Are your kids too clean? Microbiome research reveals dangers of killing germs

Brontë, 4, relaxes as sister Bridget, 3, runs around in the background Friday in Fair Oaks. Their mother says parents can fixate on super-cleanliness.
Brontë, 4, relaxes as sister Bridget, 3, runs around in the background Friday in Fair Oaks. Their mother says parents can fixate on super-cleanliness.

Parents have made an enemy of bacteria for years. They’ve sanitized tabletops, disinfected playthings and wiped down grocery store carts to keep their children safe from unseen germs.

That instinct is a natural one, experts say, but emerging research about the body’s bacteria, fungi and other cells that cover our skin, gastrointestinal tract and other areas suggests that we may be taking hygiene vigilance a little too far. That, in the long run, weakens our immune systems.

Scientists are only beginning to understand the millions of microbes that make up the human microbiome, said UC Davis microbiologist Jonathan Eisen, but researchers are finding that antibiotics, household disinfectants and other sanitizing products are also killing the “good bacteria” that help our bodies fend off disease. Many believe that the shortage of certain microbes explains recent spikes in childhood allergies and asthma.

“Our skin, anything we eat, any orifice or opening, is going to be exposed to microbes and get microbes on it and in it,” said Eisen, who jokingly calls himself a “guardian of microbial diversity.” “We’re at the point where we’re way too haphazard with killing microbes because people think they’re bad. There’s reason to believe that there are short- and long-term consequences, and we shouldn’t use these things unless we need them, and we should use them with caution.”

People in developing countries, who grow up in less sterile environments, eat mostly non-processed foods and spend more time around people and animals, have more varieties of microbes in their gastrointestinal tracts than people in the United States, recent studies show. At the same time, food allergy rates are lower in Africa and South America than in North America, Western Europe and Australia, according to the World Allergy Organization. The findings play into the “hygiene hypothesis,” or the idea that childhood infections acquired through unhygienic contact bolster the immune system against disease later in life.

Erin Byerly, a Fair Oaks parenting blogger and mother of two daughters, said there’s an expectation for American parents to keep their kids ultra-clean. Many are cautious about letting their children play in dirty places, and some even request people use hand sanitizer before touching their babies, she said.

After doing her own research about germ exposure, Byerly decided to stop worrying about dirt, dust and anything else her 3- and 4-year-old daughters might get into.

“There’s a lot of guilt with parenting and wanting to do a good job, and there’s a belief that clean is good and therefore cleaner is better and safer,” Byerly said. “It went way beyond what would have been natural. … No matter how sanitized you make an environment for a little child, they’re going to eventually grow up and be around these germs, and if their body isn’t equipped to handle it, it’s going to be a bad idea.”

Of course, too many germs can also carry risks for children, said Dr. Ralph Morris, a Minnesota physician. He helped found the “Moms Against Cooties” campaign, run by the chemical-industry-sponsored Water Quality and Health Council, to inform parents about proper infection prevention.

Let children get dirty, he said, but stay vigilant about surfaces that pose distinct health risks, such as bathroom surfaces and kitchen counters – especially after working with raw meat.

“It’s really all about a balance between exposure (to) and avoidance of environmental pathogens,” Morris said. “It’s important to have basic cleanliness and sanitation, but I think sometimes people go overboard.”

So what is the microbiome anyway?

The microbiome is made up of trillions of bacterial cells that we pick up from the world. They’re mostly concentrated in the gastrointestinal tract, but they also live in the lungs, mouth and other parts of the body.

Microbes assist in food digestion and trigger the immune system to fight illness. Some microbes appear to contribute to weight gain and others cause inflammation. A difference in microbial makeup can predispose people to certain diseases or change the way they react to drug therapies.

Recently, some doctors have been prescribing fecal transplants, essentially a dose of good microbes via fecal matter, to patients whose guts are plagued with harmful bacteria such as Clostridium difficile. The transplant of healthy microbes helps patients repopulate their gastrointestinal tracts with good bacteria.

While researchers have long suspected microbes played a role in health, they’ve only been able to study the organisms in small batches in petri dishes, said David Mills, a UC Davis microbiologist who studies the infant microbiome. Thanks to improvements in DNA sequencing over the last decade, Mills and others can now witness “communities of microbes in all sorts of environments, in levels of resolution and numbers of samples that were just insane to think about before,” he said.

Scientists can now identify gut bugs, decipher what they do and find ways to keep them healthy.

“We’re starting to think of all these microbes of an organ,” Mills said. “Our microbiome is shaped by our diet, and our antibiotic use, and the sterile environment we live in. … Once you get your microbiome, however you get it, it can stick with you for a while.”

How is it formed?

Germ exposure starts in utero and keeps forming through adulthood, making the first few months and years of a child’s life a crucial time for building a healthy microbiome.

Many experts, including Roseville allergist and immunologist Dr. Travis Miller, believe the ways babies are delivered help determine their future health. Babies born vaginally take in healthy microbes from the birth canal, organisms that babies delivered by cesarean section don’t pick up, Miller said. That may place C-section babies at a disadvantage from the get-go, he said.

One study from Henry Ford Hospital found that babies delivered by C-section are five times more likely than vaginally born babies to develop allergies, coinciding with climbing U.S. allergy rates over the last decade. A recent report from Harvard’s T.H. Chan School of Public Health showed babies delivered by C-section also have a 15 percent higher risk of obesity. Both studies pointed to the absence of birth canal microbes as a possible explanation.

Studies find that young children who are kept too clean may lack microbes with “toll-like receptors,” which tell the immune system to form antibodies against certain pathogens, Miller said.

“If those receptors aren’t being stimulated, the cells aren’t being triggered to make the protective response and the allergic response takes over,” he said. “The allergic engine is set, and you just need fuel – peanuts, grass, dust mite, the whole gamut.”

Breast milk also plays a key role in kicking off the microbiome, said Mills, of UC Davis. The complex sugars in human milk feed a microbe called Bifidobacterium infantis, which babies get from their mothers. Once the B. infantis microbes are established, they get to work keeping bad germs out of the bloodstream.

Without this breast-milk-fueled bacteria to protect it, a newborn’s gut is more vulnerable to harmful microbes, Mills said.

“The end products of B. infantis growth on breast milk prevents bad things from growing,” Mills said. “Milk is, in a sense, farming what actual survives and persists in the gastrointestinal tract. It encourages certain organisms, and it discourages certain organisms.”

How dirty is dangerous?

Land Park mother Amanda Bauer said she tries to be careful about keeping her two young daughters clean. She doesn’t carry hand sanitizer around with her, she said, but always makes sure her 7- and 9-year-olds wash their hands after going to the grocery store. Around the house, she cleans off door handles, remote controls and other heavily touched items with Lysol wipes, especially when someone is sick.

“I’m big on washing hands after they touch places where many people have touched,” she said. “But I’m not obsessive about it, because too clean isn’t too healthy either.”

Recent science supports Bauer’s beliefs. A study from Swedish researchers found that children whose families washed dishes by hand had significantly lower rates of eczema and slightly lower rates of allergies than children whose families used a dishwasher. Other studies have shown children who live with dogs and cats tend to be healthier because the pets pass on their own beneficial microbes.

That runs counter to how many American children are raised. Most are born in sterile emergency rooms, play in sanitized day care and eat washed produce. American children receive, on average, between 10 and 20 courses of antibiotics before they reach adulthood.

While those interventions have saved millions of lives, they also have robbed American children of important germs, Eisen said.

“Parents can start to try and think like a gardener or an ecologist. It’s not just about feeding your kids and protecting them from dangers – it’s about nurturing their ecosystem in some way,” he said.

On a recent Friday morning, Byerly watched her two daughters, Brontë and Bridget, play barefoot in their backyard, occasionally lying down on the back patio or climbing atop a scooter. When Brontë picked up a small, plastic dog bone in her mouth and crawled around imitating her pet, Byerly didn’t panic. She just laughed and asked her daughter to put it down.

“I see it as a little inoculation every time,” Byerly said. “I clean up major things; obviously I don’t let them roll in anything really foul. There’s a difference between everyday germs and scary germs.”

Sammy Caiola: 916-321-1636, @SammyCaiola

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