microbiome

The Microbiome Solution

by Robynne Chutkan M.D.  · 5 Aug 2015  · 298pp  · 76,727 words

. Recipes courtesy of Elise Museles of Kale and Chocolate (www.kaleandchocolate.com). Reprinted with permission. Library of Congress Cataloging-in-Publication Data Chutkan, Robynne. The microbiome solution : a radical new way to heal your body from the inside out / Robynne Chutkan MD, FASGE. p. cm. ISBN 978-0-698-19391

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1 • Getting to Know Your Gut Bacteria Chapter 1. The Zoo Inside You Chapter 2. Microbes: Your Worker Bees part 2 • Messing Up the Microbiome Chapter 3. The Hygiene Hypothesis and Our Modern Plagues Chapter 4. Pharmageddon and the Antibiotic Paradox Chapter 5. Dysbiosis—Do You Have It? Chapter 6

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: Probiotics and Other Supplements Chapter 13. Everything You Wanted to Know About Stool Transplants but Were Afraid to Ask part 4 • Recipes Chapter 14. Microbiome Solution Recipes Index Acknowledgments I am indebted to the many wonderful patients I’ve had the privilege of caring for who have taught me so

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, chlorination of the water supply, processed foods full of chemicals and hormones, microbe-depleting pesticides, increasing rates of Cesarean sections—that have ravaged our microbiome, diminishing the total number of organisms as well as the diversity of species. The result is an increase in a wide range of modern plagues

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diabetes, obesity, cancer, irritable bowel syndrome, anxiety, and heart disease. The rise of these diseases is inextricably intertwined with the full-on assault on our microbiome resulting from our super-sanitized lifestyle. A decade ago, who knew that every antibiotic dispensed during cold and flu season was potentially bringing us one

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overzealous use of antibiotics, often accompanied by a highly processed Western diet low in indigestible plant fiber—the preferred food of gut bacteria. Repopulating the microbiome can be a challenging process, but the good news is that most people do get better. Your microbes are constantly changing and evolving, and even

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essential that we learn more about where our microbes come from, what they do, and why we literally can’t live without them. Meet Your Microbiome The microbiome refers to all of the organisms that live in or on your body: all of the bacteria, viruses, fungi, protozoa, and helminths (worms,

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that crucial early microbial exposure. Gene Modulation We have about twenty-three thousand human genes and eight million microbial ones. Results from large-scale human microbiome studies suggest that genes from gut bacteria play an important role. They provide instructions for essential functions like carbohydrate metabolism and enzymatic detoxification—instructions that

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bacteria play in protecting against viral infection. Microbial health is one of the factors that determines who survives potentially deadly viruses. The very young, whose microbiome is still developing, and the very old, who have fewer microbial species and less diversity, tend to be the most vulnerable. Overzealous antibiotic use

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Gut Garden As I’ve mentioned, there’s incredible microbial variation from person to person, which makes it difficult to define exactly what the ideal microbiome looks (or smells) like. Our health depends on having the right balance, without any one species becoming unnaturally dominant or submissive, and with essential

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, psychiatric conditions like depression, poorly understood afflictions like autism, and even some forms of cancer—and clinical studies have shown significant disturbances in the microbiome in all of them. We spend huge amounts of time making sure we’re clean—scrubbing ourselves with harsh soaps, sanitizing our hands and environment

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digestive tracts through mind-body techniques of guided meditation and visualization. So it really is a pyramid approach, with nutritional therapy and rehabilitation of the microbiome being the foundation on which everything else rests. For most people, there really is no downside to using food as medicine, and there are

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food, our ability to bounce back from antibiotics is even more limited. So, avoidance of antibiotics is absolutely the number one strategy for keeping your microbiome healthy. I’ll discuss other common prescription and over-the-counter medications that threaten microbial health in Chapter 11, “A Rewilding Approach to Illness.”

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require any microscopic evaluation. The manifestations of yeast overgrowth were written all over her body. Once we got rid of the offending steroid agents, her microbiome eventually bounced back and her bloating, gas, and rectal itching resolved. Is Chemotherapy Killing Off Your Cells? In an ideal world, chemotherapy would just

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gastroenterology practice, mind-body relaxation techniques like biofeedback, which incorporates guided meditation, visual imagery, and deep breathing, are a crucial part of rehabbing the microbiome and achieving digestive wellness, and we’ve found them to be successful across a wide spectrum of GI disorders. Detecting Dysbiosis: Have You Had Any

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Major Infections? Antibiotics aren’t the only cause of dysbiosis. Gastrointestinal infections themselves can deplete the microbiome, and the subsequent decrease in microbial richness can lead to increased susceptibility to disease. Many patients trace the beginnings of their decline in health to

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inflammatory bowel disease like Crohn’s and ulcerative colitis point to a significant infectious event that marks the beginning of their illness, particularly if their microbiome was already compromised from prior antibiotic use. Many Roads Can Lead to Dysbiosis Most of the patients I see with dysbiosis have multiple risk

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high rates of dysbiosis. The following conditions are the ones I see most commonly in my office in people with dysbiosis. While alterations in the microbiome aren’t the only cause, dysbiosis often plays a central role, and rebalancing gut microbes frequently leads to a significant improvement in symptoms. TABLE

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medications—including the psychiatric drugs that are frequently prescribed—have lots of side effects and aren’t particularly effective. The finding of alterations in the microbiome as a major contributor to IBS offers exciting promise for new ways to address symptoms through restoration of microbial balance. When Bugs Work Better

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by evaluating the bacteria present in their stool, and different types of Crohn’s disease are associated with different microbial changes—further evidence that the microbiome plays a key role in these diseases. In my gastroenterology practice, a plant-based diet low in processed carbohydrates and refined sugar, in combination

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bacteria in sets of identical twins where one was well nourished and the other malnourished. It turned out that these genetically identical individuals had different microbiomes: the malnourished children couldn’t synthesize certain vitamins or digest complex carbohydrates properly. Transplanting microbes from the malnourished twins into germ-free mice created the

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gut in overweight adolescents can influence how much weight they lose with dietary restriction and increased physical activity independent of their diet, confirming that the microbiome is an incredibly important factor in determining the efficacy of dietary interventions. What About Your Genes? Your genes definitely have some influence on how

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). Maternal outcomes have improved a lot in the last century, but C-sections still come with plenty of risk, particularly to our fragile blossoming microbiome. As I mentioned in Chapter 1, babies born vaginally are colonized with Lactobacillus species and other essential microbes from their mother as they pass through

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rates of infant mortality is particularly egregious. There are undoubtedly countless additional undiscovered ingredients in breast milk that are designed to nourish the baby’s microbiome, which is why artificially made formula really can’t compare and why we continue to see the health benefits of nursing long after babies

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same is likely true for the people who eat them. As we discussed in the last chapter, overweight and normal-sized people have significantly different microbiomes, and antibiotics can induce many of those differences. Using antibiotics preventively in confined animals leads to drug-resistant bacteria that pose a real threat

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and Salmonella seem to be resistant to glyphosate, while essential bacteria like Lactobacillus and Bifidobacterium are often more susceptible, which can lead to an unbalanced microbiome and dysbiosis (see Chapter 5). Genetic Modification Bacillus thuringiensis (Bt) is a bacterium that lives in soil and produces a toxin that kills insects

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world? Remove, Replace, Restore The cornerstone of the Live Dirty, Eat Clean Plan is removing medications, practices, and foods that are damaging to your microbiome; replacing the essential bacteria that you’ve lost with a robust probiotic; and restoring the health of your gut with appropriate nutrients, supplements, and medicinal

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help avoid the pitfalls of antibiotics during pregnancy, unnecessary C-sections, the use of baby formula, and other practices that damage your baby’s burgeoning microbiome. Chapter 12, “Bugs over Drugs: Probiotics and Other Supplements,” explains exactly what to look for in a probiotic—how much live bacteria should be

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Artichokes Asparagus Bananas Chicory root Dandelion root Garlic Leeks Onions Success Secret #2: Ferment Your Food Fermented foods such as sauerkraut, kimchi, and pickles are microbiome rock stars because they contain live bacteria (probiotics) and prebiotic fiber to nourish gut bacteria. You should try to include some of these fermented foods

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diet that included jasmine rice, onions, tomatoes, squash, peas, lentils, and garlic, with bananas and mangoes for snacks. The scientists analyzed the study participants’ microbiomes before, during, and after each diet. The differences were apparent much more quickly than anyone anticipated and had unexpected genetic consequences. Not only did the

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Light Baking Almond flour Coconut flour Chickpea flour Brown rice flour Green banana flour Yellow Light Foods These foods aren’t specifically beneficial to the microbiome, but they can be enjoyed in moderation without any deleterious effects. I recommend that you limit your consumption to one serving (approximately four ounces)

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can harm skin microbes. DON’T use hand sanitizer. DON’T use antibacterial soaps and products. DON’T use antiperspirants—they can alter your skin microbiome. DON’T use mouthwash—it can destroy the microbial ecosystem in your mouth. DON’T use chemical household cleaners (see my recipe here). Beauty

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new paradigm starts to emerge that’s based on peaceful coexistence and synergy rather than toxic extermination. So go ahead, get a little dirty. Your microbiome will thank you. CHAPTER 11 |||||||||||||||||||||||||||||||||||||||||| A Rewilding Approach to Illness AS A PHYSICIAN, I realize I have inside knowledge that makes it easier for

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engages your health care professional in respectful dialogue that may include some pointed questions. Conventional medicine is finally beginning to embrace the importance of the microbiome and the role it plays in human health, but not all practitioners—or consumers—are equally enlightened. Many still consider antibiotics to be a

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and Other Supplements,” for how to choose the right probiotic. Request a narrow-spectrum antibiotic. Taking a narrow-spectrum antibiotic will minimize damage to your microbiome by targeting a narrower range of bacteria. Culture and sensitivity results from urine, stool, sputum, blood, skin, or other body parts, depending on the

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is actually sensitive to the antibiotic you’re taking, which will help avoid retreatment with additional courses of antibiotics. Eat prebiotic foods to support your microbiome. Foods high in fiber and resistant starch are especially important when you’re taking an antibiotic. Not only do they provide food for your

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ease the transition. Corticosteroids Oral or intravenous forms are the most detrimental. Long-term use of inhaled steroids or steroid creams can also affect your microbiome and lead to localized fungal infections, bacterial overgrowth, or other manifestations of dysbiosis. Note: Oral or intravenous corticosteroids should not be abruptly discontinued—ask

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t just for hippies. It’s something we should all strive for, given the consequences of antibiotics and C-sections on a newborn’s burgeoning microbiome. Allowing nature to take its course and not inducing labor prematurely, avoiding unnecessary medications and procedures during childbirth, and nursing as soon as possible

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and the utility of commercially available strains. I’ll also discuss a few supplements and herbal remedies that can have a beneficial effect on your microbiome. I hope this information will be helpful to you on your journey toward microbial optimization and better health. First, a Few Definitions Probiotics are

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doesn’t get much dirtier than incorporating someone else’s stool into your body—and the results speak for themselves. part 4 RECIPES CHAPTER 14 |||||||||||||||||||||||||||||||||||||||||| Microbiome Solution Recipes All Recipes by Elise Museles of Kale & Chocolate BREAKFASTS Sweet Potato & Kale Breakfast Hash If you like savory morning meals but crave just

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in the container of a high-speed blender and blend until smooth. Add the toppings, if you wish. Sip and savor. VARIATION: For an added microbiome boost, add ½ teaspoon grated fresh turmeric. For a thicker smoothie, add ice. Blueberry Bliss Smoothie Filled with lots of nutrient-dense ingredients, this beautiful

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my favorite cookies. With almond flour and just a touch of honey and molasses, you can satisfy your sweet tooth without wreaking havoc on your microbiome. *MAKES 12 COOKIES Ingredients 2 cups almond flour ½ teaspoon baking soda ½ teaspoon sea salt ¼ cup organic raw honey 1 teaspoon molasses 1½ teaspoons pure

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medical advice, 151 use of baby formula, 103–104 medications, problematic, 50–54, 156–57. See also antibiotics metabolic syndrome, 182 microbial imbalance. See dysbiosis microbiome decreased diversity, 7–8 definition, 3 distinctive odor, 15 external environment and, 25–27 functions of, 3, 9, 11–14 lifetime development of, 4–7

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Diet, 135 resistant starches and inulin, 126–27 in restoration and maintenance of microbial balance, 56 pregnancy antibiotic use during, 97, 102–103 baby’s microbiome, 4–5 plan and goals, 163–66 probiotics during and after antibiotic treatment, 153 to choose, 173–74 common strains, 175–76 definition, 168

Fiber Fueled: The Plant-Based Gut Health Program for Losing Weight, Restoring Your Health, and Optimizing Your Microbiome

by Will Bulsiewicz  · 15 Dec 2020  · 431pp  · 99,919 words

based on trends and pseudoscience, my program offers you a scientifically validated approach that will truly heal your gut by restoring order to your gut microbiome. Do you have a sensitive stomach? Do you have trouble processing certain foods, like beans, broccoli, and gluten-containing grains? Food sensitivity has

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purpose. We call this community the “gut microbiota.” If we’re referring specifically to the genetic code of this community, then we use the expression “microbiome.” There are five types of microorganisms residing within you. They include bacteria, yeasts, parasites, viruses, and archaea. Bacteria are living single-celled organisms that

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loss would have unintended consequences and diminish the health of that ecosystem. This is why biodiversity is critically important to any ecosystem. The human gut microbiome is no exception. Diversity of species is critically important to balance. Inside us are anywhere from three hundred to over a thousand species of

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immune system, metabolism, hormonal balance, cognition, and gene expression. The awesome power of our gut microbiota for total body health A healthy, diverse gut microbiome does so much more than just suppress pathogenic bacteria, process our drugs, and help us to process our food. It operates as the command center

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problems didn’t exist in their countries until recently, so they don’t know how to care for their patients. Evidence suggests that our gut microbiome not only changes with allergic and autoimmune disease, but it may predict or even cause these immune system conditions. For example, researchers analyzed the

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damage to the microbiota puts us at risk for immune dysregulation, manifesting with autoimmune and allergic illness. But on the flip side, a strong microbiome empowers the 70 percent of neighboring immune cells for optimal function to protect us from infection and malignancy. When we take care of our microbes

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Lupus Interstitial cystitis Autoimmune hepatitis Primary biliary cholangitis Primary sclerosing cholangitis Sarcoidosis Fibromyalgia Guillain-Barré syndrome Behçet’s disease Kawasaki disease ANCA-associated vasculitis The Microbiome Code for personalized food processing The diet industry has for a very long time told us that weight gain is within our control if

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a lowering of their blood sugar. Unfortunately, the effect only lasted a few weeks because they didn’t change their diet, so the new microbiome couldn’t be sustained. METABOLIC CONDITIONS ASSOCIATED WITH DYSBIOSIS Obesity Type 2 diabetes Coronary artery disease Hyperlipidemia Chronic kidney disease Gout Nonalcoholic fatty liver disease

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influence from your gut microbiota! In another study, researchers discovered that foods had a very different blood sugar response in each person. The gut microbiome was responsible for this unique response. Using solely an individual’s gut microbial profile, they were able to predict which foods would cause less of

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with excess estrogen, which has been associated with endometriosis, endometrial hyperplasia, and breast and endometrial cancer. No surprise, we find damage to the gut microbiome in association with each of these conditions. Alternatively, if the microbiota are too restrictive on the floodgates, you get an estrogen drought. Polycystic ovary syndrome

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an increase in androgens (or testosterone) in addition to altered estrogen. As it turns out, androgen production is also mediated in part by the gut microbiome. Clostridium scindens is a gut bacteria known to convert glucocorticoids (think cortisol) into androgens in the gut. So if you have too much C.

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predispositions—we all do. But you ultimately control your health destiny, in large part through the effects of your diet and lifestyle on your microbiome. In a letter to Science magazine in 2001, Professor Julian Davies warned that decoding the human genome was not enough to understand human biology

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four days of three broad-spectrum antibiotics can permanently destroy nine beneficial species of bacteria. The result of all these antibiotics is a “new normal” microbiome with more antibiotic-resistant microbes that leaves us vulnerable to infection, allergic conditions, osteoporosis, and obesity. I’m sure you recall all the problems

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American consumes nearly three pounds of salt per year. Three pounds! We only need a few ounces. Anything more has consequences, including in the gut microbiome, where it drives autoimmunity by inducing helper T cells, which can contribute to hypertension. Chemical preservatives, additives, and colorants Does it come as a

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Zero calories, that has to be better than sugar, right?” It’s intuitive! Turns out they’re actually worse because they induce changes in the microbiome that promote inflammation, insulin resistance, and liver injury. You will actually be less tolerant of sugar by using artificial sweeteners. And then there’s the

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universal agreement that monounsaturated fats (MUFA) and omega-3 polyunsaturated fats (PUFA) found predominantly in plant foods are healthy! We see this validated in microbiome studies that show oleic acid—a monounsaturated fat found in olive oil—and omega-3 PUFAs promote the growth of beneficial microbes, correct dysbiosis, and

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reduce bacterial endotoxin release. They even enhance microbial diversity. These fats actually protect the microbiome. And then there’s saturated fat, predominantly found in animal foods as well as in tropical oils like coconut oil and palm oil. Cardiologists are

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from” is incredibly important to gut health. The source of the protein, whether from plants or animals, can have very different effects on the microbiome. For example, plant protein increases the growth of anti-inflammatory species like Bifidobacterium and Lactobacillus while suppressing the destructive ones like Bacteroides fragilis and Clostridium

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inflammatory bowel disease), reduced Bifidobacterium (protects against irritable bowel and obesity), and increased Hungatella (produces TMAO). In other words, the Paleo diet shifted the microbiome away from health and toward disease. Even though all of the groups in the study ate a similar amount of meat, they saw dramatic differences

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, demonstrating that categorical eliminations can have unintended, potentially serious consequences. Anyone want to guess what an even more restrictive Keto/Carnivore diet does to the microbiome? In a groundbreaking study by Drs. Lawrence David and Peter Turnbaugh, a group of people cycled between a completely “plant-based diet,” which was

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called the “Carnivore diet”—100 percent animal products, no plants. So what happened? There were dramatic changes of the study’s participants in the microbiome in less than twenty-four hours. It didn’t take long. The animal-based diet saw the disturbing emergence of inflammatory bacteria like Bilophila wadsworthia

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shockingly inadequate seventeen that belong to us, our gut microbiota may contain upward of sixty thousand of these helpful enzymes. The fact that our microbiomes contain this insane number of digestive enzymes makes sense when you remember that there are three hundred thousand edible plants and potentially millions of types

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-balanced” non-vegan diet. So not only do SCFAs correct dysbiosis and heal leaky gut, but they also create a powerful link between the microbiome and immune system that serves to make the immune system work properly. Adequately fueled by SCFAs, the immune system does its job confidently and effectively

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chemical that reverses dysbiosis, heals leaky gut, strengthens the gut microbiota, optimizes the immune system, and regulates appetite and metabolism also connects the gut microbiome to cerebral function. The effects are once again broad and powerful. You know how many people with leaky gut also complain of brain fog? And

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gut microbes that thrive when that food is present and languish if that food is removed. Therefore, it makes sense that the diversity within our microbiome would be proportional to the diversity of plants in our diet. More plant-based diversity = stronger, healthier microbiota = stronger, healthier you. Although our food

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human populations? Well, you already know. Weight loss. Lower blood pressure and lower cholesterol. Reversal of insulin resistance. Less inflammation. A shift in the microbiome to produce more SCFAs. Protection from cardiovascular disease and cancer. Longer life expectancy. Study after study has shown us that legumes and whole grains are

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Because it makes us adaptable to a variable diet and environment. It also means that carbohydrate processing—including fiber—requires a healthy, properly adapted gut microbiome. When we damage the gut and reduce diversity, we also reduce the number and types of digestive enzymes in our gut. And that is

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. Since wheat is the dominant form of whole grain in the United States, you need to make sure that you’re adequately supporting your gut microbiome. Thankfully, there are some delicious gluten-free whole grains available for you to routinely consume: quinoa, buckwheat, millet, sorghum, oats, and brown rice.

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SCFAs. The point being, our gut thrives on diversity of fiber and, by creating exopolysaccharides, we are adding to that diversity to support our gut microbiome. Powerful stuff, folks. We’re only beginning to study fermented foods and the bioactive molecules the microbes create. The proteins, phytochemicals, and polyphenols in

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to prioritize: The Golden Rule—Diversity of Plants Prebiotics Probiotics I can’t wait for the day when we can analyze a person’s individual microbiome, identify the strengths and weaknesses, and then give them the exact strains in the exact proportions that they need for optimal health or to

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Shift workers are at increased risk for hypertension, hyperlipidemia, obesity, and type 2 diabetes because of what a disrupted circadian rhythm does to the gut microbiome. Our gut microbes thrive on consistency that’s anchored into these twenty-four-hour oscillations, and that means timely meals. For example, you can

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discussed in Chapter 1. Exposure to the outdoors early in life has been shown to improve immune function. Adults who exercise outdoors have more diverse microbiomes. Gardening improves mood, lowers stress, increases life satisfaction, and even promotes weight loss. Not to mention that growing your own veggies has been shown

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environment per hour. Close proximity to others has the potential for sharing among our bacterial cloud. Studies show that you’re likely to share microbiome similarities with the people you live with. These relationships have even been shown to impact our genetic expression. Even having our furry friends—dogs

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and cats—can contribute to microbiome health and protect us from disease. Our environment and the people we surround ourselves with allow a microbial exchange that keeps us alive and thriving

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you will be on the path to continuing what you started by living Fiber Fueled. Research shows that it takes twenty-eight days for the microbiome to adapt to dietary fiber, get the digestive enzymes necessary for fiber processing, and increase SCFA production. The major changes occur within twenty-eight

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its job throughout the body to keep you well. More than 225! ROCK GOD You are a Fiber Fueled God of Rock with a microbiome that is wildly diversified and working like a well-oiled machine to keep you happy and healthy. And the challenge doesn’t end after four

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testosterone), 20–21, 42 animal foods and cancer, 44, 102 digestibility of, 104 and elimination progression, 184 fad diets emphasizing, 45–47 impact on gut microbiome, 43–47 including small amounts of, 183–84 percentage of, in SAD, 38 and saturated fats, 43 and short-chain fatty acids, 102, 104 and

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blood sugar and biorhythms, 193 and exercise, 197 and fermented foods, 126 fiber’s role in balancing, 51–52 and fruits, 153 impact of gut microbiome on, 17, 18, 19 and legumes, 88 plants that benefit, 78 and prebiotic supplements, 140, 145 SCFAs’ impact on, 65–66 blueberries, 56, 81

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function and altered mental status, 109 and berries, 154 and brain fog, 13, 67 conditions associated with dysbiosis, 13, 23, 25 impact of gut microbiome on, 22–24 and neurotransmitters, 23 SCFAs’ protective role in, 67–68 and sleep deprivation, 195 and sulforaphane in cruciferous vegetables, 164 See also Alzheimer

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Taco Salad, 236–38 Thai Rainbow Bowls with Peanut Tofu, 297–99 Tuscan Kale Soup, 335–37 disease risk, environmental factors in, 25 diversity of microbiome composition central importance of, 6–7, 9 and Crohn’s disease, 61 decreases in, 19, 39, 61, 69 and diversity of foods consumed, 7

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73–93 and agricultural practices, 75 and antibiotic use, 144 benefits of maximizing, 76 central importance of, 92–93 decline in, 75 and diversity of microbiome composition, 74–75 and “eating the rainbow,” 80, 80–81, 82 and elimination of foods, 96 in Fiber Fueled 4 Weeks, 209–11, 210

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181 and Hadza of Tanzania, 68–69, 100–101 and lectins, 90–91 and legumes, 87–92 and phytochemicals, 79–83 as predictor of healthy microbiome, 74, 91, 181 and SCFA-producing bacteria, 74–75 synergistic effects of plant pairs, 81–82 and training a sensitive gut, 99–101, 115

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to recipes, 203 and Blue Zone diets, 38–39 and changes in cravings, 176–77 digestibility of, 104 grass-fed, xvi, 184 impact on gut microbiome, 43–47 including small amounts of, 183–84 in Standard American Diet, 39 medicine, food as, 167, 173 meditation, 199 Mediterranean Grain Salad, 291

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memory function, 81 menopausal symptoms, 89 metabolic conditions associated with dysbiosis, 16–19, 19 metabolic syndrome, 18 metabolism, 8, 9, 19 microbial enzymes, 125 microbiome (term), 4 microbiota of the gut damage to (see dysbiosis) digestive enzymes of, 54 digestive function, 7 and five axes of human health, 8 and

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impact of food choices on, 7 and individual responses to food, 19 number of organisms comprising, 5–6 predictor for health of (see diversity of microbiome composition) scientific research on, 3–4 as “second brain,” 22 specialization in, 8–9 time required to adapt to changes, 206 types of organisms

Dirty Genes: A Breakthrough Program to Treat the Root Cause of Illness and Optimize Your Health

by Ben Lynch Nd.  · 30 Jan 2018  · 438pp  · 103,983 words

. I laid out our master plan with Hunter. I told him that we were going to strengthen his gut, improve his digestion, and replenish his microbiome, the community of gut bacteria that are crucial for digestion as well as many other functions. During the initial phase, while his digestive system was

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—which he was relieved to hear—but I told him that we were going to find his sweet spot. As his gut healed and his microbiome became more robust, he would probably be able to increase the amount and variety of histamine-containing foods. “Okay,” Hunter said, when we had gone

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, take heart. Your friends and loved ones born with clean DAO genes may be able to hold out longer as they damage their gut and microbiome, but our bodies are forcing us to make changes. In the long run, I think we’re the lucky ones. * * * DAO: The Basics Primary function

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; cooked are typically okay ■Spinach ■Vinegars (although some people do well with unfiltered, organic apple cider vinegar) * * * Your Marvelous Microbiome Just a few years ago, almost no one had heard of the microbiome, and yet it’s one of the most important parts of your anatomy. Well, it’s not exactly your

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anatomy. Your microbiome is composed of trillions of bacteria that live in your gut and elsewhere in your body, with cells outnumbering your human cells by a factor

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of 10 to 1, and genes outnumbering your human genes by a factor of 150 to 1. The microbiome evolved along with us, so there are many functions in our body that simply wouldn’t work without the assistance of this microbial community. For

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that are vital to a number of different human functions, from digestion to the regulation of thought and mood. You want a strong, diverse, robust microbiome that includes a variety of gut bacteria in the right proportions. Because when your gut bacteria go out of balance—when you have too much

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types and not enough of others—then, my friends, you’ve got trouble. Antibiotics, which kill dangerous bacteria but also destroy big swaths of your microbiome, can contribute to this imbalance. So can stress, a long-term illness or infection, poor diet, toxic exposure, and digestive issues such as leaky gut

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, some probiotics help your body to break down histamine. So in a perfect world, you want a balance: fermented foods and probiotics to support your microbiome; but overall, a healthy rather than an excessive level of histamine in your gut. This balance is harder to achieve—but all the more important

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, parasites, viruses, and chemicals in your food and drink. This protection is carried out by built-in defenses: your stomach acid, digestive enzymes, bile, and microbiome. When any portion of this protection falters, your DAO is likely to be overwhelmed. * * * What Makes DAO Dirty? ■Too many histamine-containing foods. ■Too many

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histamine-containing liquids. ■Imbalanced microbiome. ■Small intestine bacterial overgrowth (SIBO). ■Disease or infection in the gut, caused by harmful bacteria, yeast (various Candida species), parasites, ulcerative colitis, Crohn’s disease

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, you have the DAO enzyme to process those foods. Luckily, by paying attention to diet, exercise, sleep, toxic exposure, and stress, you can replenish your microbiome, heal your leaky gut, and lower your histamine levels. All of those steps lighten the burden on your DAO, replenish your DAO enzyme, and ensure

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more energy than I’ve had in years.” Although Hunter had cut out fermented vegetables and raw sauerkraut, those foods have enormous benefits for the microbiome. I reassured him that, as his system got stronger, he’d be able to add some back in. Here are some other suggestions to support

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sprouts, and cabbage). ■Support your digestion so that you have adequate stomach acid, digestive enzymes, and bile flow. These are all essential to keep your microbiome healthy and pathogens out. (I’ll go into detail about how to do this in my discussion of the Clean Genes Protocol.) ■Counter foods that

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disorder, schizophrenia, and obsessive-compulsive disorder ■Migraine ■Obesity ■Parkinson’s disease ■Pregnancy complications ■Psoriasis ■Seizure ■Stroke ■Ulcerative colitis ■Vision loss (progressive worsening) * * * GST and Your Microbiome There are many types of GST gene, each with its own unique job. They reside mainly in the intestines and liver—but your

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microbiome also has its own GST enzymes. In fact, your microbiome is a key player in your body’s effort to get rid of xenobiotics, protecting you against chemical and oxidative stress

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. Think of your microbiome as your GST’s main backup—and make sure to protect it! * * * What Makes GST/GPX Dirty? ■Exposure to a lot of industrial chemicals, heavy

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vegetables, including foods rich in cysteine (the sulfur-containing amino acid mentioned above). Unfortunately, some people can’t seem to tolerate sulfur well. An unfriendly microbiome may be the culprit—one that’s producing too much hydrogen sulfide. If you smell like rotten eggs, with a sulfur odor coming from your

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MSM (methylsulfonylmethane) or NAC (N-acetyl cysteine). Ask your doctor to order a comprehensive digestive stool analysis (CDSA) to see what’s happening with your microbiome. Whatever the cause of sulfur intolerance, eliminating sulfur from the diet isn’t a cure-all. People on a low-sulfur diet may feel better

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you can, too. You don’t even have to wait for your Soak and Scrub. Just jump right in: ■Eat a lot of fiber. Your microbiome loves fiber! Those gut bacteria eat the fiber that your own body can’t digest, and then they help your body detox. Fiber contributes to

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superoxide being made by your dirty NOS3. A dirty NOS3 just got dirtier. As if that weren’t enough, certain types of bacteria in your microbiome also use a significant amount of arginine, further “stealing” it from your NOS3. Yet another reason to evaluate your

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microbiome. Now, at this point, you might be thinking, “Okay, fine. I’ll just take an arginine supplement.” Can you guess why that doesn’t work?

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levels ■High insulin levels ■Infection ■Inflammation ■Lack of movement—sitting, standing, lying down ■Low antioxidants ■Low arginine ■Low BH4 ■Low estrogen ■Low glutathione ■Low oxygen ■Microbiome imbalance ■Mouth-breathing ■Overeating ■Oxidative stress (too many free radicals) ■Poor methylation ■Pollution ■Sinus congestion ■Sleep apnea ■Smoking ■Snoring ■Stress ■Tongue-tie * * * NOS3 and Your

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hinders another by generating significant side effects. The exact same thing is true of food. While fermented foods might be great for me, replenishing my microbiome and healing my leaky gut, you might have a dirty DAO that can’t handle the extra bacteria. Maybe you can tolerate small amounts of

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tarragon add a lovely sweetness to this chicken soup for the soul! The Jerusalem artichoke is an amazing vegetable for liver support, and for your microbiome, too. Enjoy this hearty soup as you support all your genes. Add chicken breast or other meat of your choice to support a fast COMT

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help you detect the presence of pathogenic bacteria that increase histamine. If such pathogens are found at high levels, you’ll want to rebalance your microbiome by decreasing their presence while replenishing other types of bacteria through specific probiotics. (Doctor’s Data, Genova Diagnostics, Diagnostic Solutions [GI-MAP]) ■Identify food allergies

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elevated, you can assume that your NOS3 isn’t working well. (Quest Diagnostics, LabCorp) ■Consider a comprehensive digestive stool analysis (CDSA). This test evaluates your microbiome for the following bacteria: Streptococcus (or Enterococcus) faecalis, Mycoplasma, Bacillus, Pseudomonas aeruginosa, Halobacterium, Spirochaeta, and possibly Clostridium. If present, these are consuming your arginine, causing

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tailored to fitness, sports performance, and general well-being. ■uBiome (https://ubiome.com). This company evaluates the DNA of your microbiome, which is pretty fascinating, given that the genes of your microbiome outnumber your human genes by a factor of 150 to 1 and have an enormous impact on your health. This

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bacteria, food, and drink. —ProBiota HistaminX. Helps break down histamine from food, drink, and bacteria. Helps solve the problem of high histamine by improving your microbiome. —Pro-Digestion Intensive. A comprehensive digestive enzyme. —PreGestion. Provides stomach acid to help reduce belching and aid digestion. —Optimal Adrenal. A nonstimulating, adaptogenic blend of

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the treatment of cardiovascular disease: Reversal of arginine steal?” Cardiovascular Research, 1 June 2013, https://www.ncbi.nlm.nih.gov/pubmed/23417041. 178Bacteria in your microbiome: Cunin, R., et al., “Biosynthesis and metabolism of arginine in bacteria,” Microbiological Reviews, September 1986, http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC373073& blobtype=pdf

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, 184 bacteria, 31, 45, 117, 126, 154, 201; gut, 24, 43, 117, 119, 122-28, 155-57, 162, 178, 191, 193, 198, 280-84, 301; microbiome, 124-25; overgrowth of pathogenic, 280-81; SIBO, 6, 26, 50, 85, 120, 126, 142, 191, 194, 198, 282 Bastyr University, 11 beans, 58, 86

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; health conditions related to, 154-55; key nutrients for, 159-60; Laundry List 1, 69; Laundry List 2, 271; making the most of, 162-65; microbiome and, 155-57, 160, 162; personality sketch, 60, 154; primary function of, 152; Spot Clean, 286-87; stress and, 156, 165; sulfur and, 160-62

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, 81, 86, 88, 191, 219, 279, 289, 298; PEMT and, 191, 197-98 methylglyoxal, 157 methylphenidate, 106-7 mice, 1-2; genes, 1-2, 41 microbiome, 117, 124-25, 178; GST/GPX and, 155-57, 160, 162 migraine, 5, 8, 22, 23, 24, 78, 120, 140, 155, 167, 168, 170 milk

Everything Is Tuberculosis: The History and Persistence of Our Deadliest Infection

by John Green  · 18 Mar 2025  · 158pp  · 49,742 words

the body’s contours by making it gain or lose weight, sickening the body, killing the body. There’s even emerging evidence that one’s microbiome may have a relationship with thought itself through the gut-brain information axis, meaning that at least some of my thoughts may belong not to

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me, but to the microorganisms in my digestive tract. Research indicates that certain gut microbiomes are associated with major depression and anxiety disorders; in fact, it’s possible that my particular microbiome is at least partly responsible for my OCD, meaning that the microbes are the reason I’m

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to reach rigorous conclusions about causes of death, meaning that Holmes’s work was not so distant from that of his author. Skip Notes * Certain microbiomes are also correlated with the human body craving particular foods—meaning that when you’re hungry for carbs or protein or whatever, it may in

The End of Illness

by David B. Agus  · 15 Oct 2012  · 433pp  · 106,048 words

it hard to reduce assertions down to truthful, black-and-white conclusions. Later in the book, for example, we’ll explore the role that your microbiome, your intestinal bacteria, could be playing in your health equation, including your risk for cancer. Latitude doesn’t affect just how much sun you get

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get plenty of what they need from breast milk, formula, and, yes, even mushy baby foods probably created in a pulverizer. Mining and Minding the Microbiome Before we move on, I need to mention one more fact for your consideration. We are all different in how we metabolize our food, absorb

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to tune in to our personal nutritional needs. Certainly genetics will play a role here, too, but the larger role will be played by the microbiome—the bacteria that fill your intestinal tract and that participate in your digestion, metabolism, and overall health. We each have bacteria in our GI tract

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, and viruses), however, remain largely unstudied, leaving their influence upon human development, physiology, immunity, and nutrition almost entirely unknown. Recently, the NIH launched the Human Microbiome Project (HMP; you can learn more at www.hmpdacc.org) with the mission of generating resources enabling comprehensive characterization of the human microbiota and analysis

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probably start devouring our processed, packaged foods like the rest of us when they land in the United States—but it turns out that the microbiome plays a major role here. It controls how you metabolize your food, how fast and how much you absorb, and what enters your bloodstream, thereby

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of researchers led by Peer Bork of the European Molecular Biology Laboratory in Heidelberg, Germany, reported on three distinguishable “types” of people based on their microbiome. Each of the three types is composed of a different balance of species. People with type 1, for example, have high levels of bacteria called

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of these types of people came out of finding no link between what they call enterotypes, which are the different balances of species in a microbiome, and the ethnic background of the European, American, and Japanese subjects they studied. In other words, two Americans don’t necessarily harbor the same type

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of their individual bacterial ecosystems could define each of their risk factors for certain diseases. Bork’s team also couldn’t find a connection between microbiome types and sex, weight, health, or age. They are now trying to figure out why, thinking that one possibility is that we are each randomly

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technologies are finally helping us tune into these bacteria and their effects on us, for better or worse. One overarching feature that studies on the microbiome are revealing is the diversity of bacteria in the human body, akin to a rain forest. Different regions of the body are home to different

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digestive system running as smoothly as possible. Within the next ten years researchers will uncover mysteries of the microbiome and begin to find ways in which we can manipulate it to support health. The microbiome—not levels of vitamin D, for example—may explain why people who live at higher latitudes have

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within them. I could easily envision that if you have a high risk for breast cancer based on your personal genome, doctors may adjust your microbiome in such a way as to mitigate some of the risk. Thus the combination of technologies will win here. In addition to the active interaction

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that takes place every minute of the day between your digestive tract and microbiome, another big player on this field that many of us forget about is the brain. It lends a powerful voice to the conversation going on

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500 trillion or three pounds’ worth) than we have cells in our body (only about 80 trillion). As you already read in chapter 8, our microbiome—the totality of microbes, their genetic elements (genomes), and their interactions within us—has a lot to do with our health. It comprises the heart

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–5 downtime and, 255, 256 gut feeling and, 190, 191–93 inflammation and, 202, 203, 204–8 and keeping a regular schedule, 244, 246–47 microbiome and, 190 as microcosm of body, 204 physical activity and, 227 sleep and, 244, 253, 254, 256 vitamin C and, 153–57 brain disease, 156

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DNA repair and, 266 drugs and, 84–85, 92–93 environment and, 79, 84–85 genetics and, 37, 38, 39, 79 hormone receptor-sensitive, 84 microbiome and, 188, 190 risk indicators for, 72 and system approach to illness, 39 trade-offs and, 74–75 vitamins/supplements and, 132, 136–37, 175

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of information about, 9 kinds of, 39 late detection of, 3 lycopene and, 177–78 medical history as predictor of, 68 as metaphor, 8, 27 microbiome and, 137, 188, 190 at molecular level, 35 NCI description of, 32 oldest physical evidence of, 33 omega-3 fatty acids and, 136 oxidation and

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and, 121–22 gut feelings and, 192, 193 in history, 150–52 and keeping a regular schedule, 237, 238–39, 243–45, 246, 249, 258 microbiome and, 137, 187–90 multivitamins and, 158–59, 181 personalized treatment and, 121–22, 187 physical activity, 227 principles of health and, 3 protein in

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concerned with, 58 vitamin D and, 142, 143, 144, 145, 184–85 vitamins/supplements and, 157–58, 174–78, 194 digestion brain and, 191–93 microbiome and, 187–90 Personal Inventory Questionnaire and, 17 technology and, 268 DNA, decoding of, 118–19 DNA (deoxyribonucleic acid) as blame for illness, 22–23

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, 231 epigenetics, 205–6 epilepsy, 210 esophageal cancer, 62 estrogen, 16, 84 ethnicity: as factor in research studies, 50 European Molecular Biology Laboratory (Heidelberg, Germany): microbiome, 188 European Prospective Investigation into Cancer and Nutrition (EPIC), 30 examinations, medical: annual, 53 exercise. See physical activity/exercise exercise physiology, 224–29 Fairfield, Kathleen

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alienation and confusion about, 180 “anticancer,” 87 chemicals in, 180–81 color of, 184, 194 fast and processed, 159 fresh/whole, 182–83, 187, 194 microbiome and, 137, 187–90 natural, 179–80 shopping for, 181, 182–85 as source for antioxidants, 178 as vitamin source, 139, 178 See also diet

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, 70 heredity and, 101–3 identification of, 104 and keeping a regular schedule, 244 Mendel as father of, 101, 102 of mental illness, 118, 119 microbiome and, 187 mutations of, 38, 39, 229, 266 number of human, 96 personalized treatment and, 117, 118–19 physical activity and, 229 protein and, 96

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’s disease, 5 hope: end of illness and, 294–301 hormones gut feeling and, 191–92 and keeping a regular schedule, 239–44, 245, 246 microbiome and, 188 Personal Inventory Questionnaire and, 16, 18 physical activity and, 227 sleep and, 239–44, 245, 254 technology and, 268 See also specific hormone

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human chorionic gonadotropin (HCG), 112 Human Genome Project, 70–71 human growth hormone, 48–49, 242–43 Human Microbiome Project (HMP), 187–88 Huntington’s disease, 105 Hutchinson (Fred) Cancer Research Center (Seattle), 171 hypertension, 49, 168, 221, 233, 240, 250 hyperthyroidism, 59 hypothalamus

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, 101, 102, 103, 114 mental illness, 84, 119, 253 metabolism, 105, 119, 151, 187–90, 226–27, 229, 231, 268 metabolites, 117 metabolomics, 226–27 microbiome (intestinal bacteria), 137, 187–90, 268 “microsystems,” 50 mild cognitive impairment (MCI), 207 mitochondria, 228–29 mood, 18, 250, 253 Morris, Jeremiah, 216–19, 219n

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of the National Academy of Sciences, 140 prostate cancer deaths from, 62, 296 genetic testing and, 72 Grove’s story about, 9 lycopene and, 177 microbiome and, 188 nature versus nurture and, 80 Personal Inventory Questionnaire and, 16 physical activity and, 214 PSA test and, 56 risk in Chinese and American

Science Fictions: How Fraud, Bias, Negligence, and Hype Undermine the Search for Truth

by Stuart Ritchie  · 20 Jul 2020

the past few years, a strong contender for the ‘most hyped’ award has been research on the microbiome – the countless millions of microbes that inhabit our bodies.71 Thanks to the hype, the microbiome has been targeted by a plethora of products and treatments. So-called ‘probiotics’, drinks or pills that top

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whose gut is in better shape, helping them win the battle against the bad bacteria.75 Where we should be wary, though, is when the microbiome is invoked as a contributing factor to diseases and conditions that have no obvious link to the gut. This is where the claims and the

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reality truly begin to part ways. Reading the scientific literature, one could get the impression that the microbiome is the cause of, and solution to, a truly remarkable array of mental and physical problems. For example, studies have appeared claiming links between the

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microbiome and depression, anxiety and schizophrenia, while faecal transplants have been proposed for the treatment of, among other conditions, heart disease, obesity, cancer, Alzheimer’s disease,

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conditions, meaning that the offspring had known only the humans’ microbes for their whole lives (autism is a developmental disorder, so any influence of the microbiome would need to be in effect from the very beginning of life). Depending on whether their guts had been colonised by microbes from autistic or

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, in which the mouse could choose to spend time with either a fellow mouse or ‘a small object’. The hypothesis was that the mice with microbiomes from autistic people would choose the object over the mouse companion – but they showed no difference. As the science writer Jon Brock noted in a

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the somewhat borderline p-value of 0.03. Despite those strong criticisms, to my knowledge the authors haven’t responded. Not all studies of the microbiome are fundamentally statistically flawed like the mouse-autism paper, though many are just as shaky in terms of the over-the-top conclusions they draw

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. A 2019 study that followed a similar methodology to the autism paper argued that transferring the microbiomes of schizophrenia patients to mice can cause the rodents to display symptoms of psychosis. It concluded by saying that the results ‘may lead to new

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diagnostic and treatment strategies’ for schizophrenia, which seems more than a little premature.86 Nevertheless, it could still turn out that differences in the microbiome do play some role in the complex causes of autism or schizophrenia symptoms, or those of some of the other conditions listed above, in mice

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or in people.87 However, microbiome researchers need to accumulate solid research over time instead of thrusting into the media every small, possibly p-hacked study that finds an effect, claiming

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’ results, but fewer well-replicated ones. There have been recent calls from within the scientific community to cool down the gee-whiz hype surrounding the microbiome and its associated treatments, and to improve the quality of the research.88 In the meantime, the grossly exaggerated claims of these papers and press

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releases provide the semblance of scientific backing to a host of useless, harmful, or just plain daft microbiome-related remedies: a probiotic drink made using microbes found in the guts of elite athletes that can supposedly boost your performance; the craze for ‘colonic

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your bowels with water and comes with ghastly-sounding risks like ‘rectal perforation’; and a direct-to-consumer microbiome testing company that allows you to discover ‘the nationality of your microbiome’.89 * * * Fads like microbiome mania wax and wane, but there’s one field of research that consistently generates more hype, inspires more

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Microbes within Us and a Grander View of Life (New York: HarperCollins, 2016). 72.  Timothy Caulfield, ‘Microbiome Research Needs a Gut Check’, Globe and Mail, 11 Oct. 2019; https://www.theglobeandmail.com/opinion/article-microbiome-research-needs-a-gut-check/ 73.  Andi L. Shane, ‘The Problem of DIY Fecal Transplants’, Atlantic, 16

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Gastroenterology Journal 7, no. 8 (Oct. 2019): pp. 1051–63; https://doi.org/10.1177/2050640619854587 76.  Microbiome and depression, anxiety and schizophrenia: Jane A. Foster & Karen-Anne McVey Neufeld, ‘Gut–Brain Axis: How the Microbiome Influences Anxiety and Depression’, Trends in Neurosciences 36, no. 5 (May 2013): pp. 305–12; https

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://doi.org/10.1016/j.tins.2013.01.005; T. G. Dinan et al., ‘Genomics of Schizophrenia: Time to Consider the Gut Microbiome?’, Molecular Psychiatry 19, no. 12 (Dec. 2014): pp. 1252–57; https://doi.org/10.1038/mp.2014.93. Heart disease: Shadi Ahmadmehrabi Shadi & W. H

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. Wilson Tang, ‘Gut Microbiome and Its Role in Cardiovascular Diseases’, Current Opinion in Cardiology 32, no. 6 (Nov. 2017): pp. 761–66; https://doi.org/10.1097/HCO.0000000000000445

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.  I may have used the word ‘cause’ in that sentence, but the causal status of many claims about the microbiome is far from clear. See Kate E. Lynch et al., ‘How Causal Are Microbiomes? A Comparison with the Helicobacter Pylori Explanation of Ulcers’, Biology & Philosophy 34, no. 6 (Dec. 2019): 62; https

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gut health and autism was already raised by Andrew Wakefield, as discussed in Chapter 3. We’re a million miles from being certain whether the microbiome differences cause autism or are caused by it – for example, by the fact that autistic people often have more restricted diets. 79.  Though in some

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, no. 6 (May 2019): 1600-1618. e17; https://doi.org/10.1016/j.cell.2019.05.004 81.  Derek Lowe, ‘Autism Mouse Models for the Microbiome?’, In the Pipeline, 31 May 2019; https://blogs.sciencemag.org/pipeline/archives/2019/05/31/autism- mouse-models-for-the

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-microbiome 82.  Sharon et al., ‘Human Gut Microbiota’, p.1162. 83.  California Institute of Technology, ‘Gut Bacteria Influence Autism-like Behaviors in Mice’ (news release), 30

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Mice)?’, Medium, 14 June 2019; https://medium.com/dr-jon-brock/can-gut-bacteria-cause-autism-in-mice-582306fd7235; see also Nicholette Zeliadt, ‘Study of Microbiome’s Importance in Autism Triggers Swift Backlash’, Spectrum News, 27 June 2019, https://www.spectrumnews.org/news/study

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-microbiomes-importance-autism-triggers-swift-backlash/ 85.  Thomas Lumley, ‘Analysing the Mouse Microbiome Autism Data’, Not Stats Chat, 16 June 2019; https://notstatschat.rbind.io/2019/06/16/analysing-the-mouse-autism-data/; see also

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Jon Brock’s own analysis, at the following page: https://rpubs.com/drbrocktagon/506022 86.  Zheng et al., ‘The Gut Microbiome from Patients with Schizophrenia Modulates the Glutamate-Glutamine-GABA Cycle and Schizophrenia-Relevant Behaviors in Mice’, Science Advances 5, no. 2 (Feb. 2019): p. 8

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to see whether they were less likely than control patients to have developed heart disease. If the microbiome was a big contributor to the disease – and, given their colectomies, these were patients with very unhealthy microbiomes – we might have expected to see a reduction in their risk of disease. There were no

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from 1996 to 2014’, BMJ Open 5, no. 12 (Dec. 2015): e008702; https://doi.org/10.1136/bmjopen-2015-008702 88.  William P. Hanage, ‘Microbiology: Microbiome Science Needs a Healthy Dose of Scepticism’, Nature 512, no. 7514 (Aug. 2014): pp. 247–48; https://doi.org/10.1038/512247a. Gwen Falony et

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al., ‘The Human Microbiome in Health and Disease: Hype or Hope’, Acta Clinica Belgica 74, no. 2 (4 Mar. 2019): pp. 53–64; https://doi.org/10.1080/17843286

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.2019.1583782; and J. Taylor, ‘The Microbiome and Mental Health: Hope or Hype?’, Journal of Psychiatry and Neuroscience 44, no. 4 (1 July 2019): pp. 219–22; https://doi.org/10.1503

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colonic irrigation, everything is back to the way it was pre-irrigation. See Naoyoshi Nagata et al., ‘Effects of Bowel Preparation on the Human Gut Microbiome and Metabolome’, Scientific Reports 9, no. 1 (Dec. 2019): p. 4042; https://doi.org/10.1038/s41598-019-40182-9. The nationality of your

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microbiome: https://atlasbiomed.com/uk/microbiome/results. See also Kavin Senapathy, ‘Keep Calm And Avoid Microbiome Mayhem’, Forbes, 7 March 2016; https://www.forbes.com/sites/kavinsenapathy/2016/03/07/keep-calm-and-avoid

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-microbiome-mayhem/ 90.  Milk: Josh Harkinson, ‘The Scary New Science That Shows Milk Is Bad For You’, Mother Jones, Dec. 2015; https://www.motherjones.com/environment/

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Bik’s fake images study (2016) Boldt affair (2010) cell lines China, misconduct in Hwang affair (2005–6) Macchiarini affair (2015–16) meta-scientific research microbiome studies Morton’s skull studies Obokata affair (2014) outcome switching preprints publication bias replication crisis Reuben affair (2009) spin and statistical power and Summerlin affair

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, Texas Hume, David Huxley, Thomas Henry Hwang, Woo-Suk hydroxyethyl starch hype arsenic life affair (2010) books correlation versus causation cross-species leap language and microbiome studies news stories nutrition and press releases spin unwarranted advice hypotheses Ig Nobel Prize images, fraudulent impact factor India insomnia International Journal of Advanced Computer

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Vries’ study (2018) Fanelli’s study (2010) Ioannidis’ article (2005) Macleod’s studies mindset studies (2018) saturated fats studies spin and stereotype threat studies mice microbiome Microsoft Excel Milgram, Stanley Mill, John Stuart Mindset (Dweck) mindset concept Mismeasure of Man, The (Gould) Modi, Narendra money priming Mono Lake, California Moon, Hyung

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, Ivan Orben, Amy Organic Syntheses organised scepticism Osborne, George outcome-switching overfitting Oxford University p-value/hacking alternatives to Fine and low-powered studies and microbiome studies and nutritional studies and Open Science and outcome-switching perverse incentive and pre-registration and screen time studies and spin and statcheck and papers

Ultra-Processed People: The Science Behind Food That Isn't Food

by Chris van Tulleken  · 26 Jun 2023  · 448pp  · 123,273 words

, xylan and pectin. These aren’t digestible by any mammals. Instead, we recruit bacteria to do the job for us. I am referring to the microbiome, the trillions of bacteria, fungi and other microorganisms that live on and inside us. Most of these microorganisms are found in our guts where, whether

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, they do pretty much the same thing. (We’ll explore the effect that UPF has on the microbiome later, which is potentially one of the ways in which it causes harm.) The cow microbiome is so crucial to its survival that you could invert your idea of a cow and think of

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it as simply a vehicle for its own microbiome, a fourlegged vessel transporting the microorganisms to the plants of their choice. Once you’ve done that, you can imagine yourself in the same way

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in their gut.** The arms races of the second age, between organisms competing to eat and avoid being eaten drove fabulously complex systems like the microbiome. I left Eddie’s farm with a new respect for the complexity of the herbivore project and a head full of thoughts about how humans

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the long-term control of food intake, but there’s also a system for short-term control. Your liver, pancreas, stomach, small intestine, large intestine, microbiome, fat tissue and many other organs all detect sugars, fat, protein and other molecules in the gut and the blood after you’ve eaten. They

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fertility (and according to some experts, may even cause penile shrinkage). She also told me about how the preservatives and emulsifiers in UPF disrupt the microbiome, how the gut is further damaged by processing that removes the fibre from food, and how high levels of fat, salt and sugar each cause

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that control food intake, obesity and energy control, as well as having effects on the gut itself.27, 28 Artificial sweeteners may also disrupt the microbiome, the population of bacteria that live on and in us, forming a vital part of our digestive and immune systems. This effect was widely reported

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because of a very high-profile paper in Nature.29 Evidence from animal studies showed that sucralose disrupts the gut microbiome, even at levels approved by regulatory agencies, and certainly at levels humans frequently eat.†† So, it may be that low-calorie artificial sweeteners are contributing

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. But it is a conflict. ** This study’s findings are consistent with those of studies done in rodents.24 †† Other sweeteners may not disrupt the microbiome, but the effects on metabolism through oral taste may be the same: sweet taste in the mouth signalling sugar that never arrives may always be

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that the emulsifiers in UPF are harmful? Well, yes. And most of the harm seems to be brought about by the changes caused to our microbiome. The equations that describe a donut and the equations that describe you and me are essentially the same: we’re all double-walled cylinders. The

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layer full of antibodies and immune cells that help to keep the peace with the other residents of the gut: the microbiome. A huge amount has been written about the microbiome, but our knowledge of it is still relatively small. However, we are starting to get a toehold on some of the

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new human is colonised by between 10 and 100 trillion microbes.‡ For the first few months of life, the infant immune system and its new microbiome test and shape each other in a complex and poorly understood dance. The infant who is breastfed receives their

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microbiome from their mother as well as specific antibodies in the milk which favour the development of the useful bacteria. There’s a frenzied engagement during

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the first few years of life, until the child and a few hundred species decide to settle down together and the microbiome becomes one of the body’s largest immune organs. We provide the microbes with a warm, wet mucus home full of nutrition, and they form

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brain. In short, like Eddie Rixon’s cows, we partly live on the waste products of the bacteria in our guts. The relationship with our microbiome is one of strictly enforced boundaries, however. We need to keep colon microbes in the colon. If friendly organisms end up in the wrong place

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up in the urinary system, which can’t handle them. When the gut lining is damaged by food, antibiotics or invaders, the population of the microbiome changes: we get new species that we haven’t signed a peace treaty with. They haven’t evolved with an obligation to care for our

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others isn’t clear, but it’s possible that they all have their pathogenic origins in an increased reactivity of the immune system to the microbiome. This may happen if our diet induces a change in the population of bugs which damages the gut barrier. This barrier is made of tight

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links between cells, mucus and immune cells, which work together to keep the microbiome on a tight leash. When it’s damaged, the gut starts to leak microbes and their waste products into the rest of the body. Lots

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of things in our diet can change the population of the microbiome and the integrity of the gut wall, including fat, fibre and – not least – emulsifiers. Two of the most ubiquitous, and thus the most studied, emulsifiers

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. Ultimately, the gut started to leak so much that bacterial components could be detected in the mice’s bloodstreams. The types of bugs in the microbiome were affected, too, with reduced levels of Bacteroidales – bacteria typically associated with health – and increased levels of bacteria that break down mucus and cause inflammation

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like Helicobacter pylori, which is known to cause cancer and ulcers in humans, began to flourish. Overall, there was a reduction in diversity of the microbiome, which is one of the defining characteristics of health. Under the microscope the mouse guts were so inflamed that it looked as if they were

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the emulsifiers interrupted their ability to manage glucose, some moved towards type 2 diet-related diabetes. To check that these effects were mediated through the microbiome, the team repeated the experiments on sterile mice (born and raised without any bacteria in their guts) and found none of the effects. Then they

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. Overall, this study provided robust evidence that, in the case of these two common emulsifiers, the harmful effects are due to damage caused to the microbiome.†† The conclusion to the Nature paper proposed that dietary emulsifiers ‘may have contributed to the post-mid-twentieth-century increase in incidence of inflammatory bowel

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disease, metabolic syndrome, and perhaps other chronic inflammatory diseases’. Overeating may be driven by food additives that alter the microbiome and promote intestinal inflammation. Of course, mice aren’t people, but the effect of different components of UPF on the delicate lining of the gut

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, and the resultant effect on our brains, is becoming increasingly clear. Emulsifiers aren’t the only UPF additives that affect our microbiomes, though. Maltodextrins‡‡ are synthetic chains of sugar molecules commonly found in UPF. They add texture and shelf life and seem to increase that reward we

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colonise infants at an early age, it may be having profound effects on immune system development. Papers about the effect of different additives on the microbiome keep piling up. Trehalose, an additive sugar that was deemed safe in the US in 2000, has been linked to outbreaks of the superbug Clostridium

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asthma, systemic connective tissue disorders, juvenile arthritis, inflammatory bowel disease, immune deficiencies and leukaemia.18 § These are really your genes. You can’t separate your microbiome from you any more than you can any other organ. It has an unbroken chain of ancestors going back to long before yours were primitive

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fish. ¶ In my view, the evidence doesn’t support eating lots of other bacteria in the form of probiotics. # The microbiome has profound effects on mouse behaviour. Germ-free mice are less social and show a dramatically altered pattern of risk taking compared with mice with

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still a lot of gaps in the testing. It’s really hard to test for chronic effects mediated through the microbiome so those tests aren’t done. The words ‘obesity’, ‘dysbiosis’ and ‘microbiome’ are pretty much absent from European Food Standards Agency reports. There is an ethical question here as well. We

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to drive excess consumption. • UPF is addictive, meaning that for some people binges are unavoidable. • The emulsifiers, preservatives, modified starches and other additives damage the microbiome, which could allow inflammatory bacteria to flourish and cause the gut to leak. • The convenience, price and marketing of UPF urge us to eat constantly

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unlikely to bring about real change, because the response from industry is to do yet more processing. They do this already: if emulsifiers damage the microbiome, let’s add some probiotics. If the food’s too soft, add more gum. If it’s too dense in energy, add artificial sweeteners. Their

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has been reformulated, but the plans are still getting bigger. The Archer-Daniels-Midland Company (aka ADM; revenues around $85 billion) makes ingredients linked to microbiome damage (emulsifiers, stabilisers and modified starches) but they also make enzymes, prebiotics, probiotics, postbiotics as well as selling personalised

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microbiome services. ADM predict the market for supplements to improve the health of our microbiomes will reach $9.1 billion by 2026. Why would any company remove the emulsifiers when you could add a

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syrup, glycerol, citric acid, invert sugar syrup, palm oil, dextrose, fructose, methylcellulose (a similar molecule to carboxy-methylcellulose, which made rodent guts bleed in those microbiome studies) and soy lecithin. There’s also some apple purée, fruit concentrate and flour. Did Eddie think they were healthy? ‘We were told that the

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. First, even formula made with clean water is associated with an increased risk of fatal infection,2-5 probably because of effects on the infant microbiome. Second, Nestlé was marketing the formula in communities where the possibility of producing an uncontaminated feed was almost zero.6 In these low-income settings

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Safety 2011; 10: 342–68. 10 Naimi S, Viennois E, Gewirtz AT, et al. Direct impact of commonly used dietary emulsifiers on human gut microbiota. Microbiome 2021; 9: 66. 11 Richey Levine A, Picoraro JA, Dorfzaun S, et al. Emulsifiers and intestinal health: an introduction. Journal of Pediatric Gastroenterology and Nutrition

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survival and mucosal colonization in mice. PLoS One 2014; 9: e101789. 20 Bäckhed F, Fraser CM, Ringel Y, et al. Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications. Cell Host & Microbe 2012; 12: 611–22. 21 Dinan TG, Stilling RM, Stanton C, Cryan JF. Collective unconscious

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shape human behavior. Journal of Psychiatric Research 2015; 63: 1–9. 22 Gilbert JA, Blaser MJ, Caporaso JG, et al. Current understanding of the human microbiome. Nature Medicine 2018; 24: 392–400. 23 Holder MK, Peters NV, Whylings J, et al. Dietary emulsifiers consumption alters anxiety-like and social-related behaviors

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Chips, 140 baby food/formula, 93, 172n, 236, 274, 288–90 bacteria, 3, 4 butter and, 24 exudate, 22 first age of eating, 80–83 microbiome, 87–8, 155, 204, 213–21, 271, 272–3, 289 baked beans, 157–8 Ballarin, Oswaldo, 288, 289–90 Bank of England, 282 Barabási, Albert

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Ediacara Hills, South Australia, 84 Edmonton, Alberta, 106 Egypt, ancient, 101 electrons, 82 elephants, 100 emulsifiers, 15, 17, 18, 19, 36, 154, 155, 160, 211 microbiome and, 217–19, 271, 272–3 endocrine system, 104, 108, 131, 272 Endres, John, 233 energy density, 66, 176–7, 271, 301 Eno, 285 Environmental

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, 198, 201–4, 216, 218, 220, 227, 241 metabolism, 54, 113, 116, 123, 126, 129, 203, 271 methyl folate, 192 Mexico, 65, 200, 268, 291 microbiome, 87–8, 155, 204, 213–21, 271, 289 micronutrients, 100, 190–92 Mignon Morceaux, 254 milk, 19, 24, 25, 46, 95, 189, 196, 214, 274

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energy density, 66, 176–7, 271, 301 flavouring, 180–92 health outcomes and, 6, 7, 47, 60, 62, 189, 216, 227 height and, 8, 191 microbiome and, 87–8, 155, 204, 213–21, 271 poverty and, 9, 41–2, 45, 55, 60, 143, 144–5, 149, 233 shelf life and, 15

Entangled Life: How Fungi Make Our Worlds, Change Our Minds & Shape Our Futures

by Merlin Sheldrake  · 11 May 2020

of the planet. In the last four decades, new technologies have granted unprecedented access to microbial lives. The outcome? For your community of microbes—your “microbiome”—your body is a planet. Some prefer the temperate forest of your scalp, some the arid plains of your forearm, some the tropical forest of

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. The “loss of a sense of self-identity, delusions of self-identity and experiences of ‘alien control,’ ” observed an elder statesman in the field of microbiome research, are all potential symptoms of mental illness. It made my head spin to think of how many ideas had to be revisited, not least

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fruiting bodies house thriving communities of bacteria and yeasts—between a million and a billion bacteria per gram of dry weight. Many members of truffles’ microbiomes are able to produce the distinctive volatile compounds that contribute to truffles’ aromas, and it is likely that the cocktail of chemicals that reaches your

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send rockets into space, the biologist Joshua Lederberg became concerned about the prospect of celestial contamination (it was Lederberg who in 2001 coined the word microbiome). Humans were now able to spread earthly organisms to other parts of the solar system. More worrying was the thought that humans could bring back

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to be the rule not the exception.” Researchers have long hypothesized that lichens might involve additional symbiotic partners. After all, lichens don’t contain microbiomes. They are microbiomes, packed with fungi and bacteria besides the two established players. Nonetheless, until 2016, no new stable partnerships had been described. One of the “contaminants

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and fungi that live in their guts, many of which produce chemicals that influence animal nervous systems. The interaction between gut microbes and brains—the “microbiome-gut-brain axis”—is far-reaching enough to have birthed a new field: neuromicrobiology. However, mind-manipulating fungi remain some of the most dramatic examples

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pose a greater threat than those caused by bacteria. It is a pattern that holds through sickness and through health: Animal microbiomes tend to be dominated by bacteria, while plant microbiomes tend to be dominated by fungi. This is not to say that animals don’t suffer from fungal diseases at all

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of my scalp.” ubiquitous feature of life: For organ transplants and human cell cultures see Ball (2019). For an estimate of the size of our microbiome see Bordenstein and Theis. (2015). For viruses within viruses see Stough et al. (2019). For a general introduction to the

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microbiome see Yong (2016) and a special issue of Nature on the human microbiome (May 2019): www.nature.com/​collections/​fiabfcjbfj [accessed October 29, 2019]. dark matter, or dark life: In a sense

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that confers heat tolerance. When grown without the virus, neither fungus nor plant can survive high temperatures. The microbiome of the fungus, in other words, determines the role that the fungus plays in the microbiome of the plant. The outcome is clear: life or death. One of the most dramatic examples of

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.bbc.co.uk/​1/hi/​world/​europe/​7123414.stm [accessed October 29, 2019]. than a single organism: For a discussion of the role of truffle microbiome in odor production see Vahdatzadeh et al. (2015). When I was out with Daniele and Paride I noticed that a truffle excavated from the silty

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, require a healthy gut microflora to develop a functional nervous system in the first place (Bruce-Keller et al. [2018]). If one knocks out the microbiome of adolescent mice before they have had the chance to develop a functional nervous system, they develop cognitive defects. These include memory problems and difficulty

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unavailable: For Mary Hunt see Bennett and Chung (2001). The “crowd” need not always be “non-scientists.” In 2017, a study published by the Earth Microbiome Project in Nature attracted attention for its unusual methodology. Researchers put out a call to scientists around the world for well-preserved environmental samples for

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: Stamets et al. (2018). 8. MAKING SENSE OF FUNGI which systems systematize systems: Haraway (2016), ch. 4. yeasts were discovered: For yeasts in the human microbiome see Huffnagle and Noverr (2013). For sequencing of the yeast genome see Goffeau et al. (1996); for Nobel Prizes on yeast see State of the

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P. 2019. How to Grow a Human. London, UK: William Collins. Banerjee S, Schlaeppi K, van der Heijden MG. 2018. Keystone taxa as drivers of microbiome structure and functioning. Nature Reviews Microbiology 16: 567–76. Banerjee S, Walder F, Büchi L, Meyer M, Held AY, Gattinger A, Keller T, Charles R

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KT. 2001. Alexander Fleming and the discovery of penicillin. Advances in Applied Microbiology 49: 163–84. Berendsen RL, Pieterse CM, Bakker PA. 2012. The rhizosphere microbiome and plant health. Trends in Plant Science 17: 478–86. Bergson H. 1911. Creative Evolution. New York, NY: Henry Holt and Company. Berthold T, Centler

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networks mediate overstorey-understorey competition in a temperate forest. Ecology Letters 7: 538–46. Bordenstein SR, Theis KR. 2015. Host biology in light of the microbiome: ten principles of holobionts and hologenomes. PLOS Biology 13: e1002226. Bouchard F. 2018. “Symbiosis, Transient Biological Individuality, and Evolutionary Process.” In Everything Flows: Towards a

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. 2007. Brain states: top-down influences in sensory processing. Neuron 54: 677–96. Gilbert JA, Lynch SV. 2019. Community ecology as a framework for human microbiome research. Nature Medicine 25: 884–89. Gilbert SF, Sapp J, Tauber AI. 2012. A symbiotic view of life: we have never been individuals. The Quarterly

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PW. 2013. Nematode-Trapping Fungi Eavesdrop on Nematode Pheromones. Current Biology 23: 83–86. Huffnagle GB, Noverr MC. 2013. The emerging world of the fungal microbiome. Trends in Microbiology 21: 334–41. Hughes DP. 2013. Pathways to understanding the extended phenotype of parasites in their hosts. Journal of Experimental Biology 216

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, Yan L, Ye L, Zhou J, Zhang B, Peng W, Zhang X, Li X. 2018. Chinese black truffle (Tuber indicum) alters the ectomycorrhizosphere and endoectomycosphere microbiome and metabolic profiles of the host tree Quercus aliena. Frontiers in Microbiology 9: 2202. Lindahl B, Finlay R, Olsson S. 2001. Simultaneous, bidirectional translocation of

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? The American Naturalist 187: E1–E12. Mohajeri HM, Brummer RJ, Rastall RA, Weersma RK, Harmsen HJ, Faas M, Eggersdorfer M. 2018. The role of the microbiome for human health: from basic science to clinical applications. European Journal of Nutrition 57: 1–14. Mohan JE, Cowden CC, Baas P, Dawadi A, Frankson

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: 608–15. Redman RS, Rodriguez RJ. 2017. “The Symbiotic Tango: Achieving Climate-Resilient Crops Via Mutualistic Plant-Fungus Relationships.” In Functional Importance of the Plant Microbiome, Implications for Agriculture, Forestry and Bioenergy. Doty S, ed. Springer International Publishing, pp. 71–87. Rees B, Shepherd VA, Ashford AE. 1994. Presence of a

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in a fungal chimera. Proceedings of the National Academy of Sciences 110: 12875–880. Ross AA, Müller KM, Weese JS, Neufeld JD. 2018. Comprehensive skin microbiome analysis reveals the uniqueness of human skin and evidence for phylosymbiosis within the class Mammalia. Proceedings of the National Academy of Sciences 115: E5786–E5795

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: 5273. Toju H, Peay KG, Yamamichi M, Narisawa K, Hiruma K, Naito K, Fukuda S, Ushio M, Nakaoka S, Onoda Y, et al. 2018. Core microbiomes for sustainable agroecosystems. Nature Plants 4: 247–57. Toju H, Sato H. 2018. Root-associated fungi shared between arbuscular mycorrhizal and ectomycorrhizal conifers in a

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via enteric serotonin networks. Proceedings of the National Academy of Sciences 115: 6458–463. Vahdatzadeh M, Deveau A, Splivallo R. 2015. The role of the microbiome of truffles in aroma formation: a meta-analysis approach. Applied and Environmental Microbiology 81: 6946–952. Vajda V, McLoughlin S. 2004. Fungal proliferation at the

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222: 543–55. Zhang Y, Kastman EK, Guasto JS, Wolfe BE. 2018. Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nature Communications 9: 336. Zheng C, Ji B, Zhang J, Zhang F, Bever JD. 2015. Shading decreases plant carbon preferential allocation towards the most beneficial

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–68. Zheng P, Zeng B, Zhou C, Liu M, Fang Z, Xu X, Zeng L, Chen J, Fan S, Du X, et al. 2016. Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host’s metabolism. Molecular Psychiatry 21: 786–96. Zhu K, McCormack LM, Lankau RA

Hormone Repair Manual

by Lara Briden  · 14 Apr 2021

vulnerable to menopausal symptoms include all the modern-day problems we’ll cover in Chapter 5, such as disruption of circadian rhythm, chronic inflammation, impaired microbiome and, most importantly, insulin resistance. As we saw earlier in this chapter, menopause increases the risk of insulin resistance and, at the same time,

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immune system and cause inflammation. The things that can go amiss with digestion include food sensitivities, intestinal permeability and problems with the gut bacteria or microbiome. Food sensitivities A food sensitivity or a food intolerance occurs when a food upsets your gut bacteria or inflames your gut lining – thereby activating your

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also discussed the role of FODMAPs and SIBO in digestive problems. Let’s now move on to intestinal permeability and problems with gut bacteria or microbiome. Intestinal permeability Normally, intestinal cells are tightly joined to create a barrier to prevent microbes, toxins and food proteins from entering the body. Intestinal permeability

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pain and autoimmune disease. We’ll explore treatment in the Autoimmune thyroid disease section of Chapter 8. Gut microbiome Your gut microbiome is the sum of your gut bacteria. When you have a friendly gut microbiome, it helps to reduce inflammation, regulate the HPA axis and support a healthy mood. When you have

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an unfriendly microbiome, or dysbiosis, it can generate inflammation and interfere with many aspects of a healthy perimenopause transition. As we’ll see in Chapter 9, too many

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of a certain type of unfriendly bacteria can impair estrogen metabolism and contribute to heavy periods. Dysbiosis can also affect the health of your vaginal microbiome and worsen the symptoms of dryness and vaginal irritation that we’ll cover in Chapter 10. There’s a bidirectional relationship between the

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microbiome and perimenopause, in that problems with the microbiome can worsen perimenopausal symptoms, and, at the same time, changing hormones can alter the composition of the gut microbiome. That’s why you may be experiencing changes with your digestion. Diet

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and lifestyle to support digestive health • Reduce alcohol because it can damage the microbiome. • Eat vegetables and healthy starches because they feed friendly bacteria. • Avoid ultra-processed food because it starves friendly bacteria. • Avoid concentrated sugar because it can

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them if they are creating inflammation. • Manage stress because it causes dysbiosis. • Exercise because it improves the health of the gut microbiome. • Get enough sleep because it supports a healthy microbiome. • Ensure adequate stomach acid because it helps to reduce unfriendly bacteria. If you experience digestive bloating and heartburn, consider that it

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use a different kind of medication as an interim measure. Fermented foods such as natural yoghurt and sauerkraut are another way to support a healthy microbiome, but I advise you to proceed with caution, especially with yoghurt. First, normal yoghurt contains A1 casein, which is unaltered by fermentation and can

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see interesting developments in the coming years. In the meantime, here are a few things to understand: • Diet has a more powerful effect on the microbiome than any probiotic. • Probiotic species do not colonise your gut. In other words, they do not become established as permanent residents in your intestine but

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instead exert beneficial effects on your microbiome, intestinal wall and immune system as they pass through. • Clinical benefits have been demonstrated for specific strains (or subtypes) of certain bacteria species. You may

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Lactobacillus plantarum 299v is clinically proven to treat IBS, while the strains Lactobacillus rhamnosus GR-1 and Lactobacillus reuteri RC-14 can normalise the vaginal microbiome and relieve yeast (i.e. candidiasis or thrush) infections. • It’s better to choose a product with many individual bacteria but fewer strains or

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’ve left this topic until last because 1) avoiding toxins may not be as important as other factors such as eating vegetables to feed your microbiome, and 2) avoiding toxins can be tough to do. That said, it’s worth at least considering toxins, because they can cause problems such

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minute of every day. In other words, your body is made to detoxify. To support your body’s natural detoxification process: • Maintain a healthy gut microbiome because it assists the healthy removal of toxins via your stools. • Identify and avoid triggering food sensitivities because they can create inflammation in the gut

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HPA axis – not a good situation when you’re already in the vulnerable time of trying to recalibrate your HPA axis. • Alcohol damages the gut microbiome, activates mast cells and histamine, and promotes intestinal permeability or endotoxemia. • Alcohol stimulates appetite in women and so leads to overeating. • Alcohol can make

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liver, which we’ll cover in Chapter 10. Ultra-processed foods are devoid of the nutrients needed by you and the fibre needed by your microbiome. They also commonly contain harmful food additives, high-dose fructose (Chapter 8) and processed vegetable oils. Processed vegetable oils include oils such as soy,

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to bones or heart. Some studies have shown small benefits for some women but not others, a difference that researchers attribute to differences in gut microbiomes, and the role that plays in transforming phytoestrogens to a more active form. On the plus side, phytoestrogens that occur naturally in food do not

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cells’ ability to shift between glucose and ketones for energy. There are several ways to do that, including exercise, intermittent fasting and maintaining a healthy microbiome. One of the best ways to cultivate metabolic flexibility is to prevent or reverse insulin resistance, because insulin resistance puts the brakes on the body

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and easier than trying to stay in ketosis all the time, and starch with the evening meal will calm your nervous system, feed your gut microbiome and help you to feel full. Won’t fasting make you feel hungry? First, please don’t attempt intermittent fasting if you’re already underweight

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not have the same negative effects because most of it is converted to harmless glucose and organic acids before it can reach the liver or microbiome. According to Princeton researcher Joshua D. Rabinowitz, ‘There is a fundamental physiological difference in how smaller and larger amounts of sugar are processed in

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because it improves insulin sensitivity. If you’ve been working night shifts, try to find a way to change your job situation. Maintain a healthy microbiome because it improves insulin sensitivity and may be why frequent antibiotics can cause weight gain. If you’re in the situation of requiring frequent antibiotics

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sugar. Do not take berberine for more than eight consecutive weeks except under professional advice, because berberine has antimicrobial effects that could affect your gut microbiome. With short-term use, berberine’s antimicrobial effects are beneficial and can treat digestive problems such as SIBO and intestinal permeability. With longer-term use

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the surgery used to treat it. Another explanation is that IBS itself drives endometriosis and adenomyosis. In other words, that an underlying problem with the microbiome and/or intestinal permeability contributes directly to the inflammation and immune dysfunction of endometriosis and adenomyosis. Such an idea is supported by a recent review

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study that linked endometriosis with an imbalance of gut bacteria, and by some intriguing research into the pelvic microbiome, which are the bacteria living in the pelvis or peritoneum. According to ‘the bacterial contamination hypothesis of endometriosis’, women with endometriosis have intestinal permeability which

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the role of gut bacteria, brings us to a few strategies for keeping estrogen low: • Reduce or eliminate alcohol. • Promote a healthy digestion and gut microbiome. • Eat phytoestrogens, which have a beneficial anti-estrogen effect (page 128), in part through supporting healthy estrogen metabolism. • Consider supplementing iodine, which can downregulate estrogen

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and Replens® rehydrate vulval and vaginal tissue by increasing fluid content, mimicking vaginal secretions and lowering pH, which can help to maintain a healthy vaginal microbiome. Like lubricants, moisturisers should be free of preservatives and have a low pH and osmolality. A zinc-containing vaginal moisturising gel may soon come onto

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of 1) the epithelial cells that line the vagina, and 2) the community of friendly bacteria that live in the vagina (vaginal microbiome). In fact, maintaining a healthy vaginal microbiome has been found to prevent BV and UTIs, as well as improve GSM symptoms such as dryness, atrophy and pain. TIP Did

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you know? A healthy vaginal microbiome has low species diversity with predominantly Lactobacillus species. This is in contrast to a healthy gut microbiome, which has high species diversity. There’s a close bi-directional relationship between epithelial cells and the

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vaginal microbiome. In one direction, healthy epithelial cells make the glycogen that feeds healthy vaginal bacteria; in the

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other direction, a healthy vaginal microbiome helps to support healthy epithelial cells. Vaginal estrogen therapy is highly beneficial for both

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epithelial cells and the vaginal microbiome because it stimulates the glycogen that feeds vaginal bacteria. Beyond estrogen, diet and lifestyle strategies

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GSM include: • Not using douches or wipes because they alter vaginal pH and damage the microbiome. • Not smoking because it lowers estrogen and damages the vaginal microbiome. • Avoiding, as much as possible, antibiotics, which can damage the microbiome. • Movement, especially strength-building exercises for the core and back, can assist with the

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can also help to prevent recurrent menopausal UTIs. How it works: Vaginal strains of probiotics help to normalise the health and composition of the vaginal microbiome. What else you need to know: Vaginal probiotics can be taken orally or inserted vaginally. One vaginal product (Gynoflor®) combines the probiotic strain Lactobacillus acidophilus

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earlier, top strategies include: avoiding high-dose fructose, especially from desserts and sugar-sweetened beverages; eating whole, unprocessed foods, including vegetables to sustain a healthy microbiome; supporting a healthy circadian rhythm with morning light and protein; trying intermittent fasting; and moving your body to build muscle. Movement of any type is

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your last period. meta-analysis A meta-analysis uses statistical methods to combine the results of many different studies in order to determine wider trends. microbiome The community of microorganisms in a particular environment, such as the body or a part of the body. micronised progesterone Micronised progesterone is a form

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brain outcomes and cognitive decline: longitudinal cohort study’, BMJ, 357, 2017, article j2353. 120: Alcohol damages the gut microbiome . . .: PP Lowe, B Gyongyosi, A Satishchandran et al, ‘Alcohol-related changes in the intestinal microbiome influence neutrophil infiltration, inflammation and steatosis in early alcoholic hepatitis in mice’, PLoS One, 12(3), 2017, article

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nonalcoholic fatty liver disease, and the case for human and bacterial genes’, Advances in Nutrition, 7(1), January 2016, pp5–13. 205: Maintain a healthy microbiome because . . .: H Dutton, MA Doyle, CA Buchan et al, ‘Antibiotic exposure and risk of weight gain and obesity: protocol for a systematic review’, Systematic

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, pp411–14. 247: Such an idea is supported by a recent review study . . .: M Leonardi, C Hicks, F El-Assaad et al, ‘Endometriosis and the microbiome: a systematic review’, BJOG, 127(2), January 2020, pp239–49. 247: According to ‘the bacterial contamination hypothesis of endometriosis’ . . .: KN Khan, A Fujishita, K

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pilot study’, Journal of Menopausal Medicine, 25(1), April 2019, pp63–8. 271: In fact, maintaining a healthy vaginal microbiome has been found to . . .: AL Muhleisen & MM Herbst-Kralovetz, ‘Menopause and the vaginal microbiome’, Maturitas, 91, September 2016, pp42–50. 271: It’s believed to be autoimmune and is often associated with

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disease and 260 anovulatory cycle 48–9, 49, 54, 70, 231 problems caused by 49 anti-Müllerian hormone (AMH) blood test 83 antibiotics and gut microbiome 205 antidepressants 189 hot flushes, for 164 sleep disturbance, for 168 antihistamines 189 endometriosis/adenomyosis treatment 243 anxiety 14, 15 appearance 32–3 aromatase 51

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131 ultra-processed food 126–7 vegan or vegetarian 124 vegetables 127–9 yoghurt 115 digestive health 103–16 diet 113 fermented foods 115 gut microbiome 113–6 intestinal permeability 112–13 irritable bowel syndrome (IBS) 104 lifestyle 114 probiotics 115–16 sensitives/intolerances see food sensitivities/intolerances small intestine bacterial

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disturbance, for 171 Gottfried, Sara 93 grandmother hypothesis 41–2 Graves’ disease 211 Greendale, Dr Gail A. 180 Greer, Germaine 39 grief 38–9 gut microbiome 113–5 antibiotics, effect on 205 Hailes, Jean 63 hair loss 275–7 conventional treatments for 276 diet and lifestyle impacts 276 sex hormone-binding

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49 mental health increased risk of onset 21 metabolic flexibility 160–1 metabolic rate, resting 277–8 metabolic syndrome see insulin resistance metabolism, slowing 79 microbiome, impaired 87 migraines 14, 15, 70, 72–3, 144, 173–80, 220 diet and lifestyle impacts 176 estrogen 175 gluten-free diet 176 iron

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dryness 16, 26, 78–9 pain 34, 79 prolapse 34, 79 yeast infections 115 vaginal estrogen 140, 142–3, 268 vaginal laser therapy 269 vaginal microbiome 271 maintaining healthy 271–2 vaginal moisturisers 270 vaginal probiotics 272–3, 314 vaginal wall prolapse 267 vagus nerve 93, 94 vasectomy 67 vegan or

Brain Energy: A Revolutionary Breakthrough in Understanding Mental Health--And Improving Treatment for Anxiety, Depression, OCD, PTSD, and More

by Christopher M. Palmer Md  · 15 Nov 2022  · 402pp  · 107,908 words

—or melancholia; in fact the word “melancholy” comes from the Greek for “black bile.” (Interestingly, bodily substances—particularly feces, as it relates to the gut microbiome—are making a comeback in the theory of mental illness. More on that later.) Just as the birth of medicine transformed the way people thought

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causing both the depression and these brain changes? We just don’t know yet. Finally, let’s throw another wrench into the works—the gut microbiome. The human digestive system contains trillions of microorganisms, including bacteria, viruses, and fungi. They produce hormones, neurotransmitters, and inflammatory molecules that get released into our

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absorbed into our bloodstreams. Research suggests that these microbes play a role in obesity, diabetes, cardiovascular disease, depression, anxiety, autism, and even schizophrenia.5 But microbiome research is relatively new, and we don’t yet know the details of which specific microorganisms might be beneficial and which ones harmful, or in

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different types of organisms. More to the point, although some research in mice has found changes in depressive symptoms mediated through changes in the gut microbiome, we don’t yet know how to use this information to effectively treat depression or most other disorders.6 So, that’s a whirlwind tour

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, and social factors, ranging from things like diet and exercise, smoking, drug and alcohol use, and sleep . . . to hormones, inflammation, genetics, epigenetics, and the gut microbiome. The list also extends to relationships, love, having meaning and purpose in life, and stress levels. You can isolate any one of these factors and

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a mistake. Another way to look at it is that these mitochondria were receiving erroneous signals from somewhere else in the body, maybe the gut microbiome, or gut cells, or the liver. Or maybe it was due to insulin resistance, as I described earlier. But another distinct possibility is that the

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all mental disorders are more likely to develop an eating disorder. They are looking for ways to feel better. The Gut-Brain Axis and the Microbiome Over the past few decades, a growing body of research suggests that our intestinal tract plays an important role in both metabolic and mental health

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studies have shown that gut microbes can affect weight. In one study, researchers found that the microbiome in obese mice extracts more nutrients and calories from food than in thin mice. When this obese microbiome is transferred to thin mice, the thin mice gain weight.25 There is also increasing evidence for

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the role of the gut microbiome in mental disorders. Animal models and small human trials have shown that the gut

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microbiome appears to play a role in depression, anxiety, autism, schizophrenia, bipolar disorder, and eating disorders. There is also

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evidence for the role of the gut microbiome in epilepsy and neurodegenerative disorders. Gut bacteria get first dibs on all the food we eat. They produce a variety of metabolites, neurotransmitters, and hormones

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mentioned, about 90 percent of the body’s total serotonin is produced in the intestinal tract. This field of the gut-brain axis and the microbiome can quickly become overwhelming when one begins to think about all the different microbes, metabolites, hormones, neurotransmitters, neuropeptides, and other factors involved. However, there is

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been shown to change mitochondrial metabolism, alter the barrier function of the gut cells, and can lead to inflammation.26 Food, Fasting, and the Gut Microbiome as Treatments There are at least eight different ways that dietary interventions can be helpful in addressing mental symptoms:27 1.Addressing nutritional deficiencies, such

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, intermittent fasting (IF), and fasting-mimicking diets (more below on all three) that stimulate autophagy and mitophagy to improve metabolic health. 5.Improving the gut microbiome (more on how below). 6.Improving metabolism and mitochondrial function with a dietary intervention. This includes changes in insulin resistance, metabolic rate, the number of

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fuel source, which can be a lifeline to insulin-resistant brain cells. It also changes neurotransmitter levels, regulates calcium channels, decreases inflammation, improves the gut microbiome, increases overall metabolic rate, reduces insulin resistance itself, and most importantly, induces both mitophagy and mitochondrial biogenesis.35 After people are on this diet for

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supervision, as there are risks and side effects, and prescription medications usually need to be adjusted or stopped safely. The Gut Microbiome As mentioned, there is no question that the gut microbiome plays a role in mental and metabolic health. In terms of proven interventions, however, this field is in its infancy

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. Here are four types of interventions to consider: 1.Avoid antibiotic exposure if possible. Antibiotics are known to disrupt the microbiome, and they can sometimes directly cause mitochondrial dysfunction. In addition to not taking antibiotics unless necessary, it’s important to avoid eating foods that contain

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, and other products that commonly contain antibiotics fed to the animals. Look for “raised without antibiotics” labels. 2.Diet plays a critical role in the microbiome. Avoid highly processed foods. Eating foods high in fiber, such as fruits and vegetables, and a diet of real, whole foods is likely optimal. 3

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use of substances might be as well. Even something like the gut microbiome can be affected by sleep, light exposure, and stress. So if your microbiome is off, changing these other contributing causes might correct that issue. Alternatively, changing your microbiome might improve your sleep or stress levels. Think of everything as being

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withdrawal symptoms. All these situations can happen with all the treatments I’ve mentioned, including medications, light therapy, changes in diet, changes in the gut microbiome, supplement use, and even psychological and social interventions. Remember that you’re looking for interventions that will improve your metabolic health over the long run

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Fall of MRI Studies in Major Depressive Disorder.” Transl Psychiatry 9(335) (2019). doi.org/10.1038/s41398-019-0680-6. 5A. L. Komaroff. “The Microbiome and Risk for Obesity and Diabetes.” JAMA 317(4) (2017): 355–356. doi: 10.1001/jama.2016.20099; K. E. Bouter, D. H. van Raalte

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, A. K. Groen, et al. “Role of the Gut Microbiome in the Pathogenesis of Obesity and Obesity-Related Metabolic Dysfunction.” Gastroenterology 152(7) (May 2017): 1671–1678. doi: 10.1053/j.gastro.2016.12.048

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.” J Clin Invest 125(3) (2015): 926–938. doi: 10.1172/JCI76304. 6J. A. Foster and K. A. McVey Neufeld. “Gut-Brain Axis: How the Microbiome Influences Anxiety and Depression.” Trends Neurosci 36(5) (May 2013): 305–312. doi: 10.1016/j.tins.2013.01.005. Chapter 3 1American Psychiatric Association

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.” PLoS One 9(9) (2014): e 106463. doi: 10.1371/journal. pone.0106463. 25P. Turnbaugh, R. Ley, M. Mahowald, et al. “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest.” Nature 444(7122) (2006): 1027–1031. doi: 10.1038/nature05414. 26D. N. Jackson and A. L. Theiss. “Gut Bacteria

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) diagnostic labels diathesis-stress model diet and eating behaviors. see also specific diets eating disorders example of fasting food quality gut-brain axis and gut microbiome and obesity starvation as treatment vitamins and nutrients disease-modifying treatments dopamine drug and alcohol use. see also alcoholism; substance use disorders alcohol deaths of

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and risk for broad range of disorders that cause disorders genetics and “biological” disorders and depression and risk for metabolic disorders gut-brain axis gut microbiome H hallucinations Harman, Denham health, social determinants of. see also psychological and social factors health behaviors heart attacks contributing causes of and mental disorders and

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Artificial Intelligence: A Modern Approach

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