Now more than ever, it’s important to learn how your immune system works and the things you can do to become immunity strong. Read on to learn about biomes and how they affect the longevity of your Biological Soul. Read on to find out more—and to ensure your health and the health of others, don’t miss these Sure Signs COVID is Hurting You—Even After a Negative Test.

Poop, especially someone else’s, may not be great to get on you but it is a great way to get into those organisms that still fascinate me and have as much to do with your health than anything else in life: biomes or communities of microorganisms or microbes within and on you. When it comes to biomes, you are never alone: From before you are born, they are present everywhere in and on your body and work together to strengthen your immune system and tell it if something is friend or foe. Think of them as a kind of immune system moral compass. Bacteria are the most dominant players among your biomes and make your poop as much a living thing as a mass of dead cells and waste. In your gut alone, there are roughly 100 trillion biomes from your small intestine into your large intestine, meaning that there are also trillions of genomes that belong to bacteria visiting your body, along with millions on our skin, and many more within our lungs, mouth, and urinary, genital, and reproductive tracts. Gut bacteria play a role in regulation of immunity, development of the nervous system, and are your main source of vitamin K and vitamin B complex. It should come as no surprise then that these bacteria and all your biomes are deeply affected by what you eat. Yes, you are what you eat, as well as what you interact with, the environment around you, the stress you feel . . . and your biological soul knows it. In fact, biomes are essentially your biological soul’s soulmates, only with names you cannot pronounce and microscopic forms that look like worms and peas.

Biomes are an evolutionary marvel that have allowed us to travel to various parts of the world since the dawn of man; places where there was low oxygen at high altitudes, extreme heat, limited or unusual food sources, and so on. They permitted genetic adaptation, for example, allowing people with dark pigment from warmer climates an ability to regulate their blood pressure and heart rate as they migrated to colder parts of the globe. Most importantly, the biome was the environmental variable that allowed us to thrive and support defenses against infection, pain, and early death. They informed the immune system and allowed it to develop and adapt to the dangers of the environment. It is very likely that the immune system in early Homo sapiens was largely regulated by the biome. If there was malaria, cholera, and a whole host of other infections from environmental change, biomes eventually allowed humans to adapt and formed a natural deterrent to death from these infections.

So, it is amazing how little we think about them today—or see them as a danger and try to get rid of them. Simply put, our physical and mental well being depends on our biomes thriving within and on us. While this article speaks almost exclusively to biomes of the gut, research may eventually show biomes of other areas like the skin might be just as important to the immune system as the bowel. Digesting what this means—not just taking action to change certain aspects of your diet and your behavior—is the subject of this article and the next key to becoming immunity strong.

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Howard Hughes, the mid-twentieth-century American businessman, went from billionaire playboy to world-famous recluse and obsessive-compulsive germaphobe. He believed his neighbors made him sick by living unkempt lives, demanded that anyone who touched his food use layers of paper towels (and that most of that food was contaminated anyway), and yet still believed that everything was covered with a small layer of dirt that no amount of cleaning would help. I think all of us who lived through the global pandemic may have some understanding of Hughes’s need to socially distance from others, and stories of bacteria leading to food poisoning should make us all be conscious of safely handling our food. But the dirt part is harder to get my head around. If I saw one of my children eating dirt, playing in the cat box, or wrestling with the dog, I was sorry for whoever was doing laundry but took comfort in the fact that they might be arranging their adaptive immune system to respond to horrid infections later in life. Robust collections of healthy bacteria in a child’s bowel can build immunity at a young age that lasts through a lifetime. In other words, children who eat dirt, pick their noses and eat the snot, and luxuriate in covering themselves in mud, might have healthier immune systems because they do that.6254a4d1642c605c54bf1cab17d50f1e

As counterintuitive as all that sounds, studies of rural children who wallow and even swallow dirt when they are little reveal that they are less prone to allergies that affect suburban and urban children. Children living on a farm, being around and breathing in (and likely ingesting a bit of) manure have less allergies and healthier immune systems. There is also evidence in adults of being “dirt happy,” meaning playing in and laying in dirt acts as a natural antidepressant and mood lifter. This is something we continue to study but think about that the next time you resist the urge to lie on the ground. Howard Hughes be damned—the power of dirt might be the best thing for training immune systems!

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Don’t ignore the power of dirt! Your bowel uses the abundance of bacteria in and on the body to inform the immune system. The biomes of the bowel, as well as your skin, lung, and gastrointestinal tract, have effects on many bodily functions. They are a welcome community of organisms with their own genes and essential to good health—and have been since our ancestors began to migrate around this planet, allowing them to adapt to new environments. There is growing evidence that this power of dirt starts the moment we are born. This is called the “Hygiene Hypothesis.” According to the U.S. Food & Drug Administration, the Hygiene Hypothesis “suggests that the critical postnatal period of immune response is derailed by the extremely clean household environments often found in the developed world.” Exposing babies and young children to certain biomes in dust and dirt protects against allergies and antigens (the criminals from Chapter 1 in my book). It strengthens their immune system’s tolerance to antigens the same way they strengthened the immune systems of our nomadic ancestors. By contrast, denying the child’s exposure weakens their immune system’s tolerance. Antigen exposure at a young age essentially enlarges a child’s biomes and creates a robust immune system that can result in reduced effects of respiratory diseases like asthma and resistance to allergic diseases like eczema.1 All we just covered makes biomes adjuvants, or substances that increase your immune response to an antigen. 

Biomes are also adjuvants that assist anything that stimulates the immune system like vaccines. They do this through the flora of your bowel and your cell’s genetic library. Most vaccines contain materials like aluminum to prod the immune response as adjuvants, but these organisms within your bowel are an endogenous or inner stimulant for the immune response. I saw this in the lab when germ-free mice (sterile mice born without exposure to any organisms and fed sterile diets) were immunized with the influenza virus, and they failed to mount an immune response. A similar response was found in the mice that were given huge doses of antibiotics and had their bowels chemically sterilized. Okay, take a breath, lie down in the dirt, and contemplate all of this before we do another gut check. 

No one has explained the high rates of asthma and allergy among the urban poor children in America. Studies suggest that traffic related pollutants from auto exhaust and the aerosolization of automobile rubber tires along roads and highways are responsible for a 12 percent increase of asthma in children by age 40. I can only imagine that such pollutants affect every biome of the child’s body. The food you eat and the drugs you ingest—such as the indiscriminate use of antibiotics to treat nonexistent bacterial infections like the common cold—can alter your biomes and change your immune responses to many things, including vaccines, which are not as effective in those with altered biomes.

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“You are what you eat” is an expression usually deployed as an insult—a joke made at the expense of others about their diets by those asserting their healthy diets and fitness. But it’s no joke. What you eat has major effects on you, something the originator of the phrase, the renowned nineteenth-century French gastronome Jean-Anthelme Brillat-Savarin in Physiology of Taste, understood when he wrote: “Tell me what you eat, and I will tell you what you are.” It has been two centuries since Brillat-Savarin made connections between the external (social and political) and internal (anatomy, histology). Yet many of us still struggle to make this connection ourselves and act in spite of all the scientific advances in understanding the biomes within and on us. The 27 feet of bowel we all have helps us to digest food and absorb it. It degrades complex fats, carbohydrates, and proteins and gives you energy. But it is also part of the protective network of the body since it prevents the colonization of harmful organisms from gaining a foothold. This microbe-host relationship is vital to our wellbeing and is thus deeply affected by diet. Research has revealed unambiguous and startling differences in the health and effectiveness of gut microorganisms of thinner versus obese people. 

Studies for decades have shown that your diet can increase or decrease the risk of cardiovascular disease in both men and women, which is the most common cause of death in developing countries. Yet our food chain remains as much about class, politics, and calories than what might be right for you—and be doing to you inside and out. While food and diet research and debate are constantly evolving, we need another gut check as the health of the communities of organisms essential to our biological souls hangs in the balance—something that antibiotics not only cannot fix but can also hurt. I never understood this more than the day I met Melanie. 

Melanie’s abdominal pains felt “like she was being punched in the gut every five minutes.” Each volley of pain would be followed by a burst of watery diarrhea. She had suffered these indignities for a period of days. In taking her medical history, we learned Melanie had been on antibiotics for a urinary tract infection for some weeks and developed her bowel problem only recently. That’s when we realized she was suffering from a serious—and deadly— infection caused by a bad bacterium Clostridium difficile, or C. diff. C. diff causes inflammation and severe damage to the bowel. It is particularly insidious as it can reoccur weeks after treatment and in some cases can be fatal. Melanie was already heading in that direction when we saw her, and her diarrhea was only making her weaker. In her case, this treacherous opportunist bacterium also took advantage of a bowel in which most of the normal flora had been killed by her antibiotics and then kept taking advantage when the new round of potent antibiotics used to treat it kept killing her biomes. To be sure, any disruption of the bowel wall results in invasion of bad organisms and the subsequent inflammation, but Melanie’scase was an extreme version of a not uncommon problem (more than half a million people get C. diff every year), and one which is quite serious in a time when antibiotics are prescribed by doctors without regard for a patient’s biome. Melanie had few options left, so we deployed the exact reverse of the story that opened this piece: through a colonoscopic procedure, we transplanted stool in capsule form from a patient who had normal healthy flora into Melanie’s bowel in order to try and reseed her bowel with those normal biomes. 

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As a medical student, I can recall my microbiological mentor at Jefferson Medical College, Dr. Russell Schaedler, growing aerobic organisms (those that need oxygen to grow) and anaerobic organisms (those that grow without oxygen and produce a lot of gas). They had bizarre names, smelled horrible, and were in retrospect some of the earliest studies of the biome. Dr. Schaedler knew these organisms had a role to play in normal physiology and homeostasis. Even then, he felt that immune diseases like rheumatoid arthritis and lupus might be connected to the organisms in one’s diet. (Joint pains from the gut? Yes!) Other doctors followed. For example, an early paper from Dr. Jose Scher at New York University found that people with rheumatoid arthritis were more likely to have the Prevotella copri organism in their intestines. He felt that changes in the body’s ecosystem with the rampant and inappropriate use of antibiotics was one possible cause of the rise of autoimmune diseases in general. 

Dr. Scher also researched a nagging condition called psoriatic arthritis in patients and found that yet another unusual bug common to normal stool was absent in the bowels of those patients. All these bugs have strange names—many unfamiliar to most microbiologists, let alone laypeople—and make for impressive tongue twisters for academic discussion. Back then, I only knew one thing: these organisms were exceedingly difficult to grow in the lab, especially the ones called anaerobes that grew in the absence of oxygen. Today, growing these organisms and the cultivation, use, and study of human stool can be big business and a lifesaver for people suffering from C. diff and much, much more. 

For Melanie, unfortunately, it was too late. Her symptoms were too advanced by the time we saw her, but stool transplants do have a cure rate of 90 percent for extreme cases of C. diff and further demonstrate the power of poop. The most important question, however, is not what poop can do to cure disease, but what you can do to keep a balance of healthy biomes inside your bowel before that poop ever comes out. And that brings us back to diet. It is hard, even impossible, to keep up with the latest fad diet and even the long-established studies of how what we eat affects us. But research consistently shows a diet of meat, rich in sugar, and replete with processed foods can adversely affect the balance of these microbes in the gut and support the extraction of calories from food. A plant-based diet may be more sensible, providing fiber and vitamins without all that sugar. Research has also shown that long-established diets like the Mediterranean or Atkins that steer this way will decrease chances of inflammation as a result of what we eat. Studies in mice suggest that obesity is dependent on the biome of their bowels. A lean mouse given a stool transplant from a fat mouse results in the lean mouse gaining tremendous amounts of weight in a short period of time.

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What I advocate for is balance in everything you eat that fits your lifestyle. I do not think vitamins and other nutritional supplements can supply what you don’t eat or undo the damage of what you do. But there are practical ways to use diet to eliminate the hyperimmune state and make you immunity strong and boost your immune system, particularly prebiotics and probiotics.

Prebiotics are microbes that you ingest to encourage the growth of healthy microorganisms like bacteria or yeast that boost the health of your gut and your health overall. They are not digested by your gut but metabolized by the gut bacteria and can change the course of atherosclerosis, type 2 diabetes, and possibly even correct behavioral issues. They can be found naturally in food sources such as onions, garlic, leeks, asparagus, bananas, chicory root, and dandelion greens. Many consider foods with fiber like barley and oats as great prebiotic foods as well. Probiotics are friendly bacteria that restore your gut flora. Certain foods like yogurt, sauerkraut and kefir, tempeh (a fermented soybean product), kimchi (Korean fermented cabbage), miso (a Japanese seasoning), kombucha (fermented tea), pickles, traditional buttermilk, natto (another fermented soybean product), and many kinds of cheese are natural probiotics for your gut. All of these can boost immune function by way of biomes. For most people, the inclusion of probiotics is a natural thing. Use of prebiotics may take a little planning and thought. 

Consider this and any information you read carefully as you look at what you eat and any modification of your diet. Millions of people around the world believe in the use of probiotics, and while they are not tested in rigorous scientific trials, there is substantive evidence that the ingestion of these probiotics is safe. Just be careful to check claims on packaging to be sure you are getting more of the good stuff and less of the sugar and processed substances used to transport them. There are also prebiotics and probiotics which can be prescribed by physicians and nutritionists. Prebiotics and probiotics should be included in your diet several times per week. Everything you ingest affects your biology for better or worse, but it particularly affects your immune system. All in all, what should be clear is achieving longevity of your biological soul must include your diet and the biome of the bowel, which have been teaching your immune system good from bad since and before you were born. And to live your healthiest life, don’t miss this life-saving advice I’m a Doctor and Here’s the #1 Sign You Have Cancer.

Robert G. Lahita MD, Ph.D. (“Dr. Bob”), Director of the Institute for Autoimmune and Rheumatic Disease at Saint Joseph Health, is the author of Immunity Strong.