Microbiome Quotes

The single greatest predictor of a healthy gut microbiome is the diversity of plants in one’s diet.

A growing number of studies have made a link between animal behavior and the trillions of bacteria and fungi that live in their guts, many of which produce chemicals that influence animal nervous systems. The interaction between gut microbes and brains—the “microbiome-gut-brain axis”—is far-reaching enough to have birthed a new field: neuromicrobiology.

The “loss of a sense of self-identity, delusions of self-identity and experiences of ‘alien control,’ ” observed an elder statesman in the field of microbiome research, are all potential symptoms of mental illness. It made my head spin to think of how many ideas had to be revisited, not least our culturally treasured notions of identity, autonomy, and independence. It is in part this disconcerting feeling that makes the advances in the microbial sciences so exciting.

More specifically, he found that the consumption of thirty different plants in a given week was the greatest predictor of gut microbial diversity.

Every person aerosolises around 37 million bacteria per hour. This means that our microbiome isn’t confined to our bodies. It perpetually reaches out into our environment.

We now know that gut microbes are part of this axis, in both directions. Since the 1970s, a trickle of studies have shown that any kind of stress – starvation, sleeplessness, being separated from one’s mother, the sudden arrival of an aggressive individual, uncomfortable temperatures, overcrowding, even loud noises – can change a mouse’s gut microbiome. The opposite is also true: the microbiome can affect a host’s behaviour, including its social attitudes and its ability to deal with stress.40

During rush-hour traffic, emissions of siloxane, a microbiome-destroying ingredient in shampoos, lotions, and deodorants, are found in comparable levels to vehicle exhaust.17 Just one more reason to dread your daily commute.

Probiotics and Prebiotics If you’re suffering from gut-induced depression, how do you reset your gut microbiome to steer you back to a healthy mental state? The key is to increase probiotics and prebiotics in your diet. Probiotics are live bacteria that convey health benefits when eaten. Probiotic-rich foods contain beneficial bacteria that help your body

The microbiome affects our mood, libido, metabolism, immunity, and even our perception of the world and the clarity of our thoughts. It helps determine whether we are fat or thin, energic or lethargic. Put simply, everything about our health-how we feel both emotionally and physically-hinges on the state of our microbiome.

We inherit every one of our genes, but we leave the womb without a single microbe. As we pass through our mother's birth canal, we begin to attract entire colonies of bacteria. By the time a child can crawl, he has been blanketed by an enormous, unseen cloud of microorganisms--a hundred trillion or more. They are bacteria, mostly, but also viruses and fungi (including a variety of yeasts), and they come at us from all directions: other people, food, furniture, clothing, cars, buildings, trees, pets, even the air we breathe. They congregate in our digestive systems and our mouths, fill the space between our teeth, cover our skin, and line our throats. We are inhabited by as many as ten thousand bacterial species; those cells outnumber those which we consider our own by ten to one, and weigh, all told, about three pounds--the same as our brain. Together, they are referred to as our microbiome--and they play such a crucial role in our lives that scientists like [Martin J.] Blaser have begun to reconsider what it means to be human.

In fact, 90 percent of serotonin and 50 percent of dopamine are actually produced in the gut.

Sadly, the pharmaceutical industry has hijacked our health care system. Big Pharma runs the studies, they control the research,

fecal transplants from people with healthy microbiomes will one day provide a more effective treatment for depression than Prozac or therapy.

We are well on our way to a unified theory of biology that will merge body and environment, brain and mind, genome and microbiome.

A glass or two of red wine may be good for your heart but not for your microbiome. Studies show that just one drink per day in women and two in men can induce dysbiosis and bacterial overgrowth. Levels of good bacteria like Lactobacillus fall, while potential pathogens rise, leading to an increase in toxins and other chemicals that can cause inflammation, damage the liver, and increase permeability of the gut. Most of the overgrowth happens in the small intestine and can lead to malnourishment because the excess bacteria consume the nutrients that the small intestine would normally absorb. Some studies report an incidence of small intestinal bacterial overgrowth (SIBO) in alcoholics that’s three times that of the general population.

The fact is that hundreds of trillions of microbial “invaders,” mostly in our gut, are absolutely necessary for our survival, and there are ten times more of them than cells in the human body. Because the body cannot survive without its microbes (collectively called the “microbiome”), they are the functional equivalent of any of our other vital organ systems. In (belated) recognition of the importance of the microbiome, humans and most other organisms are now properly defined as superorganisms (complex organisms composed of many smaller organisms). (Saey

Currently, U.S. soils are degrading ten times faster than they can be replenished. Tilling also dries out soil—it was a key factor causing the Dust Bowl crisis in the 1930s—and disturbs the microbiome.

We are only beginning to understand the importance and nature of a woman’s vaginal microbiome. Babies born by Cesarean section are robbed of this initial wash. The consequences for the baby can be profound. Various studies have found that people born by C-section have substantially increased risks for type 1 diabetes, asthma, celiac disease, and even obesity and an eightfold greater risk of developing allergies.

Unfortunately, there’s no pill that can alter our gut microbiomes to be more Hadza-like. “Because they take in microbes from food they pull from the dirt, as well as air and land,” said Schnorr. “You really need continuous exposure to outside microbes.” University of Chicago microbiome scientists have in fact declared that “dirt is good.” The more time a person spends outside getting down and dirty in it, the better.

once he sticks his tongue in my mouth his bacteria become part of my microbiome for literally the rest of my life. Like, his tongue will sort of always be in my mouth until I’m dead, and then his tongue microbes will eat my corpse.

Whether one calls slime molds, fungi, and plants “intelligent” depends on one’s point of view. Classical scientific definitions of intelligence use humans as a yardstick by which all other species are measured. According to these anthropocentric definitions, humans are always at the top of the intelligence rankings, followed by animals that look like us (chimpanzees, bonobos, etc.), followed again by other “higher” animals, and onward and downward in a league table—a great chain of intelligence drawn up by the ancient Greeks, which persists one way or another to this day. Because these organisms don’t look like us or outwardly behave like us—or have brains—they have traditionally been allocated a position somewhere at the bottom of the scale. Too often, they are thought of as the inert backdrop to animal life. Yet many are capable of sophisticated behaviors that prompt us to think in new ways about what it means for organisms to “solve problems,” “communicate,” “make decisions,” “learn,” and “remember.” As we do so, some of the vexed hierarchies that underpin modern thought start to soften. As they soften, our ruinous attitudes toward the more-than-human world may start to change. The second field of research that has guided me in this inquiry concerns the way we think about the microscopic organisms—or microbes—that cover every inch of the planet. In the last four decades, new technologies have granted unprecedented access to microbial lives. The outcome? For your community of microbes—your “microbiome”—your body is a planet. Some prefer the temperate forest of your scalp, some the arid plains of your forearm, some the tropical forest of your crotch or armpit. Your gut (which if unfolded would occupy an area of thirty-two square meters), ears, toes, mouth, eyes, skin, and every surface, passage, and cavity you possess teem with bacteria and fungi. You carry around more microbes than your “own” cells. There are more bacteria in your gut than stars in our galaxy. For humans, identifying where one individual stops and another starts is not generally something we

There’s even emerging evidence that one’s microbiome may have a relationship with thought itself through the gut-brain information axis, meaning that at least some of my thoughts may belong not to me, but to the microorganisms in my digestive tract.

EATING THE RAINBOW When you start eating differently, your microbiome will start changing within two to three days. Getting five different vegetables into your diet every single day will accelerate the process of optimizing your microbiome. To enhance the benefits even further, try to make these vegetables as many different colors as you can. This means it’s much more likely that you will encourage the growth of more beneficial bacteria as well as getting maximum gut-bug diversity. But that’s not the only benefit.

If I'd been the author, I would've stopped thinking about my microbiome. I would've told Daisy how much I liked her idea for Mychal's art project, and I would've told her that I did remember Davis Pickett, that I remembered being eleven and carrying a vague but constant fear. I would've told her that I remembered once at camp lying next to Davis on the edge of a dock, our legs dangling over, our backs against the rough-hewn planks of wood, staring together up at a cloudless summer sky. I wouldv'e told her that Davis and I never talked much, or even looked at each other, but it didn't mater, because we were looking at the same sky together, which is maybe more intimate than eye contact anyway. Anybody can look at you. It's quite rare to find someone who sees the same world you see.

Drinking lots of alcohol makes the gut leakier, allowing microbes to more readily influence the brain. Could that help to explain why alcoholics often experience depression or anxiety? Our diet reshapes the microbes in our gut, could those changes ripple out to affect our minds? The gut microbiome becomes less stable in old age-could that contribute to the rise of brain disease in the elderly? And could our microbes manipulate our food cravings in the first place? If you reach for a burger or a chocolate bar what exactly is pushing that hand forward?

Even the majority of the cells in your body are microorganisms. They outnumber the cells of your body by 10 to 1. Those microbes are living, metabolizing chemicals, producing waste chemicals, and interacting with each other. Collectively, they are known as your microbiome. You are their ecosystem. It’s

registered dieticians, and other health professionals. Justin’s talk was the highlight of the event for me. It conveyed the excitement of discoveries about the human microbiome and suggested answers to puzzling questions I had about health conditions that are on the rise. Asthma, allergies, and autoimmunity have all increased in North America and other developed areas of the world. Why is the incidence of peanut allergy so much greater today than it was when I grew up in the 1950s? And what is the explanation for the spectacular increase in gluten sensitivity? That last question had bothered me greatly. Granted that gluten

If these retroviruses are affecting the immune system of the gut (and by extension the brain), you’d also expect to find abnormal bacterial populations, as well. This has become a fascinating area of scientific research, and these bacterial populations in the digestive system have become popularly known as the “microbiome.

Modern lifestyle habits have therefore primed your body for unhealthy microbial expansion. If there is no benefit to curtailing your carbon footprint or erecting levees against the equivalent to rising oceans in your body, what can you do to turn the tide against microbial expansion and invasion? Thankfully, you can do plenty.

When microbiologists first started cataloguing the human microbiome in its entirety they hoped to discover a "core" microbiome: a group of species that everyone shares. It's now debatable if that core exists. Some species are common, but none is everywhere. If there is a core, it exists at the level of functions, not organisms. There are certain jobs, like digesting a certain nutrient or carrying out a specific metabolic trick, that are always filled by some microbe-just not always the same one. You see the same trend on a bigger scale. In New Zealand, kiwis root through leaf litter in search of worms, doing what a badger might do in England. Tigers and clouded leopards stalk the forests of Sumatra but in cat-free Madagascar that same niche is filled by a giant killer mongoose called the fossa; meanwhile, in Komodo, a huge lizard claims the top predator role. Different islands, different species, same jobs. The islands in question could be huge land masses, or individual people.

Baby’s first colonizers are supposed to be predominantly lactobacilli, the microbes picked up in the vaginal canal. Lactobacillus sets up a healthy human gut with positive influence over digestion and immune functions. If other species of bacteria are baby’s first colonizers, the baby’s microbiome sets up differently, maybe harmfully.

Developers and entrepreneurs may someday be able to use CRISPR-based home testing kits as platforms on which to build a variety of biomedical apps: virus detection, disease diagnosis, cancer screening, nutritional analyses, microbiome assessments, and genetic tests. “We can get people in their homes to check if they have the flu or just a cold,” says Zhang.

1 capsule Bacillus coagulans GBI-30,6086 2 tablespoons prebiotic fiber (inulin or raw potato starch) 1 quart half-and-half or other liquid

Like death, taxes, and marital spats, fungi are an inevitable part of human life.

Here are some lethal combinations: Bonnie and Clyde, Thelma and Louise, the gliadin protein in wheat and LPS endotoxemia.

Convenience, mass food commercialization, and the lack of blood and dirt under our fingernails have contributed to a silent but massive health epidemic.

Benjamin Franklin said, “An ounce of prevention is worth a pound of cure.

As soon as we pass through the birth canal we begin to become 90 percent microbe.

Arroyo’s work, seventy-five years old, remains the standard reference on rum and its associated microorganisms—which is weird, if you think about it. As far as I can tell, no one has tried to sort through the microbiome of a dunder pit or isolate species other than the ones Arroyo recommended. Rum, especially strange, dark ones full of exotic esters, is one of the most underrated things to drink.

Before getting into CRISPR, Zayner tried a variety of synthetic biology experiments, including on himself. To treat his gastrointestinal problems, he performed a fecal transplant (don’t ask) to transform his gut’s microbiome. He did the procedure in a hotel room with two filmmakers documenting the scene, and (in case you really do want to know how it works) it became a short documentary called Gut Hack that can be found online.2

This is the science behind how UPF affects the human body: • The destruction of the food matrix by physical, chemical and thermal processing means that UPF is, in general, soft. This means you eat it fast, which means you eat far more calories per minute and don’t feel full until long after you’ve finished. It also potentially reduces facial bone size and bone density, leading to dental problems. • UPF typically has a very high calorie density because it’s dry, and high in fat and sugar and low in fibre, so you get more calories per mouthful. • It displaces diverse whole foods from the diet, especially among low-income groups. And UPF itself is often micronutrient-deficient, which may also contribute to excess consumption. • The mismatch between the taste signals from the mouth and the nutrition content in some UPF alters metabolism and appetite in ways that we are only beginning to understand, but that seem to drive excess consumption. • UPF is addictive, meaning that for some people binges are unavoidable. • The emulsifiers, preservatives, modified starches and other additives damage the microbiome, which could allow inflammatory bacteria to flourish and cause the gut to leak. • The convenience, price and marketing of UPF urge us to eat constantly and without thought, which leads to more snacking, less chewing, faster eating, increased consumption and tooth decay. • The additives and physical processing mean that UPF affects our satiety system directly. Other additives may affect brain and endocrine function, and plastics from the packaging might affect fertility. • The production methods used to make UPF require expensive subsidy and drive environmental destruction, carbon emissions and plastic pollution, which harm us all.

The First 5 in 5 × 5 × 5: The Health Defense Systems There are five health defense systems in your body: angiogenesis, regeneration, microbiome, DNA protection, and immunity. These systems maintain your health in a state of perfect balance. When mild disruptions occur in your health, the systems adjust themselves to take care of the problem and continue functioning behind the scenes, so you don’t even notice—that’s what you want your health to be like your entire life.

Literally right this second, there are over five hundred million nerves in your intestines sending feedback to your brain through the vagus nerve. That’s five times more nerves than you’ll find in your spinal cord. That is a lot of information!

You are not what you think you are. Instead of the form staring back at you when you look in the mirror, what you should imagine is your body as a collection of multiple dynamic ecosystems made up of very tiny, and very biologically diverse, organisms.

2 cups water 1 tablespoon whole cloves 1 teabag green tea 1 teaspoon FOS powder 2 teaspoons allulose (optional) Additional sweetener to taste 1 cinnamon stick (optional) In a small saucepan, combine the water and cloves and bring to a boil. Reduce the heat and cover to maintain a low simmer for 10 minutes. Add the teabag in the last 1–2 minutes of simmering, then remove from heat. Discard teabag. Stir in the FOS, optional allulose, other sweetener, and optional cinnamon stick, and serve or sip throughout the day. MATCHA,

The book was published ten years or so before I was born. Almost half a century later, we still barely acknowledge the psychological and physiological significance of becoming a mother: how it affects the brain, the endocrine system, cognition, immunity, the psyche, the microbiome, the sense of self. This is a problem. Everyone knows adolescents are uncomfortable and awkward because they are going through extreme mental and bodily changes, but, when they have a baby, women are expected to transition with ease – to breeze into a completely new self, a new role, at one of the most perilous and sensitive times in the life course.

Despite these trends, our culture pushes a Bad Energy world onto kids who cannot protect themselves. Our culture has normalized giving one-year-olds packaged, ultra-processed foods like cake, Goldfish, rice puffs, juice, and french fries. We slather toxic, artificially scented lotions and shampoos all over their tiny bodies as soon as their first hospital bath. We damage their livers and antioxidant capacity with too much acetaminophen (Tylenol) at the first sign of fussiness or a cold. We blast their microbiomes with heavy-duty antibiotics at the first sign of a possible ear infection. And we interrupt their sleep for unconscionably early school times, then force them to sit at desks in school for six or more hours a day. We create terror and chronic stress in their bodies from social media and overall media exposure. The world kids live in is inflammatory and metabolically disastrous unless parents staunchly go against the tide of “normal” American culture. The irony is that so many parents wish that parenting were easier—fewer infections, less colic, easier behavioral patterns—without thinking through the lens of energy production in their children’s bodies. We can do so much to make our lives and our kids’ lives easier by controlling the controllable.

Downstairs in the body, sleep restocks the armory of our immune system, helping fight malignancy, preventing infection, and warding off all manner of sickness. Sleep reforms the body’s metabolic state by fine-tuning the balance of insulin and circulating glucose. Sleep further regulates our appetite, helping control body weight through healthy food selection rather than rash impulsivity. Plentiful sleep maintains a flourishing microbiome within your gut from which we know so much of our nutritional health begins. Adequate sleep is intimately tied to the fitness of our cardiovascular system, lowering blood pressure while keeping our hearts in fine condition.

But even if you do not have SIBO or SIFO, it is likely—virtually guaranteed—that you have, at the very least, dysbiosis. Substantial disruptions of the bacterial and perhaps fungal species inhabiting your colon still pose implications for health, whether or not you are regular or require a stack of magazines for bowel habit success.

We live in an exciting time. We now know more than ever about our biology and about our history, allowing us to peer into the future with greater clarity than has previously been possible. But at the same time, the changes we are undergoing, brought about by our own advances in technology, medicine, transportation-- and by the growing impact we are having on the world around us-- mean that we live in a time in which the future looks increasingly less like the past. We have become an odd species, indeed, but our story is not yet over. Like all species, Homo sapiens continues to evolve, so there is one thing we can say with certainty: the people of tomorrow will not be the same as the people of today.

You leave the womb sterile, or so it is generally thought, but are liberally swabbed with your mother’s personal complement of microbes as you move through the birth canal. We are only beginning to understand the importance and nature of a woman’s vaginal microbiome. Babies born by Cesarean section are robbed of this initial wash. The consequences for the baby can be profound. Various studies have found that people born by C-section have substantially increased risks for type 1 diabetes, asthma, celiac disease, and even obesity and an eightfold greater risk of developing allergies. Cesarean babies eventually acquire the same mix of microbes as those born vaginally—by a year their microbiota are usually indistinguishable—but there is something about those initial exposures that makes a long-term difference. No one has figured out quite why that should be.

MMR, polio, and varicella are live attenuated vaccines. The contaminants and excipients include human MRC5 cells, Human WI-38 lung cells, monkey kidney cells, guinea pig cell cultures and bovine serum. Live viral vaccines are all grown in human and animal cells lines and these animal and human cell lines contain human and animal retroviruses (adventitious agents which can recombine to generate new infectious retroviruses during the manufacture.) In addition to the animal and human retroviral contaminants, the carcinogen formaldehyde, antibiotics which dysregulate the GI [gastro-intestinal] and nasopharyngal microbiomes, glutamate, and bio-incompatible contaminants including nickel and chromium (EXH 6) can synergize in toxicity and the development of neuroinflammatory, neurodegenerative and neuroimmune diseases and cancer which can become clinically apparent decades later.10

I should acknowledge, I guess, that one reason I'm interested in TB is that I have obsessive-compulsive disorder, and my particular obsessive worries tend to circle around microbes and illness. Before the germ theory of disease, we did not know that around half the cells in my body do not, in fact, belong to my body - they are bacteria and other microscopic organisms colonizing me. And to one degree or another, these microorganisms can also control the body - shaping the body's contours by making it gain or lose weight, sickening the body, killing the body. There's even emerging evidence that one's microbiome may have a relationship with thought itself through the gut-brain information axis, meaning that at least some of my thoughts may belong not to me, but to the microorganisms in my digestive tract. Research indicates that certain gut microbiomes are associated with major depression and anxiety disorders; in fact, it's possible that my particular microbiome is at least partly responsible for my OCD, meaning that the microbes are the reason I am so deeply afraid of microbes.

It’s soft and typically calorie dense, so you eat it at a rate that your body can’t keep up with when it comes to feeling full. Things like protein isolates, refined oils and modified carbohydrates are absorbed so quickly they may not even reach the part of the gut that sends the fullness signal to the brain. They’re not things you have evolved to eat. Some of the additives are well known to cause harm – be particularly aware of emulsifiers and artificial sweeteners. Emulsifiers can thin the mucus lining of the gut, allowing faecal bacteria to leak into the blood stream and inflaming your whole body. The non-nutritive sweeteners that tell your body sugar is coming but don’t supply any calories seem to cause metabolic stress and changes to the microbiome. Other additives that affect the microbiome are maltodextrins, modified starches and lots of the gums and thickeners. Flavour enhancers (glutamate, guanylate, inosinate and ribonucleotides on ingredient lists) drive excess consumption. Again, they tell your body a lie about the nutritional content of the food you’re eating when they’re added out of context.

Modern health care, drugs, and your microbiota It comes as no surprise that antibiotics absolutely decimate the gut microbiota. Just five days of ciprofloxacin wipes out about a third of gut bacteria and your gut microbiota are never quite the same. Most species recover within four weeks, but some are still absent after six months.

The body is a colony of genes. Of course, it acts and moves and procreates as a unit, and furthermore, in the case of at least one species, it feels itself, with impressive certainty, to be a unit. The gene-centered perspective has helped biologists appreciate that the genes composing the human genome are only a fraction of the genes carried around in any one person, because humans (like other species) host an entire ecosystem of microbes—bacteria, especially, from our skin to our digestive systems. Our “microbiomes” help us digest food and fight disease, all the while evolving fast and flexibly in service of their own interests. All these genes engage in a grand process of mutual co-evolution—competing with one another, and with their alternative alleles, in nature’s vast gene pool, but no longer competing on their own. Their success or failure comes through interaction. “Selection favors those genes which succeed in the presence of other genes,” says Dawkins, “which in turn succeed in the presence of them.” The effect of any one gene depends on these interactions with the ensemble and depends, too, on effects of the environment and on raw chance.

Truffle fruiting bodies house thriving communities of bacteria and yeasts—between a million and a billion bacteria per gram of dry weight. Many members of truffles’ microbiomes are able to produce the distinctive volatile compounds that contribute to truffles’ aromas, and it is likely that the cocktail of chemicals that reaches your nose is the work of more than a single organism. The chemical basis of truffles’ allure remains uncertain. In 1981, a study published by German researchers found that both Piedmont white truffles (Tuber magnatum) and Périgord black truffles (Tuber melanosporum) produced androstenol—a steroid with a musky scent—in non-negligible quantities. In pigs, androstenol functions as a sex hormone. It is produced by males and prompts the mating posture in sows.

We’ve made health too complicated with our extensive lists of foods to avoid, complex percentages of fats-to-protein-to-carb ratios, elimination diets, calorie counting, even weighing our food—and despite all these rules, we’re not getting any better. It just doesn’t need to be this complicated. Diversity of plants. That’s it. That’s all you have to remember. Done. No more annoying food lists. If you follow this one rule, it will lead you to better health. And it will always be the truth no matter what happens: No matter what changes on this planet or in our lifestyles, this core tenet of better health will stay the same.

Lactobacillus reuteri, a species that is part of the human microbiome. Erdman described her research showing how this bacteria can make wounds heal faster.

They do this already: if emulsifiers damage the microbiome, let’s add some probiotics. If the food’s too soft, add more gum. If it’s too dense in energy, add artificial sweeteners. Their solution to ultraprocessing is hyper-processing, also known as reformulation.

With a limited number of genes, humans enjoy a stable human genome. We inherit it from our parents, and it can give us a genetic predisposition for a variety of biological and pathological traits. Conversely, the human microbiota expresses one hundred times more genes than humans, is extremely plastic, and can change from individual to individual and within the same individual over time, all as the consequence of a variety of environmental factors that can shape its composition and function. Our human genome has coevolved with the trillions of constantly changing microorganisms found in and on the human body.

We’re talking about cellulose plant fiber, especially the parts of raw vegetables and fruits that your body can’t easily digest. This stuff—also known as prebiotics—is gold for your microbiome. It’s the material that serves as food for good gut bacteria. It’s pretty simple to get plenty of prebiotics: Eat the parts of vegetables you normally toss out: the end of carrots, the stump of the lettuce head, the stemmed tips of green beans. This is cellulose fiber (aka insoluble fiber). It gets down to the large intestine undigested, where the good bacteria is waiting to feast.

usually also have a lack of hundreds of other nutrients. These are nutrients like flavonoids, stilbenes, coumarins, isothiocyanates, indoles, omega-3 fatty acids, carotenes, lutein, and prebiotic fiber. These substances interact with important proteins, the genome, epigenome, microbiome, cell receptors, the cell membrane, and innumerable other mechanisms. Only a healthy, varied diet can provide all these substances. This is the first and most important step.

Also, I guess it's possible for memories to unexpectedly come back to you. In this way, the past has a life of its own. I am a container for the past, and like a microbiome, it is a whole universe inside you.

The microbiomes of those eating fiber-depleted processed foods, such as soda and refined grain products, clustered with those eating more animal foods.7515 So a junk-food vegan may not be doing their good bugs many favors.

Unlike whole foods, like brown rice or whole-grain barley, fiber supplements don’t seem to work to improve the richness of the microbiome.

Your microbiome—that is, the composition of the bacteria in your gut—also influences how many calories certain foods actually deliver. It is often claimed that our gut contains about 300,000 billion bacteria, about ten times as many bacteria as there are cells in our body. However, a recent study estimates the number of gut bacteria to be about 40,000 billion, by and large the same amount as the number of human cells that make up our body. Anyhow, the composition of the gut microbiome can determine how much food (calories) we absorb. Some Japanese people have bacteria in their intestines that are specialized in breaking down seaweed. Thus, the seaweed is better absorbed and will deliver more energy in the form of calories than it would for Europeans who do not have this type of bacteria in their gut.

There seems to be a microbiome “signature” of frailty. Fecal samples from frail individuals show a striking lack of bacterial diversity5698 and, in particular, a deficit of fiber-eating “good bacteria”5699 such as Lactobacillus.

She also told me about how the preservatives and emulsifiers in UPF disrupt the microbiome, how the gut is further damaged by processing that removes the fibre from food, and how high levels of fat, salt and sugar each cause their own specific harms. And there was one small comment that stuck. Whenever I talked about the ‘food’ I was eating, she corrected me: ‘Most UPF is not food, Chris. It’s an industrially produced edible substance.

Live dirtier, eat cleaner

In a randomized controlled trial, study subjects who substituted whole grains for refined grains saw growth of SCFA-producing bacteria Lachnospira, increased SCFA levels, and a decrease in pro-inflammatory Enterobacteriaceae. They also noted improvement in the immune system and no effect on gut inflammation.

Gut dysbiosis, studies suggest, may be a possible root cause for some conditions that we label “mental illness,” including depression, autism, anxiety, ADHD, and even schizophrenia.47 Several animal studies have shown a direct link between a decline in the health of our microbiome (as a result of poor diet and environmental influences such as stress and toxic chemicals) and a sharp rise in the symptoms associated with anxiety and depression48 in humans.

The body comprises seven dynamically interconnected, networked systems that underlie all disease—155,000 diseases, in fact. What are these systems? 1. Assimilating nutrients, digestion, and the microbiome 2. Defense and repair (immune and inflammatory system) 3. Energy production (mitochondria) 4. Detoxification 5. Transportation (circulation and lymphatic system) 6. Communication (hormones, neurotransmitters, etc.) 7. The body’s structure (from cellular structures to the musculoskeletal system)

For your community of microbes – your ‘microbiome’ – your body is a planet. Some prefer the temperate forest of your scalp, some the arid plains of your forearm, some the tropical forest of your crotch or armpit. Your gut, ears, toes, mouth, eyes, skin and every surface, passage and cavity you possess teem with bacteria and fungi. You carry around more microbes than your ‘own’ cells. We are ecosystems, composed of – and decomposed by – an ecology of microbes, without which we could not grow and behave as we do. The forty-odd trillion microbes that live in and on our bodies allow us to digest food and produce key minerals that nourish us. Like the fungi that live within plants, they protect us from disease. They guide the development of our bodies and immune systems and influence our behaviour. If not kept in check, they can cause illnesses and even kill us. We are not a special case. Even bacteria have viruses within them. Even viruses can contain smaller viruses. Symbiosis is a ubiquitous feature of life.

It is not only microbes that are benefiting from sharing our bodies, but us too. Our relationship with them is not just one of 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 on our microbes for health and happiness.

most of an infant’s initial microbiome is established during the birthing process. (This is why infants born “naturally” have different microbiomes than those born by C-section—they are exposed to different kinds of tissues.)

The following are all foods you should feel welcome to eat freely (unless, of course, you know they bother your stomach): Alliums (Onions, Leeks, Garlic, Scallions): This category of foods, in particular, is an excellent source of prebiotics and can be extremely nourishing to our bugs. If you thought certain foods were lacking in flavor, try sautéing what you think of as that “boring” vegetable or tofu with any member of this family and witness the makeover. Good-quality olive oil, sesame oil, or coconut oil can all help with the transformation of taste. *Beans, Legumes, and Pulses: This family of foods is one of the easiest ways to get a high amount of fiber in a small amount of food. You know how beans make some folks a little gassy? That’s a by-product of our bacterial buddies chowing down on that chili you just consumed for dinner. Don’t get stuck in a bean rut. Seek out your bean aisle or peruse the bulk bin at your local grocery store and see if you can try for three different types of beans each week. Great northern, anyone? Brightly Colored Fruits and Vegetables: Not only do these gems provide fiber, but they are also filled with polyphenols that increase diversity in the gut and offer anti-inflammatory compounds that are essential for disease prevention and healing. Please note that white and brown are colors in this category—hello, cauliflower, daikon radish, and mushrooms! Good fungi are particularly anti-inflammatory, rich in beta-glucans, and a good source of the immune-supportive vitamin D. Remember that variety is key here. Just because broccoli gets a special place in the world of superfoods doesn’t mean that you should eat only broccoli. Branch out: How about trying bok choy, napa cabbage, or an orange pepper? Include a spectrum of color on your plate and make sure that some of these vegetables are periodically eaten raw or lightly steamed, which may have greater benefits to your microbiome. Herbs and Spices: Not only incredibly rich in those anti-inflammatory polyphenols, this category of foods also has natural digestive-aid properties that can help improve the digestibility of certain foods like beans. They can also stimulate the production of bile, an essential part of our body’s mode of breaking down fat. Plus, they add pizzazz to any meal. Nuts, Seeds, and Their Respective Butters: This family of foods provides fiber, and it is also a good source of healthy and anti-inflammatory fats that help keep the digestive tract balanced and nourished. It’s time to step out of that almond rut and seek out new nutty experiences. Walnuts have been shown to confer excellent benefits on the microbiome because of their high omega-3 and polyphenol content. And if you haven’t tasted a buttery hemp seed, also rich in omega-3s and fantastic atop oatmeal, here’s your opportunity. Starchy Vegetables: These hearty vegetables are a great source of fiber and beneficial plant chemicals. When slightly cooled, they are also a source of something called resistant starch, which feeds the bacteria and enables them to create those fantabulous short-chain fatty acids. These include foods like potatoes, winter squash, and root vegetables like parsnips, beets, and rutabaga. When was the last time you munched on rutabaga? This might be your chance! Teas: This can be green, white, or black tea, all of which contain healthy anti-inflammatory compounds that are beneficial for our microbes and overall gut health. It can also be herbal tea, which is an easy way to add overall health-supportive nutrients to our diet without a lot of additional burden on our digestive system. Unprocessed Whole Grains: These are wonderful complex carbohydrates (meaning fiber-filled), which both nourish those gut bugs and have numerous vitamins and minerals that support our health. Branch out and try some new ones like millet, buckwheat, and amaranth. FOODS TO EAT IN MODERATION

There are some 8 million microbial genes in the gut—400 times more than in the human genome. Even more astonishing, we humans differ very little from each other genetically, sharing more than 90 percent of our genes, but the assortment of microbial genes in our guts differs dramatically, and only 5 percent of them are shared between any two individuals. The gut microbiome adds a whole new dimension of complexity and possibilities to our brain-gut emotion-generating machinery.

One can imagine a future where you might biobank microbes from your youthful skin in a tube in a freezer, which would become part of your retirement package to boost skin appearance and overall health later in life. This personal biobank could also be useful if you were diagnosed with cancer and needed a bone marrow transplant, or if you suddenly got a C. difficile infection and needed to boost your microbiome at a critical time. We might also see the application of younger persons’ microbes into commercially available products to cultivate the healthful effects of vigorous youthful microbes later in life.

If I were to boldly define the entirety of human health, there would be five essential elements: immunity, metabolism, hormonal balance, cognition, and gene expression. That would cover our bases for everything we need to thrive as humans, and what’s amazing is that the microbiota is intertwined with all five axes of human health.

we can define gut health as a state in which the hormone-producing cells produce enough of the ones that make us feel hungry when the body needs energy, and enough of the satiety-signaling molecules after a meal in order to tell the brain that it’s time to stop eating.

encompasses not only the gut’s nervous system but also its endocrine and immune systems, which together regulate metabolism and the intake of food and defend the body against pathogens.

alterations in gut microbial networks caused by diet can alter brain networks, leading to behavioral changes in social interactions, which then affect brain networks again, ultimately resulting in more changes at the level of gene expression in microbiome networks.

Each individual gut can contain up to a thousand different species of bacteria, though most of them belong to two groups—Firmicutes and Bacteroides—which make up about 75 percent of the entire microbiome.

Now we know that our gut is akin to a teeming tropical rain forest with its own diverse ecosystem, communities, and multiple signaling devices, languages that single-celled organisms use to talk among themselves.

We have a health care system that’s great at identifying problems once they exist and then trying to manage them with a combination of pills and procedures. Sure, we can improve symptoms or slow disease progression in some cases, but it always comes at a cost. It’s sick care, not health care. There is little to no focus on prevention.

Every microbiologist I spoke with agreed that antibiotic overuse is likely a bigger contributor to messing up our microbiomes—gut and skin—than hygiene itself.

The truth is that inside your digestive system lives a galaxy made up of trillions of bacteria belonging to at least ten thousand different species, plus an as-yet-undetermined number of viruses, fungi, and other microbes. This is your gut biome. You also have an oral biome with seven hundred species of bacteria and a skin biome with a thousand different species.

We think that we’re the highest-functioning organism on the planet and that our mind has complete control over our behavior, but in the hands of a simple single-celled organism, we are essentially nothing more than a giant lab rat.

Over the past fifty years, we have introduced innovation after innovation that has overlooked, depleted, and destroyed our microbiomes. It’s no coincidence that in the same time frame there has simultaneously been a stark increase in major diseases, from obesity to the current mental health crisis to the autoimmune epidemic that I treat in my clinics every day.

Microbiota Hypothesis” suggests that dust from homes with dogs may influence the development and response of the human immune system by changing the composition of the gut microbiome in ways that reduce someone’s risk for allergies and asthma.

Imagine your gut microbiota as controlling a light switch and the wiring behind the wall is your genetic code. The gut microbiota is not changing the wiring behind the wall, but it can turn the lights on or off. You can’t change your genetic code, but you can effect which genes get turned on or off.

Why I buy organic whenever possible By definition, if a food is certified organic it is not genetically modified and was not sprayed by glyphosate. I don’t think this is the only reason to buy organic produce, however. I view it as an investment in my health, our family’s health, and the health of our planet. The chemicals being used in modern agriculture aren’t affecting only us; they’re affecting the health of our soil. If you don’t have healthy soil, you can’t have nutritious food. Human health starts in the dirt. We need to protect this precious commodity. When you spend your money, you are placing your vote in a way. You are empowering an industry. I, for one, choose to empower our organic farmers and regenerative agriculture. They are healers just as our doctors are. Only with them can we enrich our soil, increase biodiversity, and heal ecosystems large (our planet) and small (your gut). Let’s rally behind them and give them the support they deserve.

For example, two commonly used emulsifiers—carboxymethylcellulose and polysorbate 80—reduce microbial diversity, induce inflammation, and promote obesity and colitis in mice. Titanium dioxide (TiO) nanoparticles, found in more than nine hundred food products, worsen intestinal inflammation. Additives such as these were snuck into our diet through the “Generally Recognized As Safe” loophole. They were GRASed into our diet. Yes, GRAS needs to be used as a verb because that’s the only way to adequately describe the careless acceptance of chemicals into our food supply by our regulatory agencies.

Got Milk? For the record, you shouldn’t. I am not advocating for training your gut to handle lactose. We learned about the effect of animal protein and saturated fat on the gut in Chapter 2—less SCFA-producing bacteria, more inflammatory bacteria, increased TMAO production, increased intestinal permeability, and increases in bacterial endotoxin. As we’ve done in the past, when we examine the whole food rather than a sum of its parts, we find that dairy products have been associated with prostate cancer and Parkinson’s disease. Also the link to bone health turns out to be a myth—a prospective study of ninety-six thousand people over twenty-two years showed that milk consumption during teenage years did not protect against hip fracture later in life. In fact, men who drank more milk as a teenager actually had increased risk of hip fracture in the study. In a study of women in Sweden, high milk intake was associated with increased risk of bone fracture, heart disease, cancer, and premature death. One of the first things I do with my patients who have gas, bloating, or diarrhea is to eliminate dairy. You would not believe how many of them are cured just by doing this. Sorry, but milk doesn’t do a body good. The irony is that lactose, which has been vilified through the years as evil, is probably the most redeeming thing about dairy because lactose is actually a prebiotic and can have a beneficial effect on the gut microbiota.

A closer look at inflammatory foods in the gut Studies keep showing that the complex carbohydrates you’ll find in whole fruits, veggies, legumes, and whole grains are anything but inflammatory. They’re actually anti-inflammatory. But we rely on our gut microbiome to process them, and if there’s damage to the gut then it’s also impaired in carbohydrate processing, which leads to digestive distress. That’s not inflammation, that’s just sloppy processing. It doesn’t hurt you beyond the acute symptoms. But what does hurt you is the effect that you see from animal product consumption—less SCFA-producing good bacteria, more inflammatory bacteria, increased intestinal permeability, release of bacterial endotoxin, creation of carcinogenic secondary bile salts/polycyclic aromatic hydrocarbons/N-nitroso compounds/heterocyclic aromatic amines, and vascular disease-fueling TMAO. Yes, it is easier for our body to digest and process meat. We don’t rely on our microbiome as much for that. So you may not feel any discomfort, but keep in mind what’s happening inside you. Silent but deadly.

How to be gluten-free and still nurture your gut So what’s a sensible approach to gluten consumption? Well if you absolutely need to be gluten-free, then I would recommend paying special attention to your whole-grain intake. 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. Get them into your belly! On the flip side, if gluten is a part of your diet, which it should be for most of you, I’m not encouraging you to go eat more processed foods. Most gluten-containing foods are processed foods. What I encourage you to eat is more unprocessed or minimally processed wheat, barley, and rye. Look for whole-grain products, like whole-grain bread and pasta when they are called for. But remember not to overdo it. Moderation is just fine.

In the words of Ben Franklin, “Early to bed and early to rise makes a man healthy, wealthy and wise.

What about fermented dairy? Why no love for kefir, yogurt, and other fermented dairy products? Let’s look more closely at these foods. As we know, fermentation transforms our food and in many cases makes it easier to digest. This is particularly true with dairy products, where fermentation will remove most lactose. In fact, most hard cheeses, kefir, and yogurt are generally well tolerated by lactose-intolerant individuals. There are also some studies suggesting that kefir, yogurt, and other fermented dairy products may have health benefits. However, these studies were largely fraught with methodological limitations or were overtly paid for by the dairy industry. So what are we supposed to make of corporate-sponsored research that is essentially a form of marketing and only being published because it makes the food look good and the conclusions are carefully guarded to protect the product? From my perspective, why take any risk when you can find delicious fermented nondairy yogurt and kefir? In particular, I love a coconut milk kefir that’s available in Canada. No matter what you choose, make sure to pay attention to the sugar content, which is one of the big issues with all commercial products of this sort. Also, it should be noted that water kefir has absolutely nothing to do with milk and is much more similar to kombucha.

The thing about processed foods is that you’re starting with something that’s healthy in its natural state, and you are modifying it. As you progressively change that food, it becomes less and less nutritionally valuable. At some point, the food that started healthy becomes poison. If you go back one hundred years, this simply wasn’t a part of our diet. Take a moment to think about that: the sheer volume of man-made chemicals we’re putting into our bodies, and the unrealistic expectation that our microbiota will be able to process and eliminate them without any damage. It’s a shock that we don’t drop dead from this stuff and a total testament to the adaptability of our microbiome, even if this is likely contributing to mass bacterial extinction. It comes as no surprise that every 10 percent increase in consumption of ultra-processed foods is associated with more than a 10 percent increased risk of developing cancer and a 14 percent risk of early death. So what happens when you hit American levels of consumption—50 or 60 percent? I don’t think that every food additive is harmful in the long term, but we don’t know and likely will never know. There’s only one foolproof way to protect yourself from the potential poisons in our diet—get rid of them!