they burrowed/ate through living cartilage.  I learned that the heparin filled granules of mast cells could be stained with berberine, which similarly stained the heparin in basement membranes of tissues and amyloids of Alzheimer’s, atherosclerosis and diabetes.  I was led by protein modeling of collagens to the binding of heparin to proteins and the revelation that basic amino acids (heparin binding domains) and sugars (heparin) are amphipathic, i.e. they have both hydrophobic and hydrophilic regions.  This is also true of plant polyphenolics.  Thus, polyphenolics, “basic” amino acids, “hydrophobic” amino acids, and sugars will all stack together.

Amphipathic Interactions

• DNA bases stack.
• Heparin binding sites of proteins are basic amino acids (Arg, Lys).
• Sugar binding sites in enzymes and lectins are hydrophobic amino acids (Trp, Tyr, Phe).
• Nuclear translocation signals, quartets of basic amino acids, bind to receptors with tryptophans.
• Tryptophans are the most highly conserved amino acids in the same proteins across great evolutionary distances.
• Hydrophobic bonding between tryptophan and a sugar or basic amino acid is ten times greater than hydrogen or ionic bonds.
• Tryptophan/Arginine ladders zip regions of proteins together.
• Polyphenols can disrupt cellular protein interactions by binding to receptors for carbohydrates/heparin, steroid hormones, amyloids, etc.
• Heparin holds dozens of hormones to receptors and changes the shapes of proteins, e.g. clotting and complement.
• Most nucleic acid binding proteins will also bind to the more negatively charged heparin.
• Bacteria use a pair of lysines to mark proteins for export.
• Peptides containing the basic amino acids of heparin binding domains (also produced by the specificity of gastric proteases) are antimicrobial, e.g. defensins, and so are plant polyphenols.
• Many drugs are active because they are domesticated plant polyphenols.

From Heparin Binding to Antigen Presentation

As soon as I realized that basic amino acids were involved in heparin binding, I started to look for the basic amino acids (R for arginine and K for lysine in amino acid sequences) in proteins known to bind heparin.  After study of hundreds of structures, it became obvious that heparin binding domains were simply a pair of basic amino acids (RR or KK or RK) with another within a distance of six amino acids.  No particular structure was necessary, as I later deduced, since binding to the heparin provided the structure.  In fact, in many X-ray crystallographic structures, the heparin binding regions on the surface of the protein are missing, because they are not in a defined shape.  I suspected that protein antigens involved in autoimmunity and allergy might be brought into cells for presentation to the immune system by interacting with HSPGs on the surface and so started to check them out for heparin binding domains.  I was very skillful at picking out pairs of Ks or Rs within sequences of hundreds of amino acids by that time, so I was shocked to see that the first dozen antigens that I checked, all had a triplet of basic amino acids.  I had discovered that autoantigens and allergens utilize a basic triplet analogous to the basic quartet used in nuclear translocation!  This also explained why proteins that interact with nucleic acids and are transported into the nucleus with a basic quartet are also prominent autoantigens.

Gut Flora and Immunity

Twenty years ago I read a curious description of leprosy that said that the course of infection could be either innocuous or devastating depending on whether the aggressive or the suppressive part of the immune system dominated.  I remained perplexed until I realized that diet and gut flora were the major determinants.  I was aware of the importance of diet at the outset of this blog, because it was clear that diet trumped genetics.  I was also aware thirty years ago in my studies of passive immunity, that milk contained bifidus factor, now known to be milk oligosaccharides, that controlled the growth of Lactobacilli that in turn controlled the development of the neonate immune system.  It was also known that bacteria-free mice had impaired immune systems.  It still took me several years for the relationship between diet, gut flora and immunity to make sense.  I began searching the literature for connections between gut flora and development of the immune system and soon noted experiments that linked filamentous bacteria with aggressive components and Clostridium spp. with Tregs.  A further refinement was linking resistant starch, a soluble fiber, with Clostridium.

My Current Views are Summarized in Three Health Diagrams

Diet, Gut Flora, Inflammation, Antigen Presentation, Tregs and Autoimmunity

Protein from the body and from food don’t normally stimulate the immune system, because there in no inflammation, the proteins lack basic triplets that enhance presentation, and antibody production and aggressive T cells are suppressed by Tregs.  Diet can throw the balance toward autoimmunity and allergy, by producing inflammation, e.g. hyperglycemia/AGE or high omega-6 fatty acids/prostaglandins, and starving gut flora needed for Treg production by eating processed food lacking soluble fiber.  The combination of inflammation and Treg deficiency causes proteins, either self or potential allergens, which have basic triplets to be presented to the immune system and stimulates attack by the immune system.

The Cure is to Cool Inflammation and Stimulate Tregs with Diet and Bacteria

I have provided an outline with The Anti-Inflammatory Diet to avoid inflammation, to stimulate existing gut flora with soluble fiber and encourage Treg production.  Mark Sisson, on Mark’s Daily Apple has provided an excellent dietary guide that also provides starch guidelines.  If you already have symptoms of autoimmune disease or allergies, then Richard Nikoley provides gut flora repair advice on Free the Animal, and Dr. B G provides more details on Animal Pharm.

Autoimmunity and allergies are not genetic destiny and they can be cured with diet and bacteria.