microbiome

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

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

Beyond Inheritance: Our Ever-Mutating Cells and a New Understanding of Health

by Roxanne Khamsi;  · 21 Apr 2026  · 335pp  · 91,958 words

thirty trillion to forty trillion cells. That number does not even include the additional thirty-nine trillion or so tiny bacterial cells in your gut microbiome. This multicellular existence is something people often overlook. We tend to think of ourselves as one entity—one body moving about in the world through

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it comes to mutations acquired as part of development and aging, the numbers can be staggering. Putting aside the many bacterial cells in our gut microbiome, each adult human body consists of upwards of thirty trillion human cells that all originated from a single fertilized egg cell. It took a lot

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the microbial passengers within us, as detailed in chapter 8. These passengers include the bacteria that help make up what’s known as our gut microbiome. There are trillions of them living in our digestive tract, and their activity might even influence our waistline. The viruses that infect us can also

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uncovered a bacterium as the main cause. More recently, we’ve gotten used to the weird idea that trillions of bacteria live in our gut microbiome. Perhaps, then, it isn’t a huge stretch to think that we might—for certain tumor types—tolerate coexisting with cancer cells as long as

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many of them play an essential role in maintaining our health. Among the many ways they support us, the friendly microbes within the human gut microbiome help us break down our meals and absorb vital nutrients. It’s a sublime symbiosis happening right inside our bellies. Just before we enter this

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life, a child will experience a rapid colonization and turnover of bacterial strains within the gut. One study of hundreds of infants suggested that their microbiomes shifted at a rate tenfold higher than in grown-ups. Anyone who has changed the diapers of a child can attest to the dramatic—and

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odorous—digestive transformation that happens in the first couple of years. Finally, by age two, the toddler will possess a stable, adultlike microbiome. And if the gods take pity on you, the child might even be potty-trained by that time. The youngster’s

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microbiome evolution, however, is far from over. As the years go by, the bacterial populations inside our bellies ebb and flow. Studies of the human digestive

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at thousands of bacterial strains from fifteen different human populations. They found that there were higher transfer rates of antibiotic resistance genes in the gut microbiomes of nonindustrialized populations—perhaps linked to the higher environmental prevalence of such resistance genes in the regions where those groups live. In contrast, they found

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REFERENCE IN TEXT One study of hundreds of infants: Daisy W. Chen and Nandita R. Garud, “Rapid Evolution and Strain Turnover in the Infant Gut Microbiome,” Genome Research 32, no. 6 (2022): 1124–36, doi.org/​10.1101/​gr.276306.121. GO TO NOTE REFERENCE IN TEXT Finally, by age two

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, doi.org/​10.4161/​gmic.20169. GO TO NOTE REFERENCE IN TEXT “may only be the tip”: Isabel Gordo, “Evolutionary Change in the Human Gut Microbiome: From a Static to a Dynamic View,” PLOS Biology 17, no. 2 (2019): e3000126, doi.org/​10.1371/​journal.pbio.3000126. GO TO NOTE REFERENCE

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IN TEXT sixteen of the microbe’s genes mutated: Shijie Zhao et al., “Adaptive Evolution Within Gut Microbiomes of Healthy People,” Cell Host & Microbe 25, no. 5 (2019): 656–667.E8, doi.org/​10.1016/​j.chom.2019.03.007. GO TO NOTE

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TO NOTE REFERENCE IN TEXT higher transfer rates of antibiotic resistance: Mathieu Groussin et al., “Elevated Rates of Horizontal Gene Transfer in the Industrialized Human Microbiome,” Cell 184, no. 8 (2021): 2053–2067.E18, doi.org/​10.1016/​j.cell.2021.02.052. GO TO NOTE REFERENCE IN TEXT over the

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ten-year study: C. Menni et al., “Gut Microbiome Diversity and High-Fibre Intake Are Related to Lower Long-Term Weight Gain,” International Journal of Obesity (2005) 41, no. 7 (2017): 1099–105, doi

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–17 autoimmunity, 65–69 AZ505 SMYD inhibitor, 146 B Babushok, Daria, 98–99, 108–9 bacteria, 21, 55, 59. See also Helicobacter pylori in gut microbiome, xviii, xxii–xxiii, 21, 178, 179–82, 191 Bacteroides fragilis (B. fragilis), 181–82 Baylor College of Medicine, 47 B cells, 53–54, 59, 66

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, 66, 83, 92 diamondback moths, 12–14 Die Mutationstheorie (de Vries), xii diet, 145, 181, 182, 217 digestive system, xxii, 177, 180. See also gut microbiome disappearing X chromosome, 82–84 Discover (magazine), 173–74 DNA repair, xvii, 158–59, 208–11 aging and, 208–11, 214–16, 218, 225–26

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, 37–38, 47–49, 80–81, 89–90, 120, 144, 151, 153, 154, 208, 227–28 convergent mutations, 144 cystic fibrosis, 153 of gut and microbiome, 180–82 H. pylori, 171–72, 175, 177–78 of immune system, 55, 65–66, 72, 75 phylogenetics, 120–21 Roux and, 30–31, 33

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, 74 Grawitz, Paul, 60 Grompe, Markus, 148–52 GSK (GlaxoSmithKline), 59 guanine, 224 Guillain–Barré syndrome, 69 Gulbenkian Institute for Molecular Medicine, 180–81 gut microbiome, xviii, xxii, 21, 178, 179–82 B. fragilis, 181–82 Cagan’s research, 203–5 evolution of, 180–82 H Haeckel, Ernst, x, 31, 32

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and, 178 Mayer’s research, 65–68 microbes, 59–60 SARS-CoV-2 and, 184–86 vaccines. See vaccines Imperial College London, 40 infants and microbiome, 180 infertility, 40–41, 118, 159–60 inflammation, 90, 91, 92, 173, 176, 207 influenza (flu), 59, 73, 91, 183, 184 inherited diseases, xii, xv

10% Human: How Your Body's Microbes Hold the Key to Health and Happiness

by Alanna Collen  · 4 May 2015  · 372pp  · 111,573 words

step in self-discovery: DNA sequencing. But rather than sequence my own genes, I would have the genes of my personal colony of microbes – my microbiome – sequenced. By knowing which species and strains of bacteria I contained, I would have a starting point for self-improvement. Using the latest understanding

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different evolutionarily as bacteria are from plants or animals. Together, the microbes living on the human body contain 4.4 million genes – this is the microbiome: the collective genomes of the microbiota. These genes collaborate in running our bodies alongside our 21,000 human genes. By that count, you are

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DNA-sequencing technology invented during the Human Genome Project enabled another major genome-sequencing programme, but one that received far less media attention: the Human Microbiome Project. Rather than looking at the genome of our own species, the HMP was set up to use the genomes of the microbes that

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live on the human body – the microbiome – to identify which species are present. No longer would a reliance on Petri dishes and an over-abundance of oxygen hold back research into

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was to be a far more comprehensive survey of the genes that make a person, both human and microbial. At the conclusion of the Human Microbiome Project’s first phase of research in 2012, not one world leader made a triumphant statement, and only a handful of newspapers featured the

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rodent models, medical science would progress at a millionth of the speed. It was by using germ-free mice that the commander-in-chief of microbiome science, Professor Jeffrey Gordon from the University of Washington in St Louis, Missouri, discovered a remarkable indication of just how fundamental the microbiota are

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tolerance, but encouragement. This realisation, combined with the technical power of DNA sequencing and germ-free mouse studies, began a revolution in science. The Human Microbiome Project, run by the United States’ National Institutes for Health, alongside many other studies in laboratories around the world, has revealed that we utterly depend

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locations like the intestines, while sparser collections of species occupy more ‘rural’ or hostile locations such as the lungs and the stomach. The Human Microbiome Project set out to characterise these communities, by sampling microbes from eighteen sites across the inner and outer surfaces of the human body, in each

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colonisation by a flood of intruders smuggled on food and floating in the air. From the mouths of their volunteers, researchers working on the Human Microbiome Project took not just one sample, but nine, each from a slightly different location. These nine sites turned out to have discernibly different communities,

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afresh. But, as we will discover, the role of the microbes living in the gut goes far beyond synthesising a few vitamins. The Human Microbiome Project began by looking only at the microbiotas of healthy people. With this benchmark set down, the HMP went on to ask how they differ

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that selection acts upon, whether animalian or microbial. Accordingly, the Rosenbergs’ idea is known as ‘hologenome selection’: selection on the host genome and the microbiome combined. The point is, the human immune system did not evolve in isolation. It was never a sterile set of nodes and tubes and roving

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direct effect of the drugs themselves. A team led by New York University’s Martin Blaser – an infectious disease doctor and director of the Human Microbiome Project – set out to determine precisely what antibiotics could do to the microbiota and metabolism. In 2012, they had shown that giving low doses

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stood up and slid a stack of newly published scientific papers towards her. As they fanned out in front of her, Carmody caught sight of ‘microbiome’ and ‘intestinal microbiota’ among the titles. ‘You might want to have a think about how this would affect your conclusions,’ the examiner said. ‘The

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fibrous bamboo stalks, but only 2 kg of that gets digested. Without its microbiota, that 2 kg would dwindle to nearly nothing. The giant panda microbiome, however – that is, the genes contained within the panda’s microbiota – carries a suite of cellulose-busting genes that are more normally found in

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associated diseases. Certainly, the quickest way to make a lab rat fat is to feed it a high-fat, high-sugar diet. It’s what microbiome scientists call ‘the Western diet’. After just a single day eating this way, rats’ gut microbes have changed composition and are making use of

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dropped since the 1940s. We simply eat fewer plant-based foods than we used to. By looking at the genes contained within the Burkina Fasan microbiome, it’s easy to see why the microbiota contains such a high proportion of Prevotella and Xylanibacter species – 75 per cent of the total

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their plant-degrading bacteria and gained species that break down proteins, synthesise vitamins and detoxify the cancer-causing compounds found in charred meat. Their microbiomes began to resemble those of herbivorous animals on the one hand and carnivorous on the other. One volunteer in the study had been a lifelong

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intolerances are not a real phenomenon, but that the origin of these conditions doesn’t lie within our genomes, but within those of our damaged microbiomes. We have evolved to eat wheat and many of us have evolved to tolerate lactose as adults, but we may have opened ourselves up

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But whatever the workings behind it, worries about the impact of delivery mode on the future development of the gut microbiota were enough to prompt microbiome scientist Rob Knight into action when his wife had to give birth to their daughter by emergency C-section in 2012. Having been involved in

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doubt that many thousands of mothers and babies are alive because of such hygiene. But it is different from what the human genome and the microbiome expect. It’s this difference and its consequences that should guide the next step in improving medical care for women and babies. Ultimately, this

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baby to cope with the onslaught of its mother’s vaginal bacteria as it slips head-first into a microbial world. The beauty of the microbiome is that, in ways that the human genome can never be, it is adaptable. As you age, as your hormones wax and wane, as

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did as a youngster. Babies, for example, need a lot of folic acid, but they can’t eat the foods that contain it. Their microbiomes, though, are full of genes that synthesise folic acid from breast-milk. Adults don’t need so much folic acid and they usually get enough

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genes that break it down. The opposite is true for Vitamin B12. The older you are, the more you need. As you age, your microbiome increases the number of genes that synthesise B12 from food. Your microbes aren’t doing this to be kind – they need these vitamins or their

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could be used to create a timeline of events reliable enough for use in forensic investigations. DNA technology utterly changed crime-scene investigation, but your microbiome is even more distinctive than your human genome – imagine what secrets it could reveal. Members of the same family tend to have very similar

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elderly. We are accompanied from the very first breath to the very last by our colony of microbes. As our bodies grow and change, our microbiomes adapt, providing us with an extension to our own genomes that can adjust within hours to better suit our needs, and their own. All

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first time in December 2014. These pills contain the same unadulterated faecal solution that Borody uses in transplants, but they are delivered orally instead. The microbiome scientist Dr Emma Allen-Vercoe, however, amidst the tighter regulations of Canada, is working on a more specifically calibrated synthetic stool. Using the same tech

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microbiotas of people living pre-industrial lifestyles? Not surprisingly, there’s quite a difference. An international team of researchers led by the pied piper of microbiome research, Jeffrey Gordon of Washington University in St Louis, Missouri, collected stools from over 200 people living in two pre-industrial, rural and traditional cultures

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Malawians overlapped, with relatively few differences between the microbes they contained. These two groups of people live over 7,000 miles apart, yet their microbiomes are more similar to one another than either is to those of people living in the US. Not only are the US microbiotas distinctly different

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these, as Western access to nutritious, vitamin-packed foods is surely second-to-none. I had it the wrong way round. In fact, US microbiomes contained more genes for vitamin-synthesising enzymes. They also had produced more enzymes for breaking down pharmaceutical drugs, the heavy metal mercury, and the bile

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salts produced from eating fatty foods. Essentially, the differences between the US and non-US microbiomes reflected the differences between carnivorous and herbivorous mammals. Where US gut microbes were specialists in breaking down proteins, sugars and sugar substitutes, the Amerindian and

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inherited and part-acquired, play an important part in an individual’s response to medicine. Microbes can activate, inactivate and toxify medicines. In 1993, the microbiome’s capacity to interfere with medications came at great cost to eighteen Japanese patients, who had developed shingles while suffering from cancer. Their shingles medication

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help to reduce side effects, improve outcomes and ensure safety. As DNA sequencing continues to reduce in price, the idea that we might monitor the microbiome to assess health risks and chart improvements becomes increasingly realistic. Our overuse of antibiotics extends to intensive farming. In his excellent book The Great Food

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captured its essence on paper, beguiled me, and reinforced my fascination with my chosen career. It’s hard to imagine that the deciphering of the microbiome, even embodied as art in such an iconic way, could have that same magical impact as the decoding of the genome. But our realisation

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our diet, and our exposures. In short, our environment: nurture. Now we have a third player, which sits uncomfortably between nature and nurture. Although the microbiome is strictly an environmental force at work on our eventual characteristics, it is genetic, and it is inherited. Not via eggs or sperm, not via

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human genes, but a good portion of the microbiome is passed from parents, especially mothers, to offspring. Many parents hope that they pass on the best of themselves to their children; films like Gattaca

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wish is not left to chance. Most parents also hope to provide their children with the happiest and healthiest environment that they can manage. The microbiome, with its genetic influence but environmental control, gives parents the power to do both of these things. Despite all the hype, our human genome

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health and happiness will take time to establish, and we don’t yet have the knowledge to diagnose health problems on the basis of the microbiome. Before I knew about the microbiota – about my microbiota – I put little thought into what I ate. I did not subscribe to the notion

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alters gut microbial ecology. Proceedings of the National Academy of Sciences 102: 11070–11075. 15. Turnbaugh, P.J. et al. (2006). An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027–1031. 16. Centers for Disease Control (2014). Obesity Prevalence Maps. Available at: http://www.cdc.gov

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in their first-degree relatives. Journal of Pediatric Gastroenterology and Nutrition 51: 418–424. 15. Grice, E.A. and Segre, J.A. (2011). The skin microbiome. Nature Reviews Microbiology 9: 244–253. 16. Farrar, M.D. and Ingham, E. (2004). Acne: Inflammation. Clinics in Dermatology 22: 380–384. 17. Kucharzik,

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(2006). Recent understanding of IBD pathogenesis: Implications for future therapies. Inflammatory Bowel Diseases 12: 1068–1083. 18. Schwabe, R.F. and Jobin, C. (2013). The microbiome and cancer. Nature Reviews Cancer 13: 800–812. Chapter 5 1. Nicholson, J.K., Holmes, E. & Wilson, I.D. (2005). Gut microorganisms, mammalian metabolism and

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early administration of antibiotics. International Journal of Obesity 35: 522–9. 8. Cho, I. et al. (2012). Antibiotics in early life alter the murine colonic microbiome and adiposity. Nature 488: 621–626. 9. Cox, L.M. et al. (2014). Altering the intestinal microbiota during a critical developmental window has lasting metabolic

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Darwinian Medicine. Birkhäuser Basel, pp. 103–115. Chapter 6 1. Zhu, L. et al. (2011). Evidence of cellulose metabolism by the giant panda gut microbiome. Proceedings of the National Academy of Sciences 108: 17714–17719. 2. De Filippo, C. et al. (2010). Impact of diet in shaping gut microbiota revealed

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The American paradox. American Journal of Medicine 102: 259–264. 8. David, L.A. et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature 505: 559–563. 9. Hehemann, J.-H. et al. (2010). Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464

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the mother in neonatal immune education. Proceedings of the Nutrition Society 69: 407–415. 12. Cabrera-Rubio, R. et al. (2012). The human milk microbiome changes over lactation and is shaped by maternal weight and mode of delivery. American Journal of Clinical Nutrition 96: 544–551. 13. Stevens, E.E

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Palmer, C. et al. (2007). Development of the human infant intestinal microbiota. PLoS Biology 5: 1556–1573. 21. Yatsunenko, T. et al. (2012). Human gut microbiome viewed across age and geography. Nature 486: 222–228. 22. Lax, S. et al. (2014). Longitudinal analysis of microbial interaction between humans and the indoor

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. (2012). Temporal dynamics of the human vaginal microbiota. Science Translational Medicine 4: 132ra52. 24. Koren, O. et al. (2012). Host remodelling of the gut microbiome and metabolic changes during pregnancy. Cell 150: 470–480. 25. Claesson, M.J. et al. (2012). Gut microbiota composition correlates with diet and health in

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136–7 coeliac disease 139–40 faecal transplants 261 and gut microbiota 227 human genome 3–4, 7–10, 43–4, 279–80 in human microbiome 8, 11, 279 and lactose intolerance 201 and leaky gut 196–7 mutations 44 natural selection 125, 126 and obesity 60 and pheromones 102

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in dirt 176 hospitals, hygiene 31–4 houses, microbes in 228–9 Human Genome Project (HGP) 3–4, 7–10, 43–4, 279–80 Human Microbiome Project (HMP) 11, 18, 19–20, 22–3, 162 human papillomavirus (HPV) 144 Humphrys, John, The Great Food Gamble 272 Hungary 33 Huntington’s

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tree of life 16–17 in vagina 205–9, 212–14, 229 and vitamins 228 see also bacteria; gut microbiota; viruses Microbial Ecosystem Therapeutics 260 microbiome 8, 11, 227–9, 279, 280 Middle East 58 midwives 32–3 migraine 238 migrants, and twenty-first-century illnesses 50–1 migration, garden

Cooked: A Natural History of Transformation

by Michael Pollan  · 22 Apr 2013  · 476pp  · 148,895 words

scientists will soon find other examples of our microbiota mediating our relationship to the rest of nature, speeding our ability to adapt. In effect, the microbiome vastly extends our genome, giving us access to a tremendous bag of tricks we did not need to evolve ourselves. So it made very good

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invent virtually every important metabolic trick known to evolution, from fermentation to photosynthesis. (According to Lynn Margulis, who until her death in 2011 was the microbiome’s most eloquent human advocate, the only important biochemical innovations to come along in the billion years since then are snake venom, plant hallucinogens, and

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Morning, Kimchi!: Forty Different Kinds of Traditional and Fusion Kimchi Recipes. Elizabeth, NJ: Hollym, 2005. On the Human Microbiome Start with the National Institutes of Health’s Web site for the human microbiome project: http://www.hmpdacc.org/. It has links to many academic articles on the subject. The articles below I

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(2004): 27–28. Turnbaugh, P.J., et al. “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest.” Nature 444 (2006): 1027–31. ———, et al. “The Human Microbiome Project.” Nature 449 (2007): 804–10. ———, et al. “A Core Gut Microbiome in Obese and Lean Twins.” Nature 457 (2009): 480–84. Walter, Jens

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fermento; I learned much from his writings on the subject in the New Yorker. Joel Kimmons at the CDC was an inspiring guide to the microbiome and so much more. One more teacher turned out to be absolutely indispensable to the entire project: Harold McGee. As any chef will tell you

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it did seem to speed the process. But what’s the rush? * Biologists use the term “microbiota” to refer to a community of microbes, and “microbiome” to refer to the collective genome of those microbes. * Robinson, Courtney J., et al., “From Structure to Function.” * This is equally true for the somewhat

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these invaders became the chloroplasts in plant cells and the mitochondria in the cells of animals. * Turnbaugh, Peter J., et al., “An Obesity-Associated Gut Microbiome with Increased Capacity for Energy Harvest,” Nature 444 (2006): 1027–31; Turnbaugh, P. J., et al., “A Core Gut

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Microbiome in Obese and Lean Twins,” Nature 457 (2009): 480–84; Turnbaugh, Peter J., et al., “The Human Microbiome Project,” Nature 449 (2007): 804–10. † This particular probiotic is found in some kinds of yogurt. (Bravo

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-Dependent Mechanism,” PloS One 7 No. 7 (2012): e42067. * Smillie, Chris S., et al., “Ecology Drives a Global Network of Gene Exchange Connecting the Human Microbiome,” Nature 480 (2011): 241–44. Arias, Maria Cecilia, et al., “Eukaryote to Gut Bacteria Transfer of a Glycoside Hydrolase Gene Essential for Starch Breakdown in

Rebel Ideas: The Power of Diverse Thinking

by Matthew Syed  · 9 Sep 2019  · 280pp  · 76,638 words

will respond to a given meal. These dimensions include such intuitive things as age, genetics, lifestyle and more. Perhaps the most fascinating dimension is the microbiome, the bacteria we all host in our gastrointestinal systems. There are around forty trillion cells and up to a thousand different microbial species in our

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the host human, and exerts a major influence on how we digest food and extract nutrients, as well as on the immune system. And these microbiomes vary from person to person. When you look at diet from this perspective, with different factors translating into different enzymes, genes, bacterial genes, and perhaps

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books that shoppers will like. To test the algorithm, one hundred new people were recruited and then measured on personal characteristics such as blood, age, microbiome and the like. This data was then fed into the algorithm. This was a significant test of the research. Would the algorithm more accurately predict

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longer-term follow-ups that measure health outcomes directly rather than via indirect indicators, such as blood sugar. Further research is required to understand the microbiome and more. The start, however, has been highly promising, and gives researchers a chance to overcome the contradictions that have bedevilled the field. Above all

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worldwide. The process is simple. You provide a stool sample and the results of a blood test. This enables the DayTwo lab to test your microbiome and to assess your blood sugar levels. This is then fed into the algorithm, allowing researchers to provide personalised food recommendations along with a searchable

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drinks. This isn’t as systematic as the experiment conducted in 2015, which measured blood sugar responses to every meal in addition to information on microbiome, but it nevertheless signals a direction of travel. Diet, like other branches of human science, is moving away from standardisation and towards personalisation. Eric Topol

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he volunteered to take a full test, tracking every meal and intake of liquid to determine blood-glucose response, as well as having his gut microbiome tested. Within weeks, he learned more about his own unique responses to food than would have been possible from trialling any number of standardised diets

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. He not only discovered that he has an unusual microbiome, but that he experienced severe blood glucose spikes for food he had been eating for years. ‘My gut microbiome was densely populated by one particular bugger – Bacteroides stercoris, accounting for 27 per cent of my

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is taking place, not just in Segal’s lab but elsewhere, seeking to build more evidence.22 The goal is to use not merely the microbiome and genome to make dietary recommendations, but other personal factors such as medication, sleep and stress. Topol writes: What we really need to do is

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

The Diet Myth: The Real Science Behind What We Eat

by Tim Spector  · 13 May 2015  · 382pp  · 115,172 words

is how evolution has facilitated the leap of microbes from one generation to the next, and how our own unique community of microbes, called our microbiome, is established. Diverse microbial gardens We are surrounded by trillions of microbes in the dirt, dust, water and air that are not interested in

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never healthy, they do much better. Microbes predict obesity better than genes Recent changes in our tiny gut microbes and to the community called our microbiome are likely to be responsible for much of our obesity epidemic, as well as its deadly consequences of diabetes, cancer and heart disease. Examining the

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cheese-research centres report mainly positive news about French cheese. Some human clinical trials have shown that cheese supplements could be used to maintain the microbiome in people taking antibiotics, which normally knock out a large proportion of our healthy species. Unpasteurised hard cheese, when given with antibiotics, has been

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bacteria species grow out of control. These often work, but they usually cause collateral damage, killing many friendly species and altering the natural community, the microbiome. This can lead to some of these pathogenic bacteria having no natural enemies and taking over; they become resistant to even the most powerful antibiotics

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species of bacteria commonly found in many commercial brands. They all ate the yoghurt twice daily for seven weeks. The US team, led by the microbiome pioneer Jeff Gordon, reassuringly found that fairly high levels of the five microbes reached the colons of the twins, particularly one of the bifidos which

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that are the major determinant. Two earlier twins studies in the US produced no conclusive evidence of a genetic influence. But when I heard microbiome expert and future collaborator Ruth Ley present the results at a meeting I thought the studies were too small, and that we could answer the

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function of the bowel via our emotions, which in turn can alter other hormones, leading in a vicious circle of symptoms to the disruption of microbiomes and even to depression. But these messenger hormones don’t work alone. We are learning that the immune system is another player in the

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stress in rodents and have done the same to young mice. When, after separating them from their mothers, they forced them to swim laps, their microbiomes were disrupted and became less diverse. The anxiety and stress were consistently reversed by giving them lactobacilli probiotics, which suggests that yoghurt, not crisps, should

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this evolutionary reason. One important message here is that strong links undoubtedly exist between how you and your brain interact with food and how your microbiome functions. People that really enjoy their food may actually, via their brains, be able to both make themselves feel happier and stimulate their microbes.

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any cramps, cravings, headaches or vomiting – maybe because of his genes or because he’d already had plenty of training. The results of Tom’s microbiome tests after the ten days of burgers and nuggets were impressive. His levels of Bacteroidetes doubled from 25 per cent to 58, and his Firmicutes

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they wanted. Unsurprisingly the fast-food mice gained considerably more weight, particularly the dangerous visceral internal fat. As well as showing major differences in their microbiomes, the fattened-up mice were in a marked pro-inflammatory state, meaning that their cells were in alert mode as if being attacked, sending out

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subject of a Chinese TV documentary.29 Over one thousand Chinese have so far been treated with his methods, many undergoing intensive investigation of their microbiomes. He has been reluctant to give away all his professional details but has published some early results of his special vegetarian diet. In one study

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as well. He decided to change his focus from plants and animals to human health. After reading a 2004 paper by Jeff Gordon, the US microbiome pioneer who suggested that gut microbes could influence obesity, his interest was reignited. Lacking big funding, he used himself as a guinea-pig to

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your body may influence your variable response to particular diets. My colleague Dusko Ehrlich was in charge of a large €20 million EU-funded microbiome project called Meta-Hit that answered some of the main questions. The researchers were able to look at gut microbes by sequencing the DNA of

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short of diverse microbes, the lowcalorie/highprotein diet wasn’t a total failure. After six weeks they did lose weight and managed to improve their microbiome diversity significantly. The problem was the rebound afterwards. The duration and intensity of the trial may not have been enough of a shake-up to

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our gut microbes may have become extinct since the introduction or farming, pesticides and antibiotics. The sad fact is that we have a very depleted microbiome compared to our ancestors. Meat, hearts and microbes From the observational studies of meat eating so far performed in Western countries, there is no clear

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eating or abstaining from regular meat can change your microbes for the better or for the worse. It should be possible, however, to improve the microbiome of a regular meat eater by having a meat/carnitine holiday. In other words, indulging in an occasional steak may not be harmful. But should

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had problems earlier, or why her twin sister with the exact same genetic make-up was unaffected, despite following a similar diet. Once again, their microbiomes may have been to blame. Studies of other patients with lactose intolerance have shown the same variable response to milk, but when patients with consistent

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inflammation and the heightened state of the body’s defences is the disruption caused to gut microbes. Studies have shown clear differences in the microbiomes of patients in the early stages of rheumatoid arthritis that can’t be explained by medications or changes in diet.19 The main bug they

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which a dramatic change in nutrition in an elderly person had preceded health problems. Paul’s research group is looking into the effects of the microbiome in the elderly, and particularly the effects of diet. In an important study they surveyed 178 Irish residents from local nursing homes aged 70 to

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rest who lived there permanently.1 They found that within six months all the permanent residents on the same dull, institutional diet developed a similar microbiome. Unfortunately, it wasn’t a healthy mix and was lacking in diversity and many of the healthy microbes. It also indicated greater levels of

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inflammation. Those elderly part-time residents who sometimes cooked for themselves and ate non-institutional meals had healthier microbiomes than those with the communally prepared food. There was some variation, but within a year of entering the long-stay nursing home all the residents

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had very similar and unhealthy microbiomes. In elderly people there are many complex reasons why the body deteriorates. These include loss of muscle through lack of physical exercise, depression, social

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and loss of cognitive function. The loss of teeth, changes in saliva, and the increasing use of antibiotics and other drugs can also affect the microbiome. With age, we see increases in the number and dysfunction of the protective Treg cells, which as we know interact with our microbes and

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in my lab looked at 400 of our older UK twins living independently who were generally frail, she found that they had a less diverse microbiome than average and lower numbers of microbes associated with suppressing inflammation and gut leakiness, such as F. prausnitzii. They also had fewer beneficial lactobacilli.

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fi films) do not build up with excess toxins or spill over with acid or need a regular de-scaling. Fasting to clean up your microbiome Many people lose some weight through juicing but this could be another form of fasting. Although fasting has no common definition, it generally means

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basis was caused by an overgrowth of microbes and an overreaction to them, while her later susceptibility to kidney infections also suggests a disordered gut microbiome as the cause. They both enjoy all foods from pickled eggs to haggis, chips and sushi. But although they used to go to the

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potty at the same time, they now have very different bowel habits and loo-visiting regimes, despite having identical diets and lifestyles. We tested their microbiomes and they were unalike in many of the normal species. On average they shared only a minority of the same microbes, the same as unrelated

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bifidobacteria, even when they start normal breast feeding.9 C-Section babies have more allergies Just as important, C-section babies, with their disrupted gut microbiome, have also a disrupted immune system that brings with it a greater risk of later immune problems such as coeliac disease and allergies, especially to

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generation. This explains why the effects and trends we are observing are magnified in children of obese mums, who themselves started life with a defective microbiome. Given that antibiotics are so difficult to escape from, is there a solution to this mess? Transforming yourself into a New Age anti-medicine organic

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this diversity comes from breast milk assisted by a healthy maternal diet, late weaning or a bit less household cleanliness. By contrast, it’s a microbiome reduced in richness and diversity that is usually associated with allergies.10 Allergies are more common in bottle-fed babies with weakened immune systems; the

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current theory, as already mentioned, is that a healthy and diverse microbiome keeps the gut immune system stimulated and in a constant state of readiness so that there will be no overreaction to strange proteins.11 Hygeine

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lighter and, more importantly, she feels a lot better. We don’t know whether the effects of the intermittent fasting would be permanent on her microbiome if she stopped, but we do see major changes in the species during fasting periods when mucus-eating microbes start their cleanup operations.6 Karen

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human blood. microbe: an organism that can be seen only with the aid of a microscope; includes bacteria, viruses, yeast and some larvae and worms. microbiome: the whole community of microbes that may be in our guts or mouths or in the soil. neurotransmitters: chemicals in the brain that allow nerve

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read and improved by old and trusted friends Robyn Fitzgerald, Roz Kadir, Bryan Fehilly and Frannie Hochberg. My colleagues in obesity genetics, nutrition and the microbiome were invaluable sources of the latest information before it was published. These include my microbe collaborators Ruth Ley and Rob Knight, plus his team from

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: origin and potential roles in health and disease. 2 Aagaard, K., Sci Transl Med (21 May 2014); 6(237): 237ra65. The placenta harbors a unique microbiome. 3 Funkhouser, L.J., PLoS Biol (2013); 11(8): e1001631. Mom knows best: the universality of maternal microbial transmission. 4 Koren, O., Cell (3

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Aug 2012); 150(3): 470–80. Host remodeling of the gut microbiome and metabolic changes during pregnancy. 5 Hansen, C.H., Gut Microbes (May–Jun 2013); 4(3): 241–5. Customizing laboratory mice by modifying gut microbiota

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The Genetic Architecture of the Human Immune System (Cell, 2015) 25 Saulnier, D.M., Gut Microbes (Jan–Feb 2013); 4(1): 17–27. The intestinal microbiome, probiotics and prebiotics in neurogastroenterology. 26 De Palma, G., Gut Microbes (May–Jun 2014); 5(3): 439–45. The microbiota-gut-brain axis in functional

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for obesity in rat offspring. 16 David, L.A., Nature (23 Jan 2014; 505(7484): 559–61. Diet rapidly and reproducibly alters the human gut microbiome. 17 Poutahidis, T., PLoS One (Jul 2013); 10; 8(7): e68596. Microbial reprogramming inhibits Western diet-associated obesity. 18 Martinez-Medina, M., Gut (Jan

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twins discordant for obesity modulate metabolism in mice. 25 Goodrich, J.K., Cell, (Nov 2014); 159(4): 789–99. Human genetics shape the gut microbiome. 26 Fei, N., ISME J (2013); 7: 880–4. An opportunistic pathogen isolated from the gut of an obese human causes obesity in germ-free

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31. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. 36 Shin, S.C., Science (2011); 334 (6056): 670–4. Drosophila microbiome modulates host developmental and metabolic homeostasis via insulin signalling. 37 Tremaroli, V., Nature (13 Sep 2012); 489(7415): 242–9. Functional interactions between the gut

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8. Dietary intervention impact on gut microbial gene richness. 10 Le Chatelier, E., Nature (29 Aug 2013); 500(7464): 541–6. Richness of human gut microbiome correlates with metabolic markers. 11 Qin, J., Nature (4 Oct 2012); 490(7418): 55–60. A metagenome-wide association study of gut microbiota in type

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the Venezuelan Amazonia: increased overweight and obesity with transculturation. 19 Schnorr, S.L., Nat Commun (15 Apr 2014); 5: 3654.doi: 10.1038/ncomms4654. Gut microbiome of the Hadza hunter-gatherers. 20 Dominguez-Bello, G., Personal communication. 21 Pan, A., Arch Intern Med (9 Apr 2012); 172(7): 555–63. Red

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a hallmark of both vertebrate and invertebrate genomes. 11 Cantarel, B.L., PLoS One (2012); 7(6): e28742. Complex carbohydrate utilization by the healthy human microbiome. 12 Georg, J.M., Obes Rev (Feb 2013); 14(2): 129–44. Review: efficacy of alginate supplementation in relation to appetite regulation and metabolic risk

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16. Seaweed and human health. 14 Hehemann, J.H., Proc Natl Acad Sci (27 Nov 2012); 109(48): 19786–91. Bacteria of the human gut microbiome catabolize red seaweed glycans with carbohydrate-active enzyme updates from extrinsic microbes. 15 Pirotta, M., BMJ (4 Sep 2004); 329(7465): 548. Effect of lactobacillus

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consensus development conference statement: Lactose intolerance and health. 11 Petschow, B., Ann NY Acad Sci (Dec 2013); 1306: 1–17. Probiotics, prebiotics, and the host microbiome: the science of translation. 12 Prentice, A.M., Am J Clin Nutr (May 2014); 99 (5 Suppl): 1212S–16S. Dairy products in global public health

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adhesion factors and vascular function in overweight men. 13 Moco, S., J Proteome Res (5 Oct 2012); 11(10): 4781–90. Metabolomics view on gut microbiome modulation by polyphenol-rich foods. 14 Langer, S., J Agric Food Chem (10 Aug 2011); 59(15): 8435–41. Flavanols and methylxanthines in commercially available

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10.1001/jamapediatrics. Association of antibiotics in infancy with early childhood obesity. 18 Blaser, M., Nat Rev Microbiol (Mar 2013); 11(3): 213–17. The microbiome explored: recent insights and future challenges. 19 Darmasseelane, K., PLoS One (2014); 9(2): e87896.doi:10.1371. Mode of delivery and offspring body mass

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

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

…

, 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

…

; 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

…

, 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

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