Too Clean for Our Children’s Good?

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The Checkup

When a toddler’s pacifier falls out of his mouth and onto the ground, does it get confiscated and boiled by anxious parents or just licked off and reinserted by the more casually inclined?

Many parents, quite reasonably, worry about germs and dirt finding their way into a child’s mouth. But many have also heard in recent years of the “hygiene hypothesis,” which holds that some exposure to germs and microorganisms in early childhood is actually good for us because it helps develop the immune system. A 2013 Swedish study, for example, showed that children whose parents just sucked their pacifiers clean had a lower risk of developing eczema.

When we talk about the hygiene hypothesis, the collection of theories that address the possible problems that can be associated with growing up less exposed to germs and dirt, we are essentially talking about growing up indoors. We’re talking about living in a world of relatively clean and controlled surfaces, where even small children who are constantly picking things up and putting them in their mouths are not going to come into contact with a very wide variety of exposures.

“The built environment is the place in which our children grow up,” said Jack Gilbert, the director of the Microbiome Center and a professor of surgery at the University of Chicago. He was one of the authors of a well-known 2016 study in The New England Journal of Medicine which compared the immune profiles of Amish children, growing up on small single-family farms, and Hutterite children, who are similar genetically but grow up on large, industrialized farms. The Amish, living in an environment described as “rich in microbes,” or alternatively, full of barnyard dust, had strikingly low rates of asthma.

Dr. Gilbert is a co-author, with Rob Knight and Sandra Blakeslee, of a book on the topic coming out in June called “Dirt Is Good: The Advantage of Germs for Your Child’s Developing Immune System.”

For the last century and a half, he said, since understanding that microbes cause disease, human beings have tried as hard as possible to wall off their bodies from the microbial world of bacteria, viruses and fungi. “We’ve deliberately separated ourselves for reasons of comfort and reasons of fear of disease.”

And it’s worked; there’s no question that increasing hygiene has saved many children from sickness and death. Scrupulously separating children from the microbes that can be found in impure water, for example, or unpasteurized milk has played a major role in reducing infant and child mortality, enabling millions of children to live and thrive. But we’ve also come to ask, in recent years, whether children who are too completely walled off from the microbial surroundings in which our species evolved may grow up with some negative consequences of our ever-cleaner homes.

That separation actually starts even before a baby is brought into its clean home environment. “All mammals are born heavily inoculated with bacteria from the maternal birth canal,” said Maria Gloria Dominguez-Bello, an ecologist who is associate professor in the Human Microbiome Program at New York University School of Medicine. For breast-fed babies, the nursing period is generally one of lower environmental exposure but intense maternal exposure, she said, and then, after weaning, babies enter a period of much more interaction with the microbes around them.

“The end of the strict lactation period is the beginning of a very intensive environmental exploration,” Dr. Dominguez-Bello said. “That happens to all mammals including our kids that lick everything they find — by the time the lactation period ends, the last half of it has been of mixed feeding milk and solids, and then we are supposed to be ready to face the world.”

Modern human habits, she said, can interfere with this early exposure at every turn; babies may be born by cesarean section, without exposure to the birth canal and its bacteria; they may be bottle-fed instead of breast-fed; they may sleep far away from their mother; and they may well be treated with antibiotics for one infection or another. (The American Academy of Pediatrics recommends breastfeeding for the first year of life, and recommends that infants should sleep in the same room as their parents but on separate safe surfaces to reduce the risk of sleep-related deaths.)

In a study published in 2016, on which Dr. Dominguez-Bello collaborated, scientists profiled the microbial development of a group of babies in the United States, examining the ways in which their bacterial populations were affected by mode of birth, by formula feeding versus breast-feeding, and by antibiotic exposure. In her research in the Amazon basin of South America, she said she has found that in rural houses and huts, most of the bacteria are related to the surrounding environment. In such settings, she said, the mother is more likely to carry the baby, and to sleep with the baby, both of them exposed to bacteria from plants and soil.

As houses become more enclosed and more subdivided, she said, spaces are increasingly separated by areas of use, and the speed at which outside air replaces inside air is decreased. “What happens is, we reduce the exposure to external environmental bacteria, so we become the main source of bacteria, our skin, our mouth, we shed bacteria, and the house becomes highly humanized, most of the bacteria in a house in a city will be human,” she said.

Walls, she said, are the best bystanders, revealing what is going on in a house, because they are not usually cleaned. After many years, she said, “you find highly oral bacteria near the sink,” fecal and vaginal bacteria “near the toilet,” and skin bacteria “in the rest of the house.”

So we need to study the health consequences of the built environment, even the more modern and more “hygienic” built environment, which is a complicated place, and by no means sterile.

“We used to live in much dustier environments,” said Marsha Wills-Karp, a professor of environmental health and engineering at the Bloomberg School of Public Health at Johns Hopkins University. Still, she said, though houses are cleaner, the built environment contains many components, including chemicals and airborne particles, not just microbes.

“Studies have shown that priming or seeding of the microbiome in the child is absolutely critical,” she said. “While you don’t want to go out and expose your child to aggressive infections, you don’t want to create such a sterile environment that their immune system doesn’t develop normally; it puts them at risk of developing immune diseases.”

And what we have learned, Dr. Gilbert said, is that early life exposure to microbes can shape not only the immune system, affecting a child’s likelihood of developing autoimmune conditions like eczema and asthma, but also the endocrine system, and even the child’s neurodevelopment.

“Different bacteria and fungi affect different diseases differently, and affect different children differently,” he said. “We don’t understand the interactions between the immune system, the genome, and all the other components of the body as well as we could.”

In an article published last October in the journal Microbial Technology, Dr. Gilbert speculated that it might be possible to develop vaccines that would help children’s immune systems develop by providing controlled exposures to some of the most important microbes and microbial components. An alternative approach would be to educate parents about defining the kinds of natural exposure that might be most helpful, given the specifics of their children and their communities.

“There are definitive ways to embrace the controlled exposure or uncontrolled defined exposure to that rich microbial world early in life,” Dr. Gilbert said.