Paleo Gut Flora Repair

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I was shocked to learn that there were some paleo (meat and veggie) eaters who were getting cured with resistant starch.  I didn’t know that some were sick and, as I said in a previous post, I would not have guessed that starch was good for anything, but spikes in blood sugar.  I was rudely awakened by the shouts of Richard Nikoley on Free the Animal, though I suspect the sanity behind the argument came from Tim and Dr. BG (though she has now modified her position)  He presented a kind of Second Coming of Paleo with resistant starch to feed the gut flora as soluble fiber.  How could I question food for flora?  (How could I question Nikoley without my karate gi?)

Paleo is not Paleo

It took me a while to realize that paleo is not the same for everyone.  I thought my Anti-Inflammatory Diet (meat/fish/eggs/dairy and veggies, without vegetable oils or sugars or grains) was paleo.  The way that I used this AID, it was high in saturated fat, low in polyunsaturated fat, high in protein, low in high glycemic carbs and ample in prebiotic, soluble fiber.  Some would say it is low carb.  Judging from comments on Free the Animal, I think I would be cast out by some of the more carnivorous (LC and VLC) in the paleo community for including prebiotic fiber.  Some people don’t want to feed their flora, microbiota.  It is a kind of “Let them eat meat,” mentality.

Gut Flora/Microbiota are Friends

I think of my gut flora as fellow travelers on my life journey and what’s good for them is good for me.  I don’t intentionally abuse them, but I also forget that they might not enjoy bourbon or the phytoalexins in herbs and spices.  I don’t begrudge them the soluble fiber that they need, and I think that they are a little happier with each apple (pectin) I feed them.  I simply forget that most people haven’t taught micro, DNA sequencing and the biochemistry of plant cell wall polysaccharides.  My wife starts to roll her eyes at any sentence containing “flora”, “antioxidant”, “inflam-“, “omega-“, “carb”, “paleo”, or even “microbiobiota.”  And the list gets longer.  I think that I'm out of touch, until I read Nikoley.

Paleo Diet without Prebiotic Fiber is Hard on Gut Flora

People get sick on paleo, because they don't feed their flora.  Gut flora are needed to supply vitamins, short chain fatty acids and immune system stimulants.  If you don’t feed your flora you get vitamin deficiencies, gut inflammation and autoimmune diseases (Treg deficiency).  It is very important to remember that feeding your flora means matching the soluble fiber with the existing flora.  Most people make the mistake of assuming that if they change their diet, then their flora will also change.  Their flora will adapt with each of their hundred different species of gut bacteria increasing or decreasing in numbers, but no new genes will be present to digest new soluble fiber.  Eating a meat diet will eventually eliminate gut bacteria needed to digest some plant materials and produce intolerances.  The missing bacteria will not be regained upon return to eating plants again.

Changing Diet Does Not Repair Gut Flora

Many people lose species of gut flora as they change from diet to diet, eat processed foods lacking soluble fiber or use antibiotics.  The loss may be permanent, but need not be.  Food intolerance and most “allergies” merely reflect missing species of bacteria, and introducing new bacteria fix the problem.  Lactose intolerance, for example, can be cured by eating live yogurt.  Similarly, many immunological problems, such as autoimmune diseases, result from species of gut bacteria that are needed for the development of the immune system, which takes place in the lining of the gut in response to gut bacteria.  New bacteria need to be introduced to fix the deficiency and diet alone is not enough.  Just to be clear;  meat-exclusive paleo can lead to autoimmune diseases, because of deficiencies in gut flora diversity/species and adding back soluble fiber can only cure the diseases, if the bacteria needed to digest the fiber polysaccharides are still present or are reintroduced.  Also note that there is soluble fiber polysaccharide sufficient in a carnivorous diet to support properly adapted gut flora.

Dairy Probiotics Do Not Repair Gut Flora Destroyed by Antibiotics

Don’t expect dairy probiotics to cure diseases caused by deficient gut flora.  Bacteria that grow on dairy cannot survive in the gut.  I know that physicians, including Dr. Oz, recommend that patients treated with antibiotics eat yogurt to repair their gut flora.  It ain’t  gonna happen.  That treatment is just for the doctor’s benefit (and provide some temporary functionality), to make her feel like she is addressing the problem responsibly.  I suggest that the antibiotic-damaged gut flora will screw up the immune system and bring the patient back to the doctor’s office even sicker.  Antibiotics are very good for business.

Health in a Crock

So, here comes the part that was missing from Nikolay’s Paleo plus RS.  He left out the missing gut flora.  RS is a panacea for those with some gut bacteria that can digest RS, but for those with profoundly crippled gut flora, e.g. some of those with autoimmune symptoms, RS is just inert fiber, not flora food.  

Fermented Vegetables Repair Gut Flora

New bacteria must be eaten, and I think that the cure, short of the real deal fecal transplant, is still available in the original, paleo form of naturally fermented, live foods.  The answer (and please forgive the fervor, because I think health can be this simple) is Fermented Vegetables, by Kirsten and Christopher Shockey.  Their book, right, is coming out in September, and I think that the most important part of this cure is that it looks and tastes fantastic.  This is not canned, dead sauerkraut.  These are culinary delights from simple recipes in which the natural bacteria do all the work.  Since they are long time friends of mine, I have coerced Kirsten into giving me some advance access to some of her recipes.  She has also tentatively agreed to share on my blog some of her personal fermentations on happy bellies.  So check back for future posts.

Pay close attention, because some of these recipes may cure what ails you.  They have the potential to repair your gut and are the healthful fix for a sickening faux “paleo” diet.  Note that homemade, live fermented veggies contain 1) fermenting bacteria responsible for acidifying the brined veggies for storage, 2) additional bacteria of the species missing from your gut flora and are just along for the ride, and 3) veggies that have their soluble fiber intact and ready to feed your gut flora.  Cooking, pasteurizing or otherwise harming the live, working bacteria in fermented vegetables destroys their benefit in contributing to your gut flora.  It only takes a few of the bacteria that do survive passage through your acid stomach to fix your gut flora.

Major Points of a Healthy Paleo Diet

• Meat/fish/eggs and veggies, without dairy, grains, vegetable oils and processed foods.
• Nikoley and others pointed out that a healthy paleo diet has soluble fiber, e.g. RS, to feed gut flora.
• Resistant starch is a unique category of soluble fiber with health benefits.  (Other types of soluble fiber may also be needed.)
• Diet alone is not enough for health, add gut flora.
• Diet and gut flora need to match.
• The natural paleo source of gut flora bacteria is homemade fermented vegetables.

Resistant Starch, Panacea, but Why?

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I am definitely not a bandwagon kind of guy (except maybe in the case of fecal transplants.)  So embracing evil, high-glycemic starch as a medicinal godsend was tough.  As a biochemist raised on structural analysis of carbohydrates, the idea of starch as a mixture of linear amylose and branched amylopectin, was straightforward.  Amylase in saliva and pancreatic solutions digests the linear alpha,1-4,glucan stretches and pullulanase (bacterial) degrades the alpha,1-6, glucan branch points.  But this suggests that starch should be digested before it gets to the colon and most of the gut flora.  This ignores the spirals of amylose that resist amylase digestion, i.e. resistant starch (RS), and that lead to the puzzling role of RS as a special food for gut flora and a health panacea.

Why is resistant starch, RS, difficult to digest and terrific for gut flora?  

There are several conceptual difficulties to understanding why RS is Real Special:

• Polysaccharides are not all simple linear chains of sugars, e.g. they branch (amylopectin) or form helices (RS, amylose).
• Sugars and polysaccharides have hydrophobic patches.  They are amphipathic like soap.
• Amylose (RS) forms a spiral with a hydrophobic surface of each sugar facing inward to make a hydrophobic core and hydrophobic patches on the outer surface that structures water to hold the spirals together.  The same principle holds together the double helices of DNA around a central hydrophobic core of stacked base pairs.
• Polysaccharides (soluble fiber) are made of many different sugars, e.g. glucans, mannans, xylans, galacturonans, etc.
• Starch is enzymatically hydrolyzed to glucose, which most gut flora can ferment.  Other sugars from other polysaccharides (e.g. pectin, polygalacturonan) must first be converted to glucose for fermentation.
• Soluble fiber polysaccharides made from multiple sugars, e.g. arabinogalactans or xyloglucans, require multiple bacterial enzymes for digestion by gut flora.
• Several hundred bacterial enzymes of the gut flora are required to digest the complex soluble fibers of food plants in a typical diet.  Resistant starch requires two.
• Food intolerances (also mistakenly called food allergies) result from missing bacteria and their enzymes to fully digest soluble fibers.
• Novel soluble fibers or sugars are used as laxatives, and they lose their loosening impact as your gut flora adapts to digest the new fiber.  Normal, softened stools are half bacteria.
• Amylose spirals are used as a storage form of glucose in seeds, potatoes, roots, etc., because enzymes can’t attack their glycosidic bonds to hydrolyze the starch into amylodextrins and glucose.
• Bacteria digest amylose by attaching the spirals to their cell walls and using wall-bound enzymes to tear the amylose apart.  It's like the different requirements of a wood chipper (pancreatic amylase) versus a man with a chain saw (bacterial amylase).
• The spirals of RS melt during cooking and become susceptible to gut amylase.  Melted amylose can sometimes slowly reform enzyme-resistant spirals, RS, when chilled.  Al dente or chilled pasta has more RS and raises blood sugar less than soft pasta.

Resistant Starch, a Unique Soluble Fiber  

Humans only produce enzymes (amylases) to degrade one of the hundreds of plant polysaccharides, linear starch.  RS is not degraded by human amylases and, as with other soluble fibers, it is degraded by bacterial enzymes in the colon and is fermented to short chain fatty acids.  The difference is that the glucose released from hydrolysis of RS is used directly by common gut bacteria, whereas the other sugars released from other soluble fibers require enzymes produced by particular species of bacteria to be converted first to glucose.  RS is a unique form of starch and a unique soluble fiber.

Short Chain Fatty Acids and Immune Cells Required for Health

Gut flora eat soluble fiber and produce short chain fatty acids, e.g. acetic, butyric, propionic acids, that feed the cells of the intestines and lower inflammation.  The development of both the aggressive and the suppressive (Tregs) halves of the immune system requires healthy gut bacteria.  The bacteria that digest RS, for example, are Clostridia (see EM right, note bacterium dissolving its way into the grain of RS), the type of gut flora that also stimulates Tregs and prevents autoimmunity.  Thus, the beneficial impact of dietary RS results from feeding gut flora.  Most people already support gut flora that can utilize RS, so most people benefit from RS in their diet.  Some people have severely damaged gut flora, dysbiosis and constipation, and they may need to eat live, fermented foods (not just dairy probiotics) to recruit enough new bacteria to benefit from RS.  Other healthy people may already have healthy gut flora that can exploit all of the soluble fiber in a compatible healthy diet, and need no further enhancement of their health by RS.  Health always requires gut flora complementary to diet and each change in diet requires accommodation by corresponding changes in gut flora.  Some changes in diet may require new species of gut bacteria.

Does Altered RS in Modern Bread Explain Gluten Intolerance?

The RS remaining in today’s superfine flour that is rapidly cooked into bread and other foods, may be very different from previous generations.  Traditional hydration and exposure to fermenting microorganisms may have produced breads with higher levels of RS that contributed to healthier gut flora.  Healthier gut flora would in turn produce less intestinal inflammation and a reduced response to gluten.

Diabetic Hypertension, Browning of the Arteries

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I decorated a flan with a drizzle of honey, and my torch produced a toasted spiral.  That was just fructose plus proteins, with a little heat, to produce advanced glycation end products (AGE) that are brown.  If you prefer, you can do the same reaction with egg whites and sugar in meringues, or by grilling brined pork chops basted with honey and anchovy paste.  Fructose is 10X better than other sugars at producing glycation, AGE and browning.

AGE and Arteries

Why do we care about the Maillard reaction and advanced glycation end products (AGEs)?  Of course, understanding the biochemistry of cooking is inherently satisfying and it helps to explain why Dr. House used vinegar to stop meatballs from browning too fast in his cooking class, but it also explains what’s cooking in atherosclerosis, cardiovascular disease.  It turns out that AGEs are highly inflammatory and inflammation of arteries leads to plaque formation.  [LDL is less important, because it only aggravates the primary event, inflammation, and that is why fish oil is more helpful for cardiovascular disease than statins.]  So increasing blood sugar is a problem, because it increases the rate of the Maillard reaction in binding blood sugar to the amino acids of proteins, such as hemoglobin to produce HgA1C, and causing vessel inflammation.  AGE in small capillaries also kills the capillaries and causes a rise in blood pressure by making harder for the heart to force blood from arteries to veins.  AGE causes hypertension and that is why salt consumption is not as important.   High blood sugar also increases the level of another powerful glycation agent, methylglyoxal, the active antibacterial agent in Manuka honey.  Honey is effective as a wound dressing, because it AGEs microbes to death!

The Trouble with AGE-ing is Inflammation

Cells detect the presence of AGEs with a surface Receptor for AGE (RAGE).  Binding of AGE to RAGE turns on the inflammation transcription factor, NFkB, with the release of inflammatory cytokines and the symptoms of inflammation.  One of my students did some computational protein modeling of the RAGE, because I was interested to see if RAGE would also bind Metformin.  Sure enough, our hunch was confirmed, indicating that Metformin might also reduce some forms of inflammation and be a treatment for diabetic high blood pressure.

Fructose vs. Inulin; AGE vs. Soluble Fiber

Fructose and the storage polymer of fructose, inulin, are similar to glucose and the storage polymer of glucose, starch.  The polysaccharides, inulin and starch can be converted to the sugars, fructose or glucose by industrial heating or enzymes.  Thus, agave inulin is converted into nectar, and corn starch is converted into syrup.  The polysaccharides are not sweet, but the sugars are.  The polysaccharides don't form AGEs with amino acids (unless they are broken up by high heat into sugars first) and fructose is 10X more chemically aggressive in forming AGEs than glucose.  Agave nectar (fructose) is a better browner than honey or high fructose corn syrup (corn syrup treated with a commercial enzyme to convert some of the glucose into sweeter fructose.)  Both inulin and some forms of starch (resistant starch), reach the colon and are digested by gut flora, i.e. they are soluble (fermentable) fiber.  The gut flora convert the resistant starch into short chain fatty acids that are anti-inflammatory.  Typical starch, e.g. corn starch or wheat flour, is digested by gut enzymes and goes directly into the blood as glucose, it is high glycemic and never reaches the gut flora.

AGE in Food

Should we fear browned foods as inflammatory.  I don't think that AGE in foods is any more of a hazard than all of the toxic phytochemicals that are touted as plant antioxidants.  I think that the gut and liver provide protection.  I brown the sugar on my flans and sear my steaks, even as I relish eating my veggies.  The body can detox these natural products in the gut better than it can handle the AGE made by high blood sugars.

Take Home Messages:

• Sugars in baked goods or blood, react with amino acids or proteins to make inflammatory AGEs.
• Blood sugar tests only measure glucose and ignore fructose, which is even more unhealthy.  So, foods laced with fructose can be low glycemic, but very unhealthy.
• The major AGE in blood is HgA1C.
• Diabetics have more stable, lower blood sugar on low carb diets, e.g. my Anti-Inflammatory Diet.  The liver produces needed blood sugar from protein.
• Diabetic use of fructose or agave nectar or honey encourages AGE, inflammation and diseases of diabetes.
• Starch (not RS) is the only polysaccharide digested by gut enzymes and is high glycemic.
• AGE is inflammatory leading to artery plaque and hypertension.
• AGE as browned foods are probably tolerated by the body.

Phytochemicals, Natural Antibiotics and Antioxidants

Plants are mean and sneaky.  They are natural organic chemists and make the nastiest toxins on earth.  Never trust a plant.  Eat them at your peril… or because they taste good.

Phytoalexins

Plants are Fast and Lethal

I was shocked when people started to laud the virtues of phytochemicals.  I thought that they must have alkaloid poisoning.  My PhD training involved separating and measuring the antifungal chemicals produced by soybean cotyledons exposed to the wall polysaccharides of a pathogenic fungus.  The plants would go crazy and produce a witch’s brew of toxins to provide protection from the fungus.  I eventually wrote a chapter on these toxic natural antibiotics, phytoalexins, for the Encyclopedia of Science and Engineering.  All plants produce these chemicals and as one might expect, seeds/nuts are provided with special protection to avoid being digested.

Lignin

Plants are Natural Chemical Killers

I developed a profound respect for the ability of plants to protect themselves.  Fungal spores germinate on the surface of leaves and their slender, threadlike hyphae attach and glue themselves to the waxy outer surface and then forcefully and enzymatically penetrate to the spongy cells below.  When the tip of the hypha touches the wall of the underlying cell, the plant nucleus lurches as its cytoskeleton reorients.  The surrounding plant cells respond in sympathy and all of these neighbors mobilize their biochemical processes to kill everything in their vicinity.  In a few hours, the plant chemicals kill the cells producing them along with the pathogen, and would continue to kill more and more of the leaf, but plant cell walls also contain enzymes that convert the phytoalexins to more wall material, lignin, and protect cells outside of the influence of the fungus.  As lignin in wood and plant litter is slowly degraded by microorganisms, it forms humus, the natural organic material in compost and soil, and also releases a potpourri of potent plant phenolics like BPA.  Compost is also a rich source of cell wall polysaccharides, a.k.a. soluble fiber, that feeds soil bacteria.

Phytochemicals are Natural Antibiotics

Most phytochemicals have evolved in plants as pathogen or herbivore defenses.  Since the nervous system is adapted to detect other organisms, it is not surprising that plants target the sensory system, brain and nerves of herbivores, and we detect the flavor and smell of plants/herbs/spices by their defensive molecules.  All of the flavor and taste components of herbs and spices are phytochemicals that kill bacteria, fungi and other pathogens.  Nicotine and caffeine are insecticides.  A detailed, worldwide study showed that spices are used in specific global areas, because of the local availability of the spices and their effectiveness against local food storage pathogens.  People develop a taste for the plant defensive chemicals that they must be exposed to for sustenance.  Cuisine represents a knife edge that separates attractive stimulation from death.  Natural or organic does not mean safe or healthy.  Plants are as dangerous to eat as pufferfish.

Phytoalexins are Useful, but Be Very Careful

Perfume Ingredients

If a grape notices a nearby fungal pathogen, it produces its phytoalexins, including resveritrol, which is a notable “antioxidant” that has been recognized as contributing to longevity.  People are encouraged to drink red wine for the health benefits of its phytoalexins.  Most of the pharmaceuticals derived from plants are phytoalexins in disguise.  Of course, the evolutionary origins of phytoalexins as natural broad spectrum antibiotics, makes it no surprise that phytoalexins are commonly toxic, carcinogenic and very dangerous to fetuses.  Morning sickness has been explained as nature’s way of telling a mother carrying a vulnerable fetus to not eat plants and potentially phytoalexins.  It is wise for women to avoid plants, perfumes and essential oils during their first trimester.  Essential oils are phytoalexin extracts from plants and many of these components are the essence of perfumes.  These same chemicals, e.g. limonene, serve dual purposes as fragrances and paint strippers, recreational drugs and insecticides.  We can smell these natural plant chemicals, because they are attacking our nervous system.  Multipurpose mixtures of essential oils, such as Vick’s Vaporub, contain menthol, camphor, eucalyptus oil and terpentine that kill bacteria and fungi (toe nail fungus) and also stimulate cold/hot sensing nerves in the skin, which triggers endorphin production and reduces underlying joint inflammation.

Fruits are Fake Seduction

Fructose is fruit sugar.  That is very appropriate.  Fructose derivatives are the most central intermediates of central metabolism, glycolysis; glucose is immediately converted to fructose after it enters a cell as the fundamental source of energy and carbon building blocks.  Fructose is not normally transported in plants or animals, because it is too chemically reactive and toxic.  It rapidly bonds and crosslinks proteins and is ten times worse than glucose in forming AGE (advanced glycation end products) such as hemoglobin A1C.  If you feed fructose to cattle, it makes their meat tough by cross linking protein fibers and it does the same thing to human skin.  Fructose in fruit is a fake, because it is cheap and sweet.  Animals eat fruit hoping to find starch, which is the only polysaccharide that animals can convert to glucose with their own (not bacterial gut flora) enzymes.  Starch quickly becomes sweet, because amylase in saliva digests the long chains of glucose molecules of starch into shorter dextrins that trigger sweet sensors in the tongue.  Fructose masquerades as starch by binding to sweet sensors a hundred times more strongly than dextrins.  The evolutionary advantage to using fructose to make plants sweet is that it takes much less energy and carbon, and it also poisons insects and microorganisms.  That is why honey is made of equal amounts of fructose and glucose, rather than sucrose, for example.  Fructose in high concentrations is toxic to microorganisms and honey can be used to dress wounds.  I can’t understand why fruits, especially juices, are recommended as part of a nutritional diet.  At best, fruit should be converted into juice.  The juice should be discarded and the pulp eaten as a source of soluble fiber, pectin, to feed gut flora. 

Phytochemicals Must be Detoxified to be Edible

Bacterial and fungal pathogens must avoid detection by plants to avoid death by phytoalexins.  Insects, similarly must avoid preformed phytochemicals that would kill or poison them with their first bite.  Pathogens and pests that are effective on one species of plant cannot eat others with different chemical defenses; plants and their pests/pathogens are mutually adapted.  Primates browse on new shoots of many different types of plants, to avoid building up lethal doses of particular phytochemicals.  The same is true of humans, who also have intestines and livers that chemically treat and neutralize plant toxins.  These same human defenses determine the rate at which other related chemicals, i.e. pharmaceuticals, most of which are derived from phytoalexins, are transformed and excreted.  Turmeric contains curcumin, which is the most potent inhibitor of inflammation yet identified.  Unfortunately, curcumin is “detoxified” in the intestine and large amounts must be eaten to suppress inflammation.  Fortunately, pepper contains another phytoalexin, piperine, which inhibits the detox system, so that most cuisines that use turmeric combine it with black pepper.

Trade Your Liver for Vegetables

The liver is the only organ that can be continually regenerated and that is because humans have evolved to eat plants, and phytoalexins take their toll on the liver.  As plants are digested and absorbed in the small intestines and transported to the liver, phytoalexins accompany the nutrients.  Most of the phytochemicals are chemically detoxified by liver enzymes, but the phytoalexins kill some liver cells with each meal and some of the phytoalexins circulate in the blood and reach other tissues.  The phytoalexins are evolutionarily adapted to bind to proteins to disrupt essential enzymes of microorganisms and herbivores, and like pharmaceuticals to which they are chemically and functionally related, they have numerous side effects.  The chemical reactivity is what is detected as the “antioxidant” property of phytoalexins.  Antioxidant is nutritionally meaningless and basically reflects the chemical toxicity of phytochemicals.  After all, you can’t easily sell chemicals that are inherently toxic.  Meat and humans are made of the same easily digestible stuff, i.e. protein, fat, plus indigestible polysaccharides in connective tissue, i.e. chondroitin sulfate and heparan sulfate.  Plants are essentially anti-human and are made of protein, vegetable oils (omega-6), digestible starch, undigestible cell wall polysaccharides, undigestible lignin and toxic phytoalexins.  Humans have adapted to eating plants with liver enzymes, liver regeneration, gut flora (to eat otherwise indigestible polysaccharides, soluble fiber to produce short chain fatty acids) and elaborate cultural habits.  We avoid most plants as too toxic and have domesticated some to produce reduced and tolerable levels of phytochemicals.  Of course this also means that the domesticated, defanged crop plants have a hard time defending themselves and we have to continually worry about blights and pestilences, and end up applying our own witch’s brew of fungicides, pesticides, and herbicides.

Polyphenols and Hormesis
I am going to add a few comments on the benefits of phytochemical "antioxidants", a.k.a. polyphenols, to clarify what I think is a misuse of the term "hormesis", which I thought meant the dilution of a toxin until it reached a magic lower concentration which was beneficial.  The trade offs of phytochemicals are nicely discussed by the Whole Health Source blogger, Dr. Stephan Guyenet.  I just don't think that the benefit of toxic chemicals stimulating the body's own antioxidant arsenal is an example of hormesis.  The point is that phytochemicals always act as toxins and stimulate toxin defenses.  Phytochemicals don't act as anti-oxidants in the body, even though they stimulate antioxidant defenses at all concentrations.  They provide a dubious benefit of unnecessarily heightening defenses with concomitant energy expenditure at low amounts and net damage at higher amounts.

Hakuna Matata and Sip the Tea

Tea Fanatic

I seem to have painted a compromising picture of plants as less than the perfect food.  They are tough and potentially toxic.  Plants clearly don’t like to be eaten and the best that can come of eaten plants is a full belly and a damaged liver.  But if you cook or ferment the plants first and bacteria start to digest and dull the chemical arsenal, plants can be safely and perhaps even enjoyably eaten.  We need not eat just safe meat.  We can also kick back and sip the tea.

Milk, Kefir and Gut Flora

Milk is a dramatic manipulator of gut flora.  It is a baby’s first food and provides necessary nutrients, but of equal importance, it crafts a community of gut microorganisms that develop the gut and immune system of babies.  Breastfed babies receive protein, fat and sugar, but they also coat their tiny stomachs and even their respiratory system with maternal lymphocytes and bacteria.  The major carbohydrate in breast milk is lactose, but there are other prebiotic oligosaccharides (HMO, human milk oligosaccharides) and polysaccharides (GAGs, glycosaminoglycans) related to heparin and chondroitin, which carefully limit which bacteria can grow in babies.  There are firm reasons why exclusively breastfed babies have diapers that smell like yogurt and look like curds and whey.

Milk Shows an Exaggerated Interaction between Food and Flora

Evolutionary selection is extreme to favor women who can successfully birth large babies and nurture them for years on breast milk.  Fewer than 5% of women in a general population need medical intervention for gestation, labor, delivery and breastfeeding.  Essentially all women and babies are genetically predisposed to healthy childbirth and milk-based child development.  Clearly, milk is powerful and an examination of the composition of milk should yield information on the interaction between food and gut flora.

Milk is the Prebiotic for Dairy Probiotics

Traditional preservation of cow's milk produces fermented kefir, butter, yogurt, cheeses, etc.  These are all controlled fermentations that begin by converting lactose into lactic acid.  Michael Pollan devoted a major section of his book, Cooked, to the cultural ramification and biology of fermentation.  It seems magical that leaving milk to sour will reproducibly yield a common dairy beverage.  When I taught microbiology, I had students spike raw cow’s milk with E. coli and then measure the decreasing survival of these common gut bacteria that are actively excluded from dairy fermentation.  One of the lessons here is that milk stops the growth of adult gut bacteria and supports the growth of lactic acid bacteria found in baby diapers and used to make fermented dairy products.

Milk is Toxic to Most Microorganisms, until Digested
Enzymes in the stomach convert milk proteins into antimicrobial peptides.  Later in the small intestines, pancreatic proteases digest and inactivate the peptides until they are converted into amino acids and are absorbed by the intestinal microvilli.  Milk is a natural antibiotic and is used ritually for cleansing wounds and pruning hooks.  Ritual fire walking ends by walking through a pool of cow’s milk.  The spread of plant disease in orchards from tree to tree is minimized by dipping pruning tools in milk.  The proteins, fatty acids and carbohydrates in milk kill or inhibit the growth of viruses, bacteria and fungi.  Early studies of the bacteria in breastfed babies showed an exclusive group of lactic acid bacteria and an absence of adult gut bacteria.  Breast milk was shown to contain a “bifidus factor” that selected for baby gut flora and this special ingredient was later shown to consist of a complex mixture of short chains of sugars, human milk oligosaccharides.  Thus, human milk is good for babies, but bad for adult gut flora because most of the protein, fat and carbs are digested and no soluble fiber remains for colon gut flora. 

Formula Kills Baby Gut Flora

Formula made from cow's milk or soy is toxic to baby gut flora and even a single bottle of formula can permanently damage it.  The disastrous impact of formula on gut flora is readily observed in the change to smelly diapers.  Mothers trying to give the best start to their babies can tell when the night nurse got lazy and just fed her baby a bottle of formula!  Use of formula in hospitals instead of mothers nursing or using donor milk greatly increases contamination of babies with deadly strains of hospital bacteria, e.g. C. dificile, and causes necrotising enterocolitis.  The only reason that babies can survive formula and the growth of adult gut flora in the first weeks of life, is that the disrupted gut flora is highly inflammatory and the inflamed gut provides some protection from infection.  Babies are tough, but there is no reason for hospitals to continue to use formula when research clearly shows that it is a risk to the health of babies.  Health concerns are forcing hospitals to encourage exclusive breastfeeding, but more work needs to be done so that donor breast milk is the alternative.

Raw Avoids Risks of Pasteurization and Ultra Homogenization
Milk straight from the udder contains natural dairy probiotics that are fit for a calf.  Dairy probiotics are different from baby gut flora and calves are different from babies, so cow milk is not appropriate for babies.  Processing cow's milk by heat (pasteurization) or extreme mixing to make ultra small fat droplets (homogenization) changes the structure of milk to increase storage shelf life, but the restructuring also produces some health risks for gut and gut flora.  Since leaves are rich in short chain omega-3 fatty acids and seeds are rich in omega-6s, grass fed cows produce healthier (higher 3/6 ratio) milk that may not store as well.

Kefir is a Yeast and Bacteria Biofilm

Commercial dairy products are uniform, because they are made from milk using defined mixtures of pure cultures of bacteria and fungi.  These dairy probiotics can substitute but not replace gut flora, because they can't grow in a healthy gut.  Kefir is a little different, because the kefir grains are biofilms of yeast and bacteria held together by a polysaccharide called kefiran made by a bacterial enzyme that rearranges the glucose and galactose sugar residues of lactose.  The point here is that if you grow your own kefir, you may end up with many species of bacteria and some may be able to contribute to your gut flora.  Many supermarket "kefirs" are just a blend of common dairy probiotics and maybe some inulin, and have no benefits over commercial yogurt.

Dairy products are nutritious, but will not benefit the health of your gut flora (fermented vegetables are a better choice), because they lack soluble fiber and do not contain gut flora, but your gut flora may adapt to the inherently disruptive nature of raw milk.

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 Diet and Gut Flora Myths

….All 190 posts here….

I just watched a Dr. Oz program on health myths, including corrections, such as recognition of the high fructose content of agave syrup (especially bad for diabetics.)  So I thought I would go ahead and correct some of the perspectives on his show that I don't think are supported by biomedical research.

The Big Truth about Diet and Gut Flora

Health results primarily from a matched Diet AND Gut Flora, with minor contributions by exercise, personal genetics, environmental toxins, etc.  You can eat the extremes of just meat or only vegetables or any mixture and be healthy, as long as your gut flora is made up of about two hundred different species of bacteria that can fully digest the soluble fiber in your diet.  Health requires a gut flora adapted to your diet.  Those bacteria, the gut flora, produce all of your needed vitamins, eliminate constipation, block inflammation and control the development of your immune system, which takes place in the lining of your intestines in response to gut bacteria.

Assorted Health Truths

Truth:  Saturated fats are healthy, but polyunsaturated omega-6 vegetable oils are inflammatory.  Oz can't bring himself to read the literature and acknowledge the heart benefits of saturated fats and meat.

Truth:  Soluble fiber, e.g. pectin in fruit or inulin in leeks or chondroitin in meat, is healthy food for gut flora, but insoluble fiber, such as in whole grains is a scam and just sucks out micronutrients.  Oz could really help the public by explaining that the hundreds of different polysaccharides produced by plants, i.e. soluble fiber, are digested by hundreds of different enzymes in gut flora.  Gut flora digest soluble fiber into sugars that are converted into short chain fatty acids that feed intestinal cells.

Truth:  GMOs have been studied intensively, are relatively boring and healthy, but organically grown veggies have not been shown to provide any additional health benefits over conventional.  Oz adheres to a very political line and attacks GMOs without any reasoned arguments and touts organic veggies without reference to supporting research.

Truth:  Grass grown beef has healthier fats with more omega-3 oils, but omega-3 plant oils, such as ALA in flax, provide only minor benefits and can't substitute for the long chain DHA and EPA in fish/algae oil.  Oz keeps pushing flax seed even though the benefits are minimal and the problems of high insoluble fiber have not been tested.

Truth:  Constipation is a sign of unhealthy gut flora and can lead to autoimmune disease, allergy or food intolerance, but laxatives such as magnesium only fix the symptoms and not the missing essential gut bacteria.  Oz is really confused about constipation and focuses on dehydration rather than the bacterial content of stools.

Truth:  Antibiotics may be essential for surgery or life threatening bacterial diseases, but antibiotic-damaged gut flora must be repaired (not just probiotics) or the immune system will be compromised.  Antibiotics are major contributors to autoimmune disease and I don't think that Oz realizes the damage that he starts or continues by not repairing gut flora after he repairs hearts.

Truth:  Dairy probiotics, e.g. Lactobacillus or Acidophilus, can provide a quick fix for some functions of gut flora, but these limited probiotic bacteria do not survive in the gut and do not substitute for normal gut bacteria.  I think that Oz still sends his patients home with yogurt after heavy antibiotic treatment and leaves his patients with damaged gut flora and long term disease risk.

Truth:  An Anti-Inflammatory Diet can reduce sources of inflammation that is the foundation for cancer, autoimmunity, allergy and most diseases, but adding new bacteria (not dairy probiotics) through social contacts and live fermented foods is essential for a healthy gut and immune system.

Truth:  All needed vitamins are supplied by healthy gut flora (as biofilm chemical signals) and healthy people do not benefit from multivitamin supplements, but people with damaged gut flora, e.g. because of antibiotic use or autoimmune disease, may require specific vitamins.

Truth:  Antioxidants are just plant defense chemicals, i.e. plant antibiotics, that are unimportant in general health, but they may alter gut flora in unpredictable ways.  Oz likes all antioxidants, but can't explain why these generally toxic chemicals are not used by plants as antioxidants.

Truth:  All of the vitamin D that we need is supplied by minimal skin exposure to sunlight, but most Americans are vitamin D deficient, because chronic inflammation blocks solar production of vitamin D in the skin.  Oz doesn't seem to understand the role of inflammation in vitamin D deficiency.

Truth:  We don't need Grains and other sources of starch, but grains also typically cause health problems, e.g. sensitivity, intolerance or celiac, for most people and can cause inflammation of the gut and disruption of the gut flora that can lead to autoimmune diseases.  Most thyroid disease and back problems are autoimmune diseases that start with celiac.  Oz still promotes whole grains even though added bran lowers nutritional quality and many people are healthier without grains.  He also seems to ignore the relationship between grain, antibiotics and autoimmune disease.

Truth:  Breakfast is not a necessary meal and there are health benefits to lengthening the time between the last and first meal of the day, but if breakfast is eaten, it should be low in sugar and starch, i.e. avoid cereal, since cereal causes a severe spike in insulin when eaten after a fast.  Breakfast makes you hungry, because even protein in the morning will raise insulin and cause an eventual abrupt drop in blood sugar that is experienced as hunger.  Why does Oz believe in breakfast?

Truth:  Food intolerances and allergies (rare) are due to missing species of gut bacteria, but these eating problems cannot be fixed by diet alone, since new bacteria (other than dairy probiotics) must be eaten.  Dairy probiotics are only useful to cure lactose intolerance.

Truth:  Hygiene should be minimal, because most people repair damaged gut flora due to antibiotics, for example, by intimate contact with friends and pets.  Antimicrobial soaps and sterile home surfaces prevent gut flora repair, because the vast majority of bacteria killed by hygiene are beneficial.  Appropriate hygiene is a real problem for Oz and he is obsessed with closing toilet covers.

Truth:  Cardiovascular disease starts with inflammation and is aggravated by fat deposits, but statins and lowered serum cholesterol only reduce heart attack risk, because statins have a weak side effect of lowering inflammation.  Diet changes and repair of gut flora, e.g. my Anti-Inflammatory Diet, fish oil supplements and wild fermented foods, are much more effective at reducing inflammation and curing cardiovascular disease without the severe risks of statins.  Oz is slowly becoming skeptical of statins, but still hasn't read the research literature critically.

Truth:  Poor health and most diseases have only minor genetic risk factors, but diet and gut flora are "inherited" directly and shared by the whole family.  When your doctor asks what diseases run in your family, she is asking about your shared gut flora.  Oz still gives the impression that genes are significant in disease and for example asks audience members if relatives have had heart disease.  He should tell them to repair their gut flora!

Summary Diet Truths

Truth:  There is nothing magic about healthy foods.  All that is needed are protein (meat, fish, eggs, dairy, beans, etc.; plant and animal proteins are equivalent), fats (from leaf and meat, not omega-6-rich seeds) and soluble fiber (to feed gut flora) from their original sources to retain naturally abundant micronutrients (vitamins, except C, are usually unimportant.)  That is my Anti-Inflammatory Diet and supplements should not be needed.  Natural, local foods are healthy, but there are no super foods and exotic does not mean better.  Variety does not compensate for low quality.  Your gut flora needs time to adjust, especially to new soluble fiber, so just change foods with the seasons, not daily, and make sure that you are sampling new bacteria in live fermented foods to make your gut community adaptable.

Transglutaminase, Gluten, Celiac, Inflammation, Autoimmunity

The point of this post is that the intestines produce an enzyme, transglutaminase (TG) that normally protects the gut from toxic plant proteins, such as grain gluten, but modern food processing and antibiotics corrupt digestion of gluten to produce intestinal inflammation and a series of related autoimmune diseases including celiac, thyroiditis, diabetes, baldness and atherosclerosis. 

Transglutaminase Links Proteins Enzymatically

Transglutaminase is a ubiquitous enzyme produced in the intestines, thyroid, heart, skin, hair follicles, etc.  This enzyme attaches to a protein (TG + ProA ~~> TG-ProA) via amino groups extending from some of the protein's amino acids, e.g. lysine or glutamine, and then the enzyme replaces itself by another protein leaving the two proteins crosslinked (TG-ProA + ProB ~~> TG + ProA-ProB).  Another alternative reaction is to leave the original glutamine without its amino group to yield glutamic acid residues.

Linking Proteins Makes Connective Tissue Tough

Transglutaminase is useful to crosslink the proteins in connective tissue.  Proteins in basement membranes form a matrix by binding to the heparan sulfate sidechains of another basement protein, perlecan.  The heparin-binding domains consist of basic amino acids that TG can react with to crosslink the proteins.

Linking Pathogen Proteins

Transglutaminase is also produced to crosslink the DNA/heparin/matrix polysaccharide-binding domains of pathogenic bacteria leading to aggregation, localization and death of the bacteria.  Inflammation resulting from activation of the inflammatory transcription factor, NFkB, stimulates production of TG.

Gluten is a Plant's Way of Saying "Don't Eat Me!"

Gliadin is a protein component of gluten that contains long stretches of glutamine residues, i.e. it is a polyglutamine protein similar to the protein that causes Huntington's disease.  Gliadin is an advantage as a storage protein for grain, because it is aggregated by the TG that protects the lining of the intestines of herbivores, such as humans, makes the animal sick and thereby discourages eating the grain.  Aggregation of gliadin/gluten inhibits digestion of the grain protein and can leave TG bound to gliadin.  Conversion of the polyglutamine stretches to polyglutamic acid stretches that are negatively charged, produces proteins that will bind to the positively charged heparan sulfates that circulate along the surface of intestinal cells leading to damage and inflammation.

Basic Triplet Leads to Antibody Production

Transglutaminase is also transported into cells, because it contains a region with a triplet of basic amino acids (...EPKQKRKLVA...).  This internalization probably contributes to enhanced presentation of TG to the immune system for subsequent antibody production.

Transglutaminase is Inflammatory

Transglutaminase interaction on the surface of cells also activates, NFkB, the transcription factor responsible for inflammation. Thus, TG turns on inflammation and part of inflammation is the activation of the innate immune system that includes production of TG.  This circular activation may produce autoinflammation that is associated with various forms of inflammatory bowel diseases.

Gluten Sensitivity is Normally Controlled By Gut Flora

Gluten sensitivity expressed by most people, is the intestinal response to the toxicity of gluten as it interacts with TG and causes inflammation.  This inflammation will also result in immune presentation of both gliadin and TG, and production of antibodies to both. Antibody production will normally be controlled by regulatory T cells of the immune system, unless spreading inflammation in the gut and/or antibiotics destabilizes the gut flora and compromises regulatory T cell development in the intestines.  

Anti-Glutaminase Antibodies Attack the Gut

Celiac results from uncontrolled production of antibodies to gliadin and TG with attack by the immune system on the aggregated gliadin/TG on the surface of the intestinal epithelium.  Celiac flare ups in response to eating even small quantities of gluten lead to further inflammation of the gut and further disruption and simplification of gut flora.

Celiac Leads to Thyroiditis and Much More

Transglutaminase is also produced by the thyroid and celiac will develop into a more generalized autoimmune disease that results in Hashimoto's thyroiditis.   TG production in the skin can result in skin rashes and may contribute to rosacea.  The base of hair follicles contains TG involved in hair production, and may contribute to some forms of hair loss.  Another substantial worry about the sequelae of celiac and gluten intolerance is the presence of TG in coronary arteries.

Antibiotics are Part of the Gluten Problem

Celiac and gluten sensitivity seem to be increasing with modern processing of grains and increased use of antibiotics.  Wheat has been gradually changed by traditional breeding, but genetic engineering has not yet been developed for wheat.  So, at least in this case, GM wheat cannot be part of the problem.  Many recent studies show that antibiotics profoundly and permanently alter gut flora.  As a result, the immune system, which is dependent on gut flora diversity is compromised, and various forms of autoimmunity and allergies develop.

Super Fine Flour Damages Gut Flora

Germ and bran are removed from all wheat before it is ground.  This is true even for whole grain flours, which have some of the germ and bran added back after milling.  Modern milling may be part of the gluten problem, because the flour is ground so fine that the grains of starch are broken.  Broken starch grains are digested by pancreatic amylases in the upper intestines, whereas some of the starch from intact grains is digested by gut flora in the colon.  Thus, modern wheat flour fails to feed gut flora like soluble fiber to produce short chain fatty acids, e.g. proprionic acid that supports Treg development; modern superfine flour supports autoimmune diseases and allergies.

Cultural Practices Make Gluten Safe

Wheat has been bred to produce bread as fast as possible from superfine flour.  This rapid bread production eliminates the exposure of gluten to enzymes from both germinating wheat seed and fermenting bacteria, which are part of traditional bread making.  Coarsely milled, traditional flour responds to soaking in water by activating enzymes that partially digest gluten, since gluten is a storage form of amino acids destined for the seedling.  Sour dough starter, a mixture of bacteria that can ferment the starch and gluten into short chain fatty acids and bubbles of carbon dioxide, has been used traditionally to provide leavening and flavor to bread.  Both flour and bacterial enzymes modify the structure of gluten to render it less toxic to the intestines.  Cultural traditions insured that gluten would be systematically detoxified by enzymes during hydration and fermentation of dough prior to baking.  Modern processing leaves wheat gluten in bread unmodified and toxic.

Prevention and Cure:  Eliminate or Detoxify Wheat and Add Bacteria

Preventing and curing diseases associated with gluten and transglutaminase is simple.  Eliminating wheat would do the trick.  Unfortunately, wheat is the mainstay in many parts of the world.  Fortunately, gluten intolerance is not uniformly observed where wheat is eaten.  This indicates that there are potentially safe ways to eat wheat and bread.  I gained insight into how to eat wheat safely from two books that were recently published:  Cooked by Michael Pollan and Artisan Bread in Five Minutes a Day by Jeff Hertzberg, MD and Zoë François.

Michael Pollan has recently become interested in gut flora and his book revealed how he built up a healthy gut flora eating homemade fermented food and compromised his work with antibiotics.  The major breakthrough that I made by reading Cooked was based on his experiments in baking whole wheat bread.  He hydrated the flour first and then used sour dough starter for lengthy fermentation.  This was the same process that I had used to make great loaves of bread (photo above) using Jeff Hertzberg’s directions in Artizan Bread in Five Minutes a Day.

The answer to gluten intolerance and most autoimmune diseases amounts to eliminating wheat or treating wheat in a safe, traditional process that inactivates the toxic properties of gluten; and maintaining a healthy gut flora (probiotics are not enough) with hundreds of different species of bacteria that promote the development of the suppressive immune system mediated by regulatory T cells:

Safe Traditional Bread 

• Remove bran and discard as toxic insoluble fiber.
• Grind wheat to retain starch grain structure.
• Soak flour to hydrate and activate wheat enzymes to start digestion/detox of gluten.
• Ferment dough with bacteria (sour dough starter) to continue digestion/detox of gluten.
• Bake.

Develop Healthy Gut Flora and Suppressive Immune System

• Avoid antibiotics that kill bacteria.
• Avoid hygiene practices, e.g. antibacterial soaps, bleaching surfaces, closing toilet covers, etc. that eliminate sources of healthy bacteria.
• Kiss your loved ones and pets, and encourage everyone to garden/play in the soil (an excellent source of thousands of different species of bacteria.)
• Recruit healthy gut bacteria by eating a variety of homemade fermented vegetables. My most highly recommended source is my friends at: http://www.fermentista.us
• Remember that cooked or pasteurized foods do not contain useful bacteria.
• Remember that dairy probiotic bacteria cannot live in the human gut and can only provide a temporary help to the immune system.
• Limit the variety of foods that are consumed and gradually change with the seasons to avoid rapid changes in nutrients to which gut flora cannot adapt.  Food intolerances indicate maladapted gut flora.
• Constipation indicates dysfunctional gut flora and a compromised immune system.