Your body hosts multiple microbial communities — in the gut, on the skin, in the lungs, and elsewhere. This collection of flora, better known as the microbiome, is home to more than 38 trillion bacteria. And they’re not alone: Viruses outnumber bacteria in the microbiome by about 10 to one, with an estimated 380 trillion viruses making up what is now called the “virome.” A healthy dose of fungi and protozoa keep them company.

“We all carry around a massive load of microbes,” notes immunology expert Mary Ruebush, PhD, author of Why Dirt Is Good: 5 Ways to Make Germs Your Friends. “The very fact that you have so many microbes of so many different kinds is what keeps you healthy most of the time.”

Some of the viruses in the micro­biome, called phages, help manage our bacterial populations; they act as natural antibiotics that target harmful bacteria while leaving helpful bugs alone. Others were long ago incorporated into our DNA, driving the evolution of the placenta, among other things.

The diverse flora that compose a healthy microbiome compete, interact, and generally occupy a lot of space, explains Ruebush. As with a thriving garden that crowds out weeds, there’s not much room left for the minority of bacteria that are dangerous to humans. “They generally can’t get enough of a foothold to start reproducing fast enough to outplace the normal flora.”

Well before 2020, healthcare providers had begun to recognize the health benefits of a thriving micro­biome. They were also realizing that an overzealous approach to cleanliness could have grim consequences for it.

Well before 2020, healthcare providers had begun to recognize the health benefits of a thriving micro­biome. They were also realizing that an overzealous approach to cleanliness could have grim consequences for it.

Some healthcare providers began to suggest less-frequent showering. Triclosan and 18 other antimicrobials were banned from household and personal-care products as researchers grew more concerned about the chemicals’ contribution to antibiotic resistance. And some of us began making our own fermented foods to cultivate more diverse microbial populations in our guts — or at least eat more high-quality yogurt.

Then along came a new corona­virus, knocking the microbiome out of the spotlight. Hand sanitizer, antimicrobial wipes, face masks, and gloves became features of everyday life. Even as research made clear that surfaces were not the primary mode of transmission, many of us felt reluctant to abandon sanitizing rituals: They helped us feel like there was something we could do to protect ourselves and one another.

Today, as the pandemic continues to evolve, we’re equipped with new forms of protection: vaccination, natural immunity, more knowledge, and better treatments. Meanwhile, our renewed attachment to hyper­sanitizing might actually be weakening our immune systems, even as we strive to help them thrive and protect us from whatever comes next.

Learn why developing a more accurate understanding of the risks and rewards of microbial exposure can leave us even healthier and better protected in the long run.

Microbes and Immunity

That thriving garden of bacteria, ­viruses, fungi, and protozoa in the micro­biome both trains and develops the immune system, playing a critical role in preventing illness. A depleted or imbalanced microbiome can leave us more susceptible to infection by bacteria, viruses, and parasites. It’s also associated with certain types of cancer, autoimmune diseases, and chronic conditions such as irritable bowel syndrome.

The seeds of our protective micro­bial garden are planted mainly in childhood. The “old friends” hypothesis argues that early exposure to beneficial microbes (the “old friends”) that co-evolved along with humans is essential for the immune system to develop properly. These microbes teach the immune system to recognize invaders and react to them appropriately.

“If you don’t have that exposure, the immune system doesn’t get educated.” And a poorly educated immune system is prone to misbehave.

“If you don’t have that exposure, the immune system doesn’t get educated,” explains Mitchell Grayson, MD, chief of the Division of Allergy and Immunology at Nationwide Children’s Hospital in Columbus, Ohio. A poorly educated immune system is prone to misbehave.

“Our immune system is designed to negotiate life with microbes,” explains functional-medicine physician Kara Fitzgerald, ND, IFMCP. “If you take the microbes out, our immune system is still going to react, often against the self — with autoimmunity — or against a benign environmental compound, such as pollen, dander, or food, as happens with allergies.” (For more on allergies, see “Taking On the Allergy Epidemic“.)

The more diverse organisms you’re exposed to as a child, the more likely you are to have better protection from illness. You’re also less likely to ­develop immune disorders. “In the first 10 years of life, we’re hardwired to be experimenting with the environment immunologically,” explains ­Ruebush. “If the body is happily ­occupied dealing with things that could endanger it, then it’s not developing allergies, asthma, and autoimmunity.”

Eager young immune systems find their microbial teachers mainly through contact with other people and the great outdoors. In the United States, Amish children who grow up interacting with animals, soil, and airborne sediment and microbes on their farms report lower rates of asthma and allergies than their genetically similar counterparts whose communities use modern agricultural technology.

Researchers have concluded that the hands-in-the-dirt life of the Amish produces less-reactive airways and lower levels of allergy-related cells. This is just one example of support for the hygiene hypothesis, which states that too much cleanliness leads to immune dysfunction.

In the 2000s, Finland was found to have the world’s highest rate of autoimmunity-based type 1 diabetes among children. Finland shares a border — as well as a genetically similar population and subarctic environment — with Russia; there, however, the rate of type 1 diabetes was six times lower.

Researchers found that Russian children spend the first years of their lives fighting off a host of infections, including hepatitis A, the parasite Toxoplasma gondii, and the stomach bug Helicobacter pylori. These exposures are far less common across the border in wealthier Finland.

Without question, industrialized nations’ advances in sanitation have prevented countless early deaths — but the flip side of this positive development is that they may also be contributing to immune disorders. “In modernized societies where we bathe every day and use antibacterial soaps, our higher rates of autoimmunity and allergies might be related to us being too clean,” says Grayson.

One in 12 Americans is diagnosed with an auto­immune condition (a number that’s rising steadily); industrialized nations in Asia are catching up.

Exposure to other people matters, too. A study published in 2020 found that most toddlers who engaged with multiple kids in a childcare environment were better protected against developing asthma than those who stayed home. And kids living with older siblings tend to report lower rates of asthma and allergies, possibly because they’re exposed to their siblings’ germs at a young age. Pets also play a salutary role.

In short, letting kids play in the dirt, preferably in the company of other children, seems to be a great strategy for long-term immunological health.

“When you create a hygienically controlled atmosphere, diseases like autoimmunity and allergy can occur,” notes Fitzgerald. “Paradoxically, what you don’t want to happen can happen. The wholesale damage from an ­attempt to control microbes leads to less immunological control.”

The Gut–Skin Axis

The gut microbiome is not the only garden worth tending. The skin has a community of microbes of its own — one as large and diverse as that in your gut.

“The skin and the gut are both massive organs at the interface of self and not-self, and the skin- and gut-­associated immune systems are ­responsible for making decisions around what’s safe and not safe, what to react to or not,” says Fitzgerald. “Further­more, what’s happening on the skin can influence the gut, and what’s happening in the gut can impact the skin.”

The intimate relationship and communication between these organs is called the gut–skin axis. Both can affect the immune system.

The skin is a barrier that repels bad bugs, antigens, toxins, and harmful UV light, Fitzgerald explains. It relies on a thriving microbiome for its integrity.

“If we disrupt that with excessive hygiene or toxins in the lotions and potions we put on, we’re disrupting this living, interacting ecosystem and breaking down that barrier.”

“If we disrupt that with excessive hygiene or toxins in the lotions and potions we put on, we’re disrupting this living, interacting ecosystem and breaking down that barrier.”

In his book Clean: The New Science of Skin and the Beauty of Doing Less, James Hamblin, MD, explains how bathing temporarily alters the skin micro­biome, either by removing some microbes or altering the resources available to them. And that’s not always a good thing.

“Like the microbes that fill our guts, the microbes on our skin rarely cause disease,” he writes. “If anything, they may help protect us from disease.”

Handwashing is a time-tested strategy for warding off contagious bugs and harmful pathogens. Yet there’s wisdom in not overdoing even this protective measure.

Creating holes in the skin’s micro­bial garden creates openings for weeds — those less desirable bugs — to take up residence. Along with the excessive use of antibiotics, antibacterial soaps and cleaning products are driving the evolution of “superbugs” — pathogens that can’t be killed by the usual sanitation methods or drugs.

The best routine, says Ruebush, is good old soap and water. “Warm, soapy water is good enough for just about anything you want to clean.”

The Immunity Muscle

During 2020, much of the world didn’t experience normal cold or flu seasons. Although COVID ran rampant, other common viruses were notably absent, including respiratory syncytial virus (RSV), a highly contagious virus that normally circulates in the winter and can be particularly dangerous for children.

When RSV made a surprising, out-of-season return in the summer of 2021, it caused dramatic spikes in child infections and hospitalizations around the world. Experts blamed the surge on “immunity debt” — the failure to build up immunity against common viruses, in this case due to widespread mitigation measures for COVID.

How does the immune system usually stay up to date and out of debt? Through exposure.

Whether from vaccination or infection, the immune system learns how to combat pathogens through practice. (Vaccines act more like a friendly ­tutor to the immune system; infections provoke a real-time battle.)

Like a muscle, the immune system needs exercise to stay in shape. “White blood cells multiply in response to challenge: Each exposure to a germ gives you more immune cells to respond faster and more aggressively the next time that germ tries to attack.”

Like a muscle, the immune system needs exercise to stay in shape. “White blood cells multiply in response to challenge: Each exposure to a germ gives you more immune cells to respond faster and more aggressively the next time that germ tries to attack,” explains Ruebush.

B and T cells are two critical components of the adaptive immune system. They recognize specific attackers, produce antibodies to destroy them, and regulate the action of other immune cells. These cells can have long lifespans, providing protection against pathogens they’ve met before, sometimes for decades.

“But if we don’t keep them on their toes by showing them they’re doing a great job guarding the environment, they can become quiescent and die,” notes Ruebush. “Then you need to start from scratch, with immune cells learning by bumping into pathogens, which happens slowly.”

Keeping these cells busy helps them stay in fighting shape. “In normal circumstances, if you’re less than perfect about personal hygiene, relaxed about your environment, and hugging people at church, that gives those cells more of a kick in the butt to keep them interested in what’s going on around them,” she says.

There’s even evidence that battling a cold recently may provide some immune protection against the virus that causes COVID.

There’s even evidence that battling a cold recently may provide some immune protection against the virus that causes COVID. In a study pub­lished in Science in 2020, researchers found that T cells trained to respond to common-cold-causing coronaviruses will cross-react to the virus’s spike protein.

Multiple studies have also found that a recent cold correlates to less severe symptoms in those who later contract COVID.

While vaccination remains the best tool to prevent severe outcomes from COVID, this research suggests that keeping your immune system primed by engaging with the world may be a worthwhile addition to your immunological toolkit.

“What keeps our immune response strong is being experienced in dealing with things in the environment and managing them,” says Ruebush. “That makes us stronger and causes us to react more normally to the things around us.”

Striking a Balance

So, what’s the best way to balance the need to protect ourselves from illness and the need to protect our immune systems from depletion?

All of our experts agree that vaccination is a critical tool. “People should be vaccinated for the things we can be vaccinated against,” says Grayson. It’s a gentle and effective way to educate the immune system and keep it on its toes.

Beyond that, Grayson encourages a more relaxed approach to protecting against germs. “Sometimes having a cold is a good thing, because it jazzes the immune response,” he notes.

While the desire to ward off colds and flu is understandable, he thinks masking solely for this may be shortsighted. “At some point, if you stop wearing a mask, you’re not going to have an immune response to that ­virus. Your illness might be more severe ­because your immune system won’t have seen it for that period of time.”

Once you’re vaccinated for COVID,  he suggests, take the long view if you do get an infection. “If you get exposed to COVID as a vaccinated person and have a mild or asymptomatic case, that’s a booster response, and over time you’ll be less likely to get sick from it.”

Fitzgerald adds that hypervigilance can carry immunological costs of its own, noting that “the stress hormone cortisol can suppress the immune system.” Still, she recommends going at your own pace when relaxing protocols, especially if you’re anxious about letting your guard down.

“Don’t push yourself if you’re not ready,” she says. “We need to engage in good immune-supportive self-care and ultimately have our eyes on moving back out toward the world.”

The Facts About Surface Transmission

Most marketing campaigns for cleaning products want you to believe that the surfaces in your environments are teeming with terrifying bacteria and viruses, waiting to leap onto your skin and food and make you ill. You need the company’s arsenal of sprays, solutions, and wipes to keep them at bay.

Not so fast. It’s true that some viruses, such as influenza and respiratory syncytial virus, can transmit via droplets and surfaces — and you really don’t want to share a spoon with an actively sick person. But the risk of catching COVID-19 from surfaces has been overblown.

Research now suggests that COVID spreads primarily through airborne transmission — that is, we breathe it in more than we touch it in. Surface transmission of COVID is rare.

“Research is clear that all the sanitizing we’ve been doing to prevent COVID-19, like endlessly cleaning surfaces, hasn’t been worth the tradeoff. We need to back off of that,” says functional-medicine physician Kara Fitzgerald, ND, IFMCP.

While it might seem like a harmless exercise in caution, disinfecting surfaces does have consequences. Antimicrobial cleaning products don’t discriminate between harmless or beneficial bugs and bad ones. Ridding your environment of good bugs can create more openings for unwanted ones. Wipes may serve to spread germs around rather than destroy them, and each discarded sheet winds up in a landfill.

“I’m not too worried about surfaces,” says immunology expert Mary Ruebush, PhD. “But I do worry about how many chemicals we introduce in our desire for cleanliness, especially around kids.” Not only do many cleaning products contain antimicrobials, but they often also host hormone-disrupting ingredients, like phthalates.

Ruebush notes that pathogens we ingest orally are less likely to cause disease than those we breathe, because they have to live through the acid bath of the stomach. “I’m more cautious with things I’m breathing,” she says. “I try not to touch my face too much, but I’ve gotten rid of chemicals in my home, and I clean with soap and water.”

Article by Mo Perry for Experience Life. This article was originally appeared as “Making Peace with Microbes” in the April 2022 issue of Experience Life.