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Brain Maker  by David Perlmutter, M.D.


Italics are Dr. Stingl's Comments


Death begins in the colon.

-Élie Mechnikov (1845-1916) 1908 Nobel prize winner for the discovery of phagocytosis


And so does health. Metchnikov noticed the longevity and health of the peasants in the Northern Caucasus, who kept their prized possession, kefir, a secret. He experimented on himself with fermented lactobacillus isolates (he also attempted suicide twice after the death of his first wife and severe illness of his second, but thankfully, he was unsuccessful). Many believed that this kefir concoction held special powers; a gift from the gods, an elixir of life, a miracle drink. It was Metchnikov who said that the good bacteria in our gut must outnumber the bad. Hippocrates the third century B.C.E. physician and father of modern medicine said, “All disease begins in the gut.” New scientific evidence is indicating that 90% of all human illness can be traced back to an unhealthy gut.

Dr. Perlmutter notes that this new knowledge about our gut biome can help with ADHD, asthma, autism, allergies and food sensitivities, chronic fatigue, mood disorders including depression and anxiety, diabetes and craving for sugar and carbohydrates, overweight and obesity as well as weight loss struggles, memory problems and poor concentration, chronic constipation or diarrhea, frequent colds or infections, intestinal disorders including celiac disease +IBS+Crohn's, insomnia, painful joint inflammation and arthritis, high blood pressure, atherosclerosis, chronic yeast problems, skin problems such as acne and eczema, bad breath including gum disease and dental problems, Tourette's, extreme menstrual and menopausal symptoms and many more. The intenstinal flora that residing in the delicate folds of our intestine: aid in the digestion and absorption of nutrients, create a physical barrier against bad bacteria & harmful viruses and parasites, detoxify, influence the immune system, help us handle stress, assist in a good night's sleep and help control inflammation. Popular antidepressants such as Paxil, Zoloft and Lexapro increase availability of serotonin in the brain but the reason dietary changes can be more effective is 80 to 90% of the serotonin in our bodies is manufactured by the nerve cells in our gut. The gut has its own immune system, the “gut-associated lymphatic tissue” (GALT) representing 70 to 80% of our body's total immune system. Fat people have more firmicutes bacteria in their gut whereas lean people have more bacteroidetes.

Our gut biome starts at birth. Passing through the birth canal we are 'baptized” in vaginal microbiome, dominated by beneficial lactobacillus. Babies born by C-Section have a: five-fold increased risk of allergies, triple the risk of ADHD, twice the risk of autism, 80% increased risk of celiac disease, 50% increased risk of becoming obese as an adult and 70% increased risk of type-1 diabetes. There are three forces working against our gut biome: 1) exposure to substances like environment chemicals, food (sugar, gluten,etc.), water (chlorine), and drugs (antibiotics), 2) lack of nutrients, and 3) stress. There is an association between Alzheimer's with higher degrees of sanitation in Western industrialized countries compared with countries with lower degrees of sanitation and parasite infestation such as Costa Rica and Sudan (an association is not causation). Good gut bacteria can help prevent (and even assist in reversing with ReCODE) Alzheimer's. A leaky gut as indicated by bacteria produced lipopolysaccharide (LPS) in the blood is associated with not only Alzheimer's, but a multitude of diseases that have inflammation in common. Fecal microbial transplantation (FMT), a procedure not without risks because it involves transplanting tissue from a donor human to a recipient, has nonetheless produced some amazing results for multiple sclerosis as well as other diseases. Gastric bypass surgery appears to work for obesity and diabetes, not because of the mechanical restriction imposed by a smaller stomach, but rather by a change in the gut microbial communities by increased circulating bile acids and binding the farnesoid-X receptor (FXR). Eighty percent of the antibiotics used in the U. S. are fed to livestock to alter their gut biome which causes them to pack on weight. There has been a huge increase in autism spectrum disorders in America since 1970. Again, Dr. Perlmutter relates an amazing anecdotal story of autism treated with FMT. When gut bacteria process dietary fiber they produce three main short-chain fatty acids: acetic, propionic and butyric. Clostridial bacteria species produce propionic (PPA) in abundance and autistic children have been found containing a larger number of Clostridial bacteria. When PPA was fed to pregnant rats and their offspring, the pups brains showed changes similar to autism. When PPA was injected into rats they displayed autistic behavior. This was blocked by pre-treatment with the glutathione enhancer n-acetyl cysteine (NAC). NAC, L-carnitine and omega-3s have been suggested as potentially useful for autism. Children with autism may have lowered mitochondrial activity (PPA compromises mitochondrial function).

Trouble in Bugville

The risk of developing diabetes is twice as great for women who drank artificially sweetened beverages compared to those drinking sugar sweetened beverages. (No, it is not OK to drink sugar-sweetened drinks – the artificial sweeteners affect the gut bacteria). Besides causing fatty liver disease, high fructose diets also cause bacteria to leak from the gut. Gluten causes leaky gut and disrupts the gut microbiome. Antibiotics, birth control pills, environment chemicals and herbicide laden GMO foods may all adversely affect the gut biome.

Feeding your microbiome

Dr. Perlmutter recommends Live-cultured yogurt, kefir, kombucha tea, tempeh, kimchi, sauerkraut, pickles, pickled fruits and vegetables (not in vinegar), cultured condiments, and fermented meat, fish and eggs. Eat a low carb high fiber diet with high quality fat.

Veggies: leafy greens and lettuces, collards, spinach, broccoli, kale, chard, onions, mushrooms, cauliflower, Brussels sprouts, artichoke, alfalfa sprouts, green beans, celery, bok choy, radishes, watercress, turnip, asparagus, garlic, leek, fennel, shallots, scallions, ginger, jicama, parsley, water chestnuts

Low-sugar fruit: avocado, bell peppers, cucumber, tomato, zucchini, squash, pumpkin, eggplant, lemons, limes

Healthy fat: extra-virgin olive oil, sesame oil, coconut oil, grass-fed tallow, and organic or pasture-fed butter, ghee, almond milk, avocados, coconuts, olives, nuts and nut butters, cheese (except blue cheeses), and seeds (flaxseed, sunflower seeds, pumpkin seeds, sesame seeds, chia seeds)

Protein: whole eggs, wild fish (salmon, black cod, mahimahi, grouper, herring, trout, sardines); shellfish and mollusks (shrimp, crab, lobster, mussels, clams, oysters); grass-fed meat, fowl, poultry, and pork (beef, lamb, liver, bison, chicken, turkey, duck, ostrich, veal); wild game

Herbs, seasonings, and condiments: mustard, horseradish, tapenade and salsa (if they are free of gluten, wheat, soy and sugar). No ketchup.

Enjoy red wine, tea and coffee.

Choose foods rich in prebiotics. They reduce febrile illnesses, reduce inflammation, enhance absorption of minerals, lower risk of cardiovascular disease, promote a sense of fullness or satiety, and reduce glycation. Dr. Perlmutter's top food sources of natural prebiotics: Acacia gum (or gum arabic), raw chicory root, raw Jerusalem artichoke, raw dandelion greens, raw garlic, raw leek, raw onion, cooked onion and raw asparagus. It is easy to work in the cooked onion. If you Google foods containing inulin you will see the same plus bananas (which you should eat green for the resistant starch) and jicama.

Drink filtered water.

Fast every season (or more often than 4 times a year). Just keeping 12 hours between eating in the evening and the following morning has the same beneficial effect, especially if you are in mild ketosis.


Dr. Perlmutter recommends five core bacteria for probiotics: Lactobacillus plantarum, Lactobacillus acidophilus, Lactobacillus brevis, Bifidobacterium lactis, and Bifidobacterium longum. We recommend Lifeway brand Organic Whole Milk Kefir with the prebiotic psyllium seed(husk has plenty of soluble fiber, but seed creates more butyrate) which contains all of these bacteria except Lactobacillus brevis which is in Dr. Mercola's Kinetic-Culture; however, it also contains Lactobacillus Rhamnosus, Streptococcus Diacetylactis, Lactobacillus Casei, Saccharomyces Florentinus, Leuconostoc Cremoris, Bifidobacterium Breve, and Lactobacillus Reuteri.


DHA, Tumeric, Coconut Oil, Alpha-Lipoic Acid, Vitamin D

Meals and Homemade Fermented Foods

Dr. Perlmutter advocates home fermentation of vegetables using “wild” fermentation and some starter cultures. A 2003 book by Sandor Katz has generated quite a following. Using salt tolerance as a method to select species, the bacteria and fungi (yeasts and molds) which are allowed to propagate exist on the vegetables, your skin and your kitchen countertop. Hopefully, the final product contains the species that will optimize our health. Hopefully, we are not amplifying bad species or ingesting compounds which are injurious to our health. Fermented foods tend to be high in salt, which can raise blood pressure. A recent study in mice fed an amount of salt comparable to a high salt diet in humans reduced blood flow to the brain and impaired cognition independent of blood pressure by a gut-initiated TH17 response.


One of our promises as physicians in the Hippocratic Oath we took is “Primum non nocere”

First Do No Harm


More diversity in the gut biome has viewed as positive with good evidence, but restriction or elimination of some species appear to be necessary to be on “The Path to Health”. We are in our infancy in understanding our gut biome, holding a candle glimpsing at morsels of wisdom in a giant cavern of dark ignorance. There is ample evidence that fermentation produces healthy compounds although randomized controlled trials (RCTs) are lacking.

Health benefits of fermented foods.

Crit Rev Food Sci Nutr. 2019;59(3):506-527. doi: 10.1080/10408398.2017.1383355. Epub 2017 Oct 20.

Lactic acid bacteria (LAB) have been some of the most studied microorganisms. During fermentation, these bacteria synthesize vitamins and minerals, produce biologically active peptides with enzymes such as proteinase and peptidase, and remove some non-nutrients. Compounds known as biologically active peptides, which are produced by the bacteria responsible for fermentation, are also well known for their health benefits. Among these peptides, conjugated linoleic acids (CLA) have a blood pressure lowering effect, exopolysaccharides exhibit prebiotic properties, bacteriocins show anti-microbial effects, sphingolipids have anti-carcinogenic and anti-microbial properties, and bioactive peptides exhibit anti-oxidant, anti-microbial, opioid antagonist, anti-allergenic, and blood pressure lowering effects. As a result, fermented foods provide many health benefits such as anti-oxidant, anti-microbial, anti-fungal, anti-inflammatory, anti-diabetic and anti-atherosclerotic activity. However, some studies have shown no relationship between fermented foods and health benefits.

Adv Food Nutr Res. 2019;87:147-185. doi: 10.1016/bs.afnr.2018.09.001. Epub 2018 Dec 7.

Microbial Ecology of Fermented Vegetables and Non-Alcoholic Drinks and Current Knowledge on Their Impact on Human Health.

While kombucha is often hyped as a "super-food," only antioxidant and antimicrobial properties toward foodborne pathogens are well established; and it is unknown if these properties incur beneficial impact, even in vitro or in animal models. To conclude, plant-based fermented foods and drinks are usually safe products; few negative reports can be found, but more research, especially human dietary intervention studies, are warranted to substantiate any health claim.

Nutrients. 2018 Apr; 10(4): 448.

Published online 2018 Apr 4. doi: 10.3390/nu10040448

Fermented Food and Non-Communicable Chronic Diseases: A Review.

The strongest evidence for a beneficial effect is for yoghurt on risk factors of type 2 diabetes. The literature on fermented plants is characterized by a wealth of in vitro data, whose positive results are not corroborated in humans due to the absence of Randomized Controlled Trials (RCTs). Finally, none of the RCTs were specifically designed to address the impact of food fermentation on health.


Home Fermentation Safety


Dr. Stingl has experience with fermentation because he owned a winery. He would never start a ferment without a starter culture and he would never allow oxygen to get to the ferment. (The way to make a small fortune owning a winery is to start with a large fortune.) Vegetable starter cultures from Cutting Edge, Caldwell's and Body Ecology all contain Lactobacillus plantarum, Pediococcus acidilactici and Leuconostoc mesenteroides (ssp cremoris in body ecology), which are naturally occurring bacteria on cabbage. Dr. Mercola's Kinetic Culture is far more likely to contribute to long term health and a diverse gut microbiome.


We recommend anyone considering home-fermentation read the following three links. Our goal is not to just avoid acute food poisoning, but create a food product that will enhance our long term health.

In the United States, acute food poisoning from home-fermented foods is very rare. However, that does not mean they are good for your health. You can drink a 2 liter bottle of soda every day without getting food poisoning, but that does not mean it is good for your health.

Home fermented raw milk or raw meat? We absolutely love this story because it is an honest account of fermentation told with humility from Lea Harris (who found mold at the bottom of an innocent looking ferment after finding mold at the top) and her discussion of CO2.


In terms of acute food poisoning, home-fermented vegetables are safer than raw vegetables. What is the worst possible case? Botulism, which can be fatal. Clostridium Botulinium spores are heat resistant, but the toxin (one of the most lethal substances known) produced under low-oxygen conditions is destroyed by boiling. However, the leading cause of botulism in China is home fermented foods.

The CDC estimates produce causes nearly half of all food borne illnesses. Annually, 9 million in the U.S. get sick from food poisoning, 55,000 are hospitalized and 1,000 die. E. Coli occurs more commonly in beef and vegetable row crops, listeria in dairy and fruits, Campylobacter in raw milk and salmonella in everything. Studies have shown that intentional inoculation into lactic acid fermentations with pathogenic bacteria showed poor survival of the pathogens. However, it is not fool-proof.

A study looking at Diverstiy of Microorganisms in Global Fermented Foods and Beverages found Enterococcus Faecium in Goyang (wild vegetables) in India and Nepal and Jiang-sun (bamboo shoots) in Taiwan. This is a nasty virulent bacteria that you do not want to ingest (just ask any Intensive Care physician or nurse).

Pathogenic Properties of Enterococcus Faecium

Numerous sources for home fermentation advise just scraping off any mold that may appear but the toxins can already be in the liquid. This may not make you acutely ill, but after you become familiar with Dr. Bredesen's ReCODE, you will understand how these toxins can contribute to chronic disease.

Toxins in Fermented Foods: Prevalence and Preventions Mini Review

Toxins (Basel). 2019 Jan; 11(1): 4.

Mycotoxins (aflatoxins, fumonisins, sterigmatocystin, nivalenol, deoxynivalenol, zearalenone, ochratoxin, and alternariol), bacterial toxins (shiga toxin and botulinum), biogenic amines, and cyanogenic glycosides are the common toxins found in fermented foods in addition to the pathogenic microbes. Fermented milk products and meat sausages are extremely vulnerable to contamination. The authors recommend use of specific starter culture, optimized fermentation process, and pre- and post-processing treatments.

Homemade kombucha tea carries significant risk with scant evidence of health benefits.

It gets worse. Pickled foods doubled the risk of esophageal cancer and increased the risk of gastric cancer by 50%. A high salt diet raises the risk, as well as Helicobacter pylori. However, eating non-fermented unsalted fruits and vegetables reduces the risk of cancer.

Pickled Food and Risk of Gastric Cancer-a Systematic Review and Meta-analyses of English and Chinese Literature

Pickled Food increased the risk of gastric cancer by 50% in East Asia.

Pickled vegetables and risk of oesophageal cancer: a meta-analysis.

Pickled Vegetables doubled the risk of esophageal cancer.

Fermentation does not remove pesticides. Because of Dr. Bredesen's ReCODE, we think it is important to ingest as little pesticide and toxins as possible. We would like to note that Rotenone, a pesticide approved organic labeling, is a mitochondrial poison that is extremely toxic to fish and causes a Parkinson's like disease when injected into animals. A study found a 15 minute soak in a sodium bicarbonate solution (1 teaspoon per two cups of water-) was more effective in removing the pesticides thiabendazole (deeper penetrating) and phosmet from apples than the standard industry practice of water and bleach wash. Bicarbonate of soda wash was found to be effective in the removal of 10 typical pesticides from spinach. If you cannot find or afford organic strawberries, a study comparing tap water, wash ozone water wash, ultrasound cleaning, and boiling found 5 minutes of ultrasound cleaning was the most effective removing up to 91.2% of pesticides; boiling was almost as effective (but who wants to boil strawberries?) Organophosphate pesticides were removed from raw cucumbers with bicarbonate wash (31-99%, although the stronger and more dangerous alkali sodium carbonate worked better on trichlorfon and dimethoate), ultrasonic cleaning (50-84%) and 48 hours at 5 degrees C (61-90%)(! From other sources as well – which is hard to explain). The problem of removing pesticides is complex with many variables: Efffect of handling and processing on pesticide residues in food

The Environmental Working Group publishes a widely popular list of 47 fruits and vegetables ranked by the risk of pesticides (ranked by the likelihood of finding multiple pesticides) 2019 list based on 2017 and as far back as 2002 from USDA and FDA data : Listed from the “dirtiest” to the “cleanest”:

  1. Strawberries (The top 12 are the 'dirty dozen')

  2. Spinach

  3. Kale

  4. Nectarines

  5. Apples

  6. Grapes

  7. Peaches

  8. Cherries

  9. Pears

  10. Tomatoes

  11. Celery

  12. Potatoes

  13. Sweet Bell Peppers

  14. Cherry Tomatoes

  15. Lettuce

  16. Cucumbers

  17. Blueberries

  18. Hot Peppers

  19. Plums

  20. Green Beans

  21. Tangerines

  22. Raspberries

  23. Grapefruit

  24. Winter Squashes

  25. Snap Peas

  26. Carrots

  27. Oranges

  28. Summer Squashes

  29. Mangoes

  30. Bananas

  31. Sweet Potatoes

  32. Watermelons

  33. Honeydew Melons (The bottom 15 are the 'clean fifteen')

  34. Mushrooms

  35. Broccoli

  36. Cantaloupes

  37. Cauliflower

  38. Cabbage

  39. Kiwis

  40. Asparagus

  41. Eggplant (2006 data)

  42. Papayas

  43. Onions

  44. Frozen Sweet Peas (2003 data) – Pesticide Action Network found 12.1% of Frozen Sweet Peas contained Dimethoate, 3.3% contained o-Phenylphenol, 2.3% contained Omethoate and a total of 12 different pesticides based on 2006 data

  45. Pineapples (2002 data)

  46. Sweet Corn

  47. Avocados


Consumers Reports publishes the Consumers Guide to Residual Pesticide Risk with a logical assessment called the Dietary Risk Index (DRI) based upon not only the number of pesticides per sample, but also the average level of each sample, frequency of finding it, serving size, toxicity of each pesticide, more complete information concerning noncancer as well as cancer, and domestic vs. imported. They note the DRI scores are improving over time.

  1. Very High Risk: Green Beans, Sweet Bell Peppers, Hot Peppers

  1. High Risk: Peaches, Tangerines, Plums(Chile), Nectarines(Chile), Apples(USA), Strawberries, Cantaloupe(USA), Winter Squash, Cucumbers, Summer Squash, Snap Peas, Tomatoes, Sweet Potatoes, Cherry Tomatoes

  1. Always Buy Organic: Peaches, Tangerines, Nectarines, Strawberries, Cranberries, Green Beans, Sweet Bell Peppers, Hot Peppers, Sweet Potatoes, Carrots


The California Department of Pesticide Regulation (CDPR) publishes annual data on pesticide residue, the latest being 2017:

Illegal Pesticides by Country:

Vietnam 100% of samples tested contained illegal pesticides (14/14) !

Guatemala 13% (8/62)

Mexico 7% (68/986)

USA 2% (41/2206)

Organic does not mean “not treated with pesticides”. In 2017, 288 organic samples were tested covering 69 commodities from 12 countries. 42 (14.6%) contained pesticide residue. Three contained illegal pesticides:

Organic Lemons – Mexico

Organic Limes – Mexico

Organic Kale – California !!

Conventional (Nonorganic) Produce Containing Illegal Pesticides

100% of Dragon Fruit (5/5) and Litchi Nuts (4/4) !

91% of Logan from China

50% of Cilantro (10/21)

50% of Mint from California (½)

35% of Cactus Pads and Pears from Mexico (15/43)

33% of Parsley from US (2/6)

25% of Radish Tops (2/8)

17% of Snow Peas (13/75)

16% of Green Onions (4/25)

10% of Tomatilloes from Mexico (8/80)

9% of Chili Peppers from Mexico (7/81)

9% of Chayote (Mirliton Squash) (5/54)



Our current recommendation: Wash under running tap water (with chlorine) all your vegetables and fruits, even organic, using a vegetable brush when appropriate. (Removing the external dirt without sacrificing the nutrient rich skin is a constant source of opinions from our volunteers.) If you are going to cook your vegetables immediately at sterilizing conditions, leave on the skin. Stainless steel ultrasonic cleaners are inexpensive on Ebay and we suggest using one with sodium bicarbonate solution (1 teaspoon per pint of cold tap water or less) for 5 minutes, especially for conventional (nonorganic) produce. Always fill the ultrasound cleaner at least 2/3s of the way full with the heat off. Pour the water down the drain (with the pesticides). Rinse with filtered water. If you find certain produce has a residue of bicarbonate of soda that you can taste, ultrasound clean it again in plain filtered water. If you are going to ferment the produce, you will need to use cold filtered water for the second ultrasound cleaning to remove the chlorine from the tap water: the pH of your produce is important for fermentation (it is only the beginning – stay tuned). (Did you know municipal tap water has more chlorine than your swimming pool? If you have a pool, just test your tap water with a test strip.

It is far better to eat the produce with pesticides than forgo it altogether.

Stay tuned. It it just the beginning.

We want to be clear that we did not suggest a sugar/refined carbohydrate tax in the United States.

We would also like to be clear that we are not against it.

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