by Sanjay Gupta
Today, decoding our microbiome—from the communities deep inside our guts to the colonies that cover our skin—is one of the most promising fields of scientific study. We are at the very beginning of an exciting journey to understanding and leveraging the power of the human microbiome, and the pandemic gives us all the more reason to study this “superorgan” and unlock its secrets. It may hold the future key to our health and ability to combat future pathogens, including COVID’s cousins yet to be born.
The ecosystem, or “rainforest,” that comprises a human biome includes a diverse collection of microorganisms, mainly bacteria, fungi, yeasts, parasites, and viruses. Their collective genetic material far outnumbers our own DNA. The bacteria that thrive in our intestines are especially important. They have a commanding say in everything about us, from the efficiency and speed of our metabolism to our risk for all manner of ills, COVID-related conditions among them. They assist with digestion and the absorption of nutrients; you can’t nourish yourself effectively without them. They also make and release important enzymes and other substances that your body requires but cannot make sufficiently on its own. These include vitamins (notably B vitamins) and neurotransmitters, such as dopamine and serotonin.
An estimated 90 percent of the feel-good hormone serotonin in your body is not made in your brain. It’s produced in your digestive tract, thanks to your gut bugs. This intestinal flora and their effects on your hormonal system help you handle stress and even get a good night’s sleep.
That’s my brief summary on gut bacteria. The main point I want to get across is the following: Of all the actions that these microscopic organisms perform to keep you healthy, perhaps the most vital are the ones that regulate and support your immune system, which is directly tied to your risk for a poor outcome from an infection like COVID. Put simply, your microbial friends help shape your immunity.
The majority—at least 80 percent—of our body’s total immune system is made up of gut-associated lymphoid tissue (GALT), the largest mass of lymphoid tissue in the body that’s rich in immune cells such as those B and T cells. The GALT lies throughout the intestine, covering a stunningly vast area (up to 300 square meters, which is a little larger than a tennis court!).11 Indeed, our immune system is headquartered in the gut because the intestinal wall is a biological gateway to the outside world. Aside from skin, it’s where we have the greatest chance of encountering foreign material and organisms. The GALT is in constant communication with other immune system cells throughout the body, notifying them if cells in the gut encounter a potentially harmful substance. Because gut bacteria can control certain immune cells and help manage the body’s inflammatory pathways, the gut and its inhabitants are said to be your immune system’s largest “organ.” You may already know that the skin is the largest physical organ. Biologically speaking, the gut and the skin are one and the same, as they present barriers between our insides and outsides that are colonized with microbes. Those microbes can help and hinder how our insides and outsides perform; in fact, the skin and intestinal lining share similar origins in utero during embryonic development. The immune system is dynamic and constantly changes alongside the microbiome throughout our lifetime.
The concept of “you are what you eat” was born when French author Anthelme Brillat-Savarin wrote: “Tell me what you eat and I will tell you what you are,” in his 1826 work, The Physiology of Taste: Or, Meditations on Transcendental Gastronomy. And now we have plenty of science to show us how this is so, with the microbiome taking center stage. The composition and strength of your microbiome reflect your nutrition and, in turn, your entire physiology. If there’s one thing we scientists have learned in just the past decade or so, it’s that changes in diet result in adjustments to our microbiome—sometimes in as little as a few days with nutritional tweaks. As our ancestors’ diet evolved over time, their gut inhabitants did too, from microbes that could easily break down the fibrous foods plentiful in the early human diet to other microbes better equipped to process the animal proteins, sugars, and starches prevalent after the advent of agriculture and animal husbandry about ten thousand years ago. But as we all know, Westerners have taken the consumption of animal protein, sugars, and starches to the extreme, and the result is a diet high in empty calories and deficient in such nutrients as fiber, essential fatty acids, and other micronutrients that help nourish a healthy microbiome and, in turn, a strong immune system. As the saying goes, we are overfed and undernourished. That is true, but you now understand that your immune system can also be compromised by your diet. If we make bad food choices, we are at greater risk of becoming infected and less able to defend ourselves against a pathogen once it does take hold.
Your gut’s microbiome is in constant conversation with the brain through what’s called the gut-brain axis. Gut bacteria make chemicals that communicate with the brain through nerves and hormones; the communication is a unique and complex two-way highway. So not only is the gut’s community a key to immunity and levels of inflammation, but it’s also a linchpin to our entire nervous system. You probably don’t think of your gut and brain being strongly connected the way you see your limbs linked up to your brain. But you’ve no doubt experienced this hidden connection through nerve-racking experiences that leave you, for example, feeling sick to your stomach (“butterflies in your stomach”). The vagus nerve (derived from the Latin word for “wandering”—vagary—because this nerve has the longest course of all cranial nerves) is the primary channel of information between the hundreds of millions of nerve cells in your central nervous system and your intestinal nervous system. There’s also an axis to your skin to complete the loop, called the gut-brain-skin axis. Hence, when you experience strong emotions, such as fear or embarrassment, your stomach may hurt and your skin may turn “white as a ghost” or flush red.
The vagus nerve is meant to relay messages, but it also helps the health of the gut lining. The gastrointestinal tract is lined with one single layer of surface (epithelial) cells all the way from the esophagus to the anus. The intestinal lining, the body’s largest mucosal surface, has three main jobs. First, it serves as the means for the body to obtain nutrients from foods. Second, it blocks the entrance into the bloodstream of potentially harmful particles, chemicals, bacteria, and other organisms and components of organisms that can pose a threat to health. The third function of this cellular barrier is perhaps less well known and deals with its immune function: It contains chemicals called immunoglobulins that bind to bacteria and foreign proteins to prevent them from attaching to the gut’s lining. Immunoglobulins are antibodies secreted from immune system cells on the other side of the gut lining and transported into the gut via the intestinal wall. This function ultimately allows such pathogenic organisms and proteins to be pulled from the body, pass on through the intestines, and be excreted.
A key point to remember is that intestinal microbes help control your gut’s permeability, or how easily substances pass through the one-cell-thick intestinal epithelium. In addition to the single-cell-thick lining, there are also goblet cells that produce mucus that attaches to the cell wall and makes it “thicker.” This process of mucus production depends on back-and-forth interplay with the gut microbiome (the mucus layer typically consists of two layers—and the inner layer is renewed every hour). In other words, your gut’s microbiota play a key role in shaping that intestinal barrier structure and its permeability. Microbial imbalances can cause damage to that wall. If there are problems with the integrity of the cells that line the gut due to a microbial disturbance, there can be problems with controlling the passage of nutrients from the digestive tube into the body. And if that gateway is compromised in any way, so is the body’s immune system and its resistance to a pathogen like COVID.
The strength and function of your microbiome may play a much bigger role in your immunity and reaction to an infection like COVID than you can imagine—and that science is just beginning to be uncovered. Studies in the past year alone have highlighted
the significance of the microbiome in people’s prognosis with COVID.12 Associations found between gut microbiota composition (that is, strains and volume of species) and levels of inflammatory markers in patients with COVID suggest that the gut microbiome is involved in determining the magnitude of the infection. What has been of particular interest to me is the growing possibility that imbalances in the gut’s biome, or gut dysbiosis, after COVID clears the body could be a major cause of long-hauler or post-COVID symptoms—brain fog, fatigue, and other persistent symptoms. Experts have also hypothesized that it is an imbalanced gut microbiome that may at least partly explain why older adults and adults with conditions such as obesity or type 2 diabetes seem to be at greater risk of serious COVID illness.
The close relationship between our gut bugs and immunity is likely a two-way street: as infections alter our microbiome, our microbiome alters our immune function and vice versa. Given that the gut is the largest immunological organ in the body and its resident microbes are known to influence immune responses, scientists are focused on teasing out how the gut microbiome affects the immune system’s specific response to a COVID infection. And if a connection between the gut microbiota and COVID severity is found, interventions like probiotics or even fecal transplants, to reestablish an individual’s healthy microbiome, may help patients in the future. The fecal transplant is an emerging procedure in medicine where a doctor restores the balance of bacteria in a person’s gut by taking specially filtered stool from a healthy donor and transferring it into the gastrointestinal tract of the individual with an unhealthy or imbalanced microbiome. Although the procedure is usually reserved for serious gastrointestinal infections such as C. diff, future research will surely find other beneficial uses for it in medicine.
The probiotic market, however, has exploded in the past decade. The term probiotic is derived from the Latin pro, meaning “for,” and the Greek word bios, meaning “life.” Probiotics are the beneficial bacteria you can consume via pill or through such fermented foods as cultured yogurt, cheese, kimchi, and kombucha. Lactic acid fermentation, in fact, is the process by which foods become probiotic, or rich in beneficial bacteria. In this process, good bacteria convert the sugar molecules in the food into lactic acid. In doing so, the bacteria multiply and proliferate. This lactic acid in turn protects the fermented food from being invaded by pathogenic bacteria, because it creates an acidic environment that kills harmful bacteria. That is why lactic acid fermentation is also used to preserve foods. To make fermented foods today, certain strains of good bacteria, such as Lactobacillus acidophilus, are introduced to sugar-containing foods to kick-start the process. Yogurt, for instance, is easily made by using a starter culture (strains of live active bacteria) and milk. None of this is new; throughout history, fermented foods have provided probiotic bacteria in the diet.
The ideal composition and species of microbes that make up a healthy microbiome remain unknown, and studies on the value of taking supplemental probiotics have been mixed. We are still in the “we don’t know yet” phase as we conduct studies to inform how to support the health of our microbiome. Given how rapidly we are learning about the relationship between gut health and immune health, we may soon be at the point where we will be able to “prescribe” certain strains of probiotics to help treat or even cure a slew of conditions. In fact, certain strains have already been identified that can significantly and positively support the immune system, such as strains in the Bifidobacterium, Lactobacillus, and Saccharomyces genera that are readily available in commercial products, notably fermented foods.
To fully appreciate the microbiome, experts have emphasized to me that it helps to not be reductionist, describing strains as good or bad. After all, studies around the world show that people of different cultures and environments exhibit wildly different microbiomes, which means that one helpful strain of bacteria in one part of the world might be less helpful in another. What seems to be most important is a significant diversity of microbes: the more diverse, the healthier. And there’s no better way to consume a rich array of healthy bacteria than to consume them through wholly natural sources, such as sauerkraut, pickles, kimchi, and other fermented vegetables. Once in the gut, these bacteria need to be nurtured by basic lifestyle habits in addition to a good diet, such as regular exercise and restful sleep, which also contribute to the well-being of the microbiome.
Prebiotics are increasingly talked about as well. These are the compounds in certain foods that also promote the growth and activity of beneficial microbes in the gut but are not in and of themselves microbes. They are types of dietary fiber found in many fruits and vegetables, such as chicory root, Jerusalem artichoke, garlic, onion, leek, banana, asparagus, and dandelion greens (toss some of those in a salad!). We live in symbiosis with the microbes in our guts, so it’s important to give them a wide variety of things like fibrous fruits and vegetables so they can stay healthy.
Move, Sleep, and Chill
Three other keys to maintaining optimal health and immune function are staying active, sleeping well, and reducing stress.
Movement Mitigates COVID
Just twenty-two minutes of moderate exercise a day can strengthen your immune system, and we know now that regular physical activity lessens the severity of COVID—so much so that inactivity is listed by the CDC as a risk factor for severe COVID.13 For someone who doesn’t exercise on a regular basis, 22 minutes a day (150 minutes a week) might sound a bit overwhelming, but those minutes don’t have to entail signing up for a gym membership, investing in a treadmill, or revamping your schedule. With the right strategies, you can accomplish your daily exercise goal with very little disruption to your day. Moderate exercise can include walking (at least 4.0 miles an hour), lawn-mowing, and some household chores like vacuuming and mopping.
We humans evolved to move, and move frequently. I know I’m not the first person to tell you this, but it bears repeating that when you avoid routine exercise that gets your heart beating at a faster clip, your blood pumping at a speedier pace, and your skin to sweat, you put yourself at higher risk for the same things a Western diet will do: more inflammation and more chronic disease. Exercise is nature’s panacea for the body, providing more health benefits than any drug—and with almost no side effects. It reduces risk for all manner of ills, rapidly flushes out stress hormones, and boosts mood while balancing blood sugar and metabolism in general. Activity improves the health of every organ system, including the brain (and, yes, that all-important lung capacity). If I told you that more than anything else you can do, a mere two minutes of activity every hour can boost your health and make you smarter, wouldn’t you want to rethink your sedentary ways? A few years ago, it just hit me one day: we were thinking about it backward. It’s not that activity should be thought of as the cure but rather inactivity as the disease. Just move. Every time you are about to sit, ask yourself: Could I stay standing instead? Other tips:
• Take regular walks. Walking is so accessible to most people that it’s easy to dismiss its benefits. But a brisk walk is one of the most underrated, health-boosting exercises available to humankind. You probably already walk at least a little bit each day. Would it be possible for you to add in a five- or ten-minute walk around the neighborhood before getting in your car to go somewhere? Pair the walk with talking on the phone with a friend or family member or listening to your favorite podcast.
• Practice short bursts of activity. Break up your twenty-two-minute minimum with a quick interval training session consisting of four rounds of five exercises for one minute each. These could include body-weight exercises like push-ups, squats, lunges, hip bridges, and jumping jacks. Add in a couple minutes of warm-up and cool-down, and you’ll easily hit your twenty-two-minute mark.
• Pick up an old sport you used to play like tennis or cycling. If you have kids, play fun games with them that get your heart pumping.
• Track your movement. Most smartphones now come with apps that track your miles. Unless
you made a serious effort to exercise during the height of stay-at-home orders, many of us fell far behind the 10,000-steps-a-day rule. Accountability goes a long way toward helping us stay on track with fitness goals. A recent study published in the British Journal of Sports Medicine found that people walk almost an extra mile per day when using an activity tracker on their phone or watch.14 And study participants who had fitness trackers with exercise prompts did even more. It doesn’t matter how you track your fitness—whether you use smart technology or simply keep a journal, the act of recording your progress will help keep you on track.
People who recover from COVID could be managing damaged lungs for months that prevent them from engaging in vigorous exercise. Their cardiovascular health could also be compromised as a result of both the effects from the infection and the recovery process that disrupts their fitness routines. Be patient with yourself. In addition to following advice from your doctor, I want to share something that has significantly helped many patients support recovery and strengthen their lungs: performing deep breathing exercises, which also have the added benefit of lessening feelings of anxiety and stress.
Deep breathing can be done anywhere, anytime. A practice twice daily will get you started and give you a foundation. All you have to do is sit comfortably in a chair or on the floor, close your eyes, and make sure your body is relaxed—releasing all tension in your neck, arms, legs, and back. Inhale through your nose for as long as you can, feeling your diaphragm and abdomen rise as your stomach moves outward. Take in a little more air when you think you’ve reached the top of your lungs. Slowly exhale to a count of twenty, pushing every breath of air from your lungs. Continue for at least five rounds of deep breaths. Another variation on the theme is to try the yawn-smile technique. This exercise incorporates motion with deep breathing, which helps increase coordination and build strength in the arms and shoulders. It also opens up the muscles in your chest to expand the diaphragm. And it’s simple: Sit upright on the edge of your bed or in a sturdy chair; reach your arms up straight overhead and create a big stretching yawn; then lower your arms down to your sides and finish by smiling for three seconds. Repeat for one minute. You can find online videos of these practices.
