For most people, the thought of drinking a glass of live bacteria is about as appetizing as downing a cup of lake water. But bacteria is what were buying when we succumb to the probiotic craze that has swept supermarket shelves.

Probiotics are microorganisms that wiggle through yogurt, kefir and other fermented foods, then take up residence in our intestinal tracts. Scientists used to see them, at best, as hitchhikers in the body, and at worst, the cause of sickness and disease.

But now they believe the trillions of microbes that swarm through us play a key role in keeping us healthy hence the avalanche of probiotic foods, supplements and household products now available for sale. One company touts its "ProBugs" kefir, and there are even probiotic mattresses and air fresheners that spritz microbes into the air.

While doctors downplay the effectiveness of supplements touting probiotic benefits, they acknowledge the change may be jarring for families that have been told for decades that they should be killing bacteria with antibiotics and sanitizing sprays and wipes.

Until recently, we presumed that all bacteria were potential pathogens. And while we were doing a great job of eradicating infectious disease, we were seeing an increase in allergic and autoimmune disease, in which the immune system attacks itself, said Dr. Darla Shores, a pediatric gastroenterologist and assistant professor at the Johns Hopkins University School of Medicine in Baltimore. "We now know that 'good' bacteria are very important to normal immune system function."

That's one reason Julie Thompson, a mother of six in Provo, Utah, serves her family a diet heavy in fermented foods, such as sauerkraut, sourdough bread and homemade yogurt.

Thompson said she can tell a difference in her children when theyve consumed too much "bad" food outside the home, and she believes the regiment keeps the family healthy.

I personally can tell a difference in my own health physically, emotionally and even spiritually when Im eating foods that are good for me, she said, noting that fermented foods are the original probiotics, used to promote health since ancient times.

Fighting the wrong battle

The war on microbes began in the late 19th century when scientists realized that germs caused disease and we set out to kill them with pasteurization, sterilization, chlorinated water and an array of antibacterial products that now include antibacterial clothing and paint.

This improved public health and is one reason for our increased lifespans. But tens of thousands of helpful microbes die every time we try to wipe out the bad ones, and in recent decades, scientists have hypothesized that reducing exposure to microbes has weakened our immune systems.

Weve been in this crazed, antibacterial, antiseptic world where we think bacteria are the enemy, but the right bacteria are our friends, said Dr. Vincent Pedre, an internist in New York City who specializes in gut health.

Moreover, it looks like the eradication of helpful bacteria has been especially damaging to children.

Microbes that colonize the intestinal tract in the first 100 days of life help determine whether children develop allergies or asthma, how they fight off other infections and disease, and if they become obese, says Marie-Claire Arrieta, an assistant professor at the University of Calgary and co-author of Let Them Eat Dirt.

For children to be healthy, their intestinal microbes have to be healthy, too, and microbial health is determined by factors as diverse as what children eat, the medicines they take, how much time they spend outside, and even how they were delivered. But research has shown that this community of animalcules that live in our bodies can be changed, and in relatively short time in ways both good and bad.

Small things considered

In the womb, babies have no microbes at all; they begin to acquire their collection at birth. Babies delivered vaginally get a dose of their mothers microbes as they swallow amniotic fluid and move through the birth canal; in essence, they get a bath of beneficial microbes that are crucial to development, Arrieta said.

Babies born by C-section, however, start with a disadvantage; their first microbes come with contact of skin in a sterile operating room. This is thought to be such a problem that researchers are looking into how to transfer the microbes in other ways, such as swabbing the baby with gauze dampened with the mother's bodily fluids.

The microbe colony is also influenced by how much weight a woman gains during pregnancy and whether the baby is breast-fed or receives formula. "Also, if you are hospitalized in the NICU or need antibiotics, that may change which organisms set up shop in you. Its not one particular event, but a whole host of factors," Shores said.

The medical term for a microbe imbalance is dysbiosis, and it has been linked to a range of disorders that include inflammatory bowel disease, metabolic syndrome and asthma. Research done by Arrieta and her colleagues suggests that taking antibiotics in infancy makes children more likely to develop asthma because the medicine destroys protective bacteria.

"Our findings indicate that in humans, the first 100 days of life represent an early-life critical window in which gut microbial dysbiosis is linked to the risk of asthma and allergic disease," Arrieta and her co-workers wrote in their report.

In another study, scientists implanted feces from obese mice into thin ones, and found the thin mice gained weight, suggesting that microbes play a role in how we process energy.

While the connection is a hypothesis, not yet proven in humans, there is really strong suggestive data that makes a case for taking better care of our microbiomes, and those of our children, Arrieta said, adding that diet "affects the microbiome the most.

Good bacteria thrive on fiber found in raw vegetables and fruits, as well as fermented foods, which is one reason parents should introduce these types of foods as soon as babies can eat them, said Pedre, the New York City internist and author of a book called Happy Gut.

The father of a 12-year-old who loves salad, Pedre said he introduced his son to vegetables early in life by giving him pureed soup in a bottle. Its important to expose babies to a variety of foods and flavors while theyre receptive to everything.

What I tell people is to eat the rainbow. Eat the rainbow of foods that come naturally from the earth. Diversity is the key to health; you dont want a narrow microbiome. Its pretty simple, but you have to start when theyre really young.

Probiotics pros and cons

In his book I Contain Multitudes, Ed Yong, a writer for The Atlantic, argues that, contrary to their reputation as champions of microbe health, probiotic products found in supermarkets such as yogurt and kefir do minimal good because they contain bacteria that are transient and chosen not because of their importance to humans but because they're good travelers and easy to grow.

Arrieta agrees that such products are typically not good invaders of the gut.

Its really hard for any new species to go into an established ecosystem and stay; normally, ecosystems reach a balance and its hard for an invader to come in, she said.

She also notes that, like other health supplements, the Food and Drug Administration does not regulate the manufacturers claims. I could make a probiotic today and sell it tomorrow, and I wouldnt have to prove that its effective, only that its safe, she said.

As for probiotic pills and capsules available in the U.S., she encourages people to look at evidence of their effectiveness from scientific studies, available at a website, USprobioticguide.com.

Researchers are still learning what long-term effect, if any, probiotics have on our health, Shores said. As for supplements in pills, they are useful for certain health conditions, such as if someones microbiome needs to be rebuilt after using antibiotics, but I dont think an otherwise healthy person needs to be on probiotic supplements to have a healthy microbiome, as long as natural sources of probiotics are obtained from the diet," she said.

The care and feeding of microbes

Until a few years ago, the word gut was mostly used to describe a beer belly, Pedre said. With the advance of research on microbes, its now commonly used to describe gut flora, the garden of microbes that populate our digestive system not just the stomach and intestines, but supporting organs like the liver and pancreas. Together, those organs comprise the enteric nervous system, populated by more than 200 million neurons that communicate with the brain but operate independent of it.

The gut is sometimes called the body's second brain, and its processes can affect our moods, which is why anxiety and fear is sometimes experienced as butterflies in the stomach or gut feelings.

Conversely, when things are good in the gut, it positively affects our mood and behavior. Animal studies suggest the introduction of beneficial bacteria can improve anxiety and depression, and there is ongoing research about the benefits of fecal transplants in human beings to combat obesity.

But there are many things families can do to ensure good gut health, like making homemade kefir, avoiding antibiotics and antiseptics except when medically necessary, getting a dog, and letting your children play in dirt and go barefoot in grass.

Ultimately, building a healthy microbiome depends most on feeding children a diverse diet that is low in sugar and high in fiber. Arrieta also says she gives her children a fermented food every day.

If your children are reluctant to trade hot dogs and French fries for brown rice and broccoli, Arrieta suggests trying something that worked for one of her friends.

She told them that they have little bugs and critters living inside them, and the only thing they eat is vegetables, and if they dont get to eat vegetables, they will die. Faced with the knowledge that their inner pets would suffer if they didnt eat right, the children were more willing to eat more things.

Its not that they love broccoli, but they do it, Arrieta said.