We know which species make us sick, but we must learn which species make us healthy.

It was a revelation. Germs cause disease. When Louis Pasteur and Robert Koch discovered and developed what would later be called the germ theory in the 1860s, this was a radical, then revolutionary idea—one so good it seems obvious in retrospect.

At the heart of their work was the notion that individual species cause disease by invading our bodies. Over the next century, the notion of “germs” changed our behavior. It led us to scrub our hands and actively fight specific pathogens (as researchers came to call dangerous germs) and to cure the diseases they cause. These changes saved millions, maybe billions of lives. Every day you rub shoulders with the success of this theory. How could there be anything wrong with it?

New research, however, is beginning to question, if not germ theory itself, at least some of the actions we have taken on its behalf. These studies come from very different groups of scientists, largely working separately and apparently without much awareness of one another. But I believe that they are unwittingly part of the slow unraveling of a new, broader theory of disease, the ecological theory of disease.

Here’s the thinking. In the late 1980s, microbiologists and public-health researchers began to notice differences between rural and urban kids. Rural kids seemed less likely to develop allergies. A new idea was floated—perhaps they had been exposed to more bacteria that had helped their immune systems to “balance” themselves. This idea, often called the hygiene hypothesis, has since found support in empirical studies worldwide.

Country kids whose fingers still plunge regularly into the rich bacteria of soil (and farm animals) have fewer allergies. But it isn’t just farm living: Sometimes the exposure to a wilder bacterial life can be subtle. For example, a recent study in Australia found that pregnant mothers living with dogs were less likely to have children with allergies. These studies note fundamental differences between the immune systems of dirty kids and clean kids. Conclusion: In some ways it is better to be dirty.

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