CHAPTER 1
MEET YOUR GENERAL CONTRACTOR: YOUR MICROBIOME
Before we dive into your room-by-room Gut Renovation, I want to introduce you to your general contractor, the head honcho whoâs calling the shots in this overhaul: your microbiome. The microbiome is an overall term for the many trillions (yes, trillions) of microbes (bacteria, viruses, and fungi) that live in and on your body. You canât see them, but your microbiome is living in and on every part of youâfrom your skin to your genitals to your colon. Even your ears and eyes have their own microbiome!
Much as the general contractor leads every aspect of a home renovation, the microbiome influences almost every part of your health. And as with a general contractor, a lot of this work happens behind the scenes! All of those microorganisms in your microbiome are an integral part of you. And there are a lot. You have somewhere around twenty thousand to twenty-five thousand human genes; your microbiome has as many as eight million genes. In your gut alone, your microbiome makes up about four pounds of biomass. Compare that to your brain, which weighs only about three pounds. For as long as humans have existed, so have the bacteria on us and in us. Youâre not just a person, youâre a superorganism! Your assortment of microbes is different from anyone elseâs, even from a twinâyour microbiome is as unique as a fingerprint.
How do we know this? In 2007, the National Institutes of Health launched a research initiative called the Human Microbiome Project, which aimed to identify and characterize the composition of the human gut microbiome. Thanks to those brave researchers sifting through a ton of stool, the discoveries from the project not only led to a much greater understanding of whatâs brewing inside our guts, but also jump-started game-changing research into how these bugs function in our body.
So what are all those bacteria doing?
A LOT. Basically, theyâre keeping you alive and healthy. In your gut (your small intestine and colon), theyâre performing vital functions that affect your entire body. Your gut bacteria help you digest your food, extract the nutrients you need to survive, and produce some of the vitamins your body depends upon. Pretty useful houseguests, arenât they? They also bolster your immune function, make anti-inflammatory compounds, produce neurochemicals that affect your mood and cognition, and support your health in myriad other waysâas you will be learning throughout this book.
More than two thousand years ago, Hippocrates said, âAll disease begins in the gut,â and modern science seems to be proving him right. Research shows that your beneficial bacteria can influence everything from your body weight to your risk of developing obesity-related diseases (like type 2 diabetes), chronic inflammatory disorders (such as inflammatory bowel disease), heart disease, mental health problems (including depression and anxiety), and age-related musculoskeletal conditions (like osteoporosis and sarcopenia).
What has also become clear is that the connection works in both directions. Your gut microbiome not only affects other parts of your body and your well-being, but your microbiome is also affected by your lifestyle and your overall health.
Why Diversity Matters
We often associate bacteria with infection and illness. I certainly doâin my office we spend a lot of time and effort on washing our hands, cleaning surfaces, and sterilizing equipment to get rid of bacteria. In any setting where harmful bacteria can be passed on, that makes sense.
Your gut is different. The wide variety of bacteria in the human microbiome consists of mostly beneficial bacteria, not harmful ones. (Otherwise, youâd be in trouble.) Your microbiome naturally goes through ups and downs, blooms and die-offs, in bacterial species and in numbers. A healthy gut has about 85 percent beneficial species, which means that a substantial number of harmful bacteria are always hanging around looking for a chance to multiply and throw the balance off. In a healthy gut, if that happens you might have a day or two of feeling a little off, but usually the balance fixes itself without you even noticing.
You can never fully get rid of the badâor what I call unfriendly!âbacteria, but with the right care and habits you can maximize the effectiveness of good bacteria. That way, the bad guys will be crowded out by the good guys so they canât reproduce into large enough numbers to be harmful.
Sometimes the unruly houseguestsâthe unfriendly bacteriaâdo get the upper hand and trash the place. That might be because you unknowingly ate food contaminated with bad bacteria like salmonella or E. coli and got food poisoning. Or maybe you caught a virusâwhat we doctors very scientifically call a stomach bug. After a few days of throwing up and/or diarrhea, your immune system clears out the bad guys, the good bacteria take over again, and your digestion gets back to normal.
At least, thatâs what usually happens. Sometimes, however, the bad bacteria linger, and your digestion takes a long time to return to normal. Or the bad bacteria donât cause an actual illness but still crowd the good bacteria, reducing their numbers. Your microbiome is incredibly dynamic, changing quickly in response to your diet and environment. And so consistent bad habits mean that the balance of your microbiome in your gut is regularly set off course. As the balance and diversity of bacteria deteriorates, so does your health, because you now have a problem called dysbiosis.
Understanding Dysbiosis
Modern life doesnât make things easy for your gut microbiome. Weâre constantly doing things to it that the bacteria donât like. Top of the list is our diet. Many of us eat the aptly named Standard American Diet, or SAD. Itâs mostly high-calorie, low-nutrition, ultraprocessed foods filled with sugar, salt, bad fats, preservatives, and food additives. This sort of junk food now makes up more than half of the average Americanâs diet. On top of a bad diet, we attack our gut bacteria with alcohol, antibiotics and other drugs, environmental toxins, lack of sleep, and plenty of stress. Those lifestyle choices can all throw your microbiome into an imbalance that canât self-correct. You feel your digestive system just isnât working right, but because your symptoms are vague and variable, you ignore them or maybe pop some over-the-counter pills.
Dysbiosis is basically what happens when thereâs a major reduction in the diversity of your microbiome and/or an overgrowth of unfriendly bacteria. The symptoms can vary a lot from person to person, and from day to day, even hour to hour, in the same person. The most common digestive symptoms include upset stomach/nausea, constipation, diarrhea, and gas and bloating. You may also have fatigue and brain effects such as brain fog, inability to concentrate, anxiety, and depression.
Not everyone will have every symptom, of course, and the symptoms can range a lot in how severe they are and how often you have them. But even without any digestive symptoms, dysbiosis can wreak havoc on your body in many ways. It has been implicated in everything from skin disorders to diabetes.
Throughout this book weâll talk about how your microbiome and gut health interact with all the aspects of your life, and the strategies you can employ to prevent or fix dysbiosis. Two important tactics are improving your diet and using probioticsâgood bacteriaâto restore a better balance in your microbiome. But there are many more ways to optimize your gut, as you will soon learn!
Gut Barrier Function
When food reaches your small intestine in its digestive journey, itâs basically a soup of partially digested food, as well as anything toxic you may have accidentally eaten. (I know, gross!) While you want the nutrients from your food to be absorbed into your bloodstream, you donât want to absorb anything else. Lining your small intestine is a single layer of cells closely laid next to each other, sort of like subway tiles, with very little space between them. The spaces between the cells are called tight junctions. The junctions can open up just enough to allow digested food particles, water, and micronutrients to pass through into the bloodstream, while blocking larger particles and the rest of the intestinal contents. In this way, the lining of your intestine forms an important barrier. It keeps the toxic or foreign particles in your intestine from sneaking into your bloodstream, where they can trigger inflammation. The good bacteria in your gut help maintain this barrier, both by secreting protective mucus to layer onto the gut wall and by producing compounds that keep the junctions tight.
But what if that barrier gets compromised? When the tight junctions of your small intestine open up too widely or stay open too long, or if the delicate walls of your small intestine develop tiny holes and cracks, you have intestinal permeabilityâaka a leaky gut.
When the gut becomes permeable for whatever reason, larger food particles, bacteria, and other intestinal contents leak out into your bloodstream. Your immune system sees the escaped contents and responds to them as if they were dangerous invaders, which in a sense they are. The immune response triggers inflammation, which in turn can lead to many of the same symptoms as dysbiosis. You can get bloating, gas, nausea, and cramps, but now with the possible addition of food sensitivities and aching joints. Long term, itâs possible that the chronic inflammation caused by a leaky gut can lead to autoimmune illnesses such as rheumatoid arthritis or other chronic diseases like diabetes or even heart disease. It can also produce food allergies that wonât go away.
What causes these breaches in the integrity of the intestinal lining? One cause is dysbiosis that goes on for a long time, but there are many others. The same low-nutrient, low-fiber diet that causes dysbiosis can cause leaky gut by constantly bombarding your gut with damaging substances, including the artificial sweeteners, preservatives, food additives, food colorings, emulsifiers, and residue of agricultural chemicals that abound in processed and packaged foods. Alcohol can damage the gut, as can the many environmental toxins that weâre exposed to every day: air pollution, cleaning supplies, cosmetics, personal care products, fire retardants, fabric softeners, and everything else. Having a bad bout of food poisoning or a stomach flu can also increase intestinal permeability.
Radiation therapy for cancer and a range of powerful drugs for cancer and other serious conditions can also trigger leaky gut. If you have an underlying condition, like celiac disease or Crohnâs disease, youâve got a good chance of developing a leaky gut, because the inflammation from these diseases can directly damage your intestinal lining. And then thereâs that all-purpose enemy of digestion, stress.
So while a leaky gut can be caused by many factors, you have control over so many of them! Youâre the general contractor of your microbiome, after all. To start, changes in gut flora need to occur to correct dysbiosis. Restoring the numbers of good bacteria and the diversity of species leads to tighter junctions in the gut lining as well as more protective mucusâboth of which strengthen and reinforce this important barrier.
Your Home Surveillance System: Understanding Immunity
From start to finish, your digestive tract is constantly in contact with bacteria. Keeping those bacteria inside the long digestive tube is important to protect the rest of your body from infection. Some are inevitably going to escape, however. Your body is ready for them: at least 70 percent of all the infection-fighting immune cells in your body are found in the gut. You can think of them as your bodyâs alarm system.
Having an alarm system is a good thing, right? After all, you want your gut immune system to go after the bad microbes. But as anyone with a home alarm system knows, itâs easy to set off a false alarm. You donât want your immune system going off by mistake, because thatâs what triggers autoimmune diseases, where the body attacks itself. Ideally, you want your immune system to be balanced between tolerating a few bad microbes and reacting swiftly when the level of bad microbes reaches the danger point.
We call this immune tolerance. The best way to maintain it is by having a diverse range of gut bacteria. Diversity helps the cells of your immune system distinguish between dangerous microbes that need to be attacked and those that donâtâand to distinguish between invaders and your own cells.
When your immune system does need to respond, a complex cascade of steps gets triggered. Imagine youâre making dinner and you slice your finger while chopping the onions. Thatâs sort of like an alarm system when one of the safety protocols is breached. Your bodyâs alarm is quick to respond; bacteria from the environment immediately enter the gash and your immune system kicks in to throw them out. The area around the cut swells, gets red, feels hot, and hurts, all of which are signs of acute inflammation. Basically, the first immune cells to rush to the scene send out chemical signals that tell the blood vessels around the cut to get leakyâthe cells that line the blood vessels open up a little to let more immune cells, platelets (for clotting), and fluid from your blood into the area. That makes the area around the cut swell even more.
Just as an alarm system would signal for backup, so does your body. The immune cells that rush in start sending out more chemical messengers called cytokines. The cytokine messages help control the inflammatory response. They tell more immune cells to come to the cut to kill off invaders.
If the cut is a small one, your immune system can easily kill off any invading bacteria. Your finger may be a little red, swollen, and sore for a few days until it heals up. But if the cutâs a bad one, or if you just get unlucky and particularly dangerous bacteria get in, your finger could develop an infection. Now your immune system has to work harder to get rid of the invaders. The cytokines tell more immune cells to join in, and also make you run a fever and feel tired so youâll slow down and have more energy for fighting the infection.
Acute inflammation may make you feel pretty lousy for a few days, but when the worst is over, the inflammatory response dies down.
The tricky thing about acute inflammation in the gut is that it isnât visible the same way a cut on the finger is, but your body has a lot of the same recovery mechanisms. Your gut gets swollen and painful with cramps and bloating. It doesnât work well, so you may get diarrhea and may even pass some blood. You feel fatigued and achy, lose your appetite, and run a fever.
Your body is constantly on the lookout for things that can harm you. Your immune system goes...