But the link isn’t disease-causing germs. It’s early and ample exposure to harmless bacteria — especially the kinds encountered living close to the land and around livestock and other young children. In other words, dirt, dung and diapers. Just as disease-causing microbes clearly bring on inflammation, harmless microorganisms appear to exert a calming effect on the immune system.

A second misconception common among vaccine-shunning parents is that there’s something “natural” about the 6 to 10 respiratory infections the typical American child gets every year (or even the two to four we adults experience). Common, yes; natural no, not if “natural” represents the forces that shaped the human immune system during all but the last sliver of our 250,000 years as Homo sapiens. Colds, flus and most other contagious diseases found a central place in our lives only after we and our domestic animals began crowding together in large settlements some 5,000 years ago.

Yet the most compelling reason to get a flu shot this year is a new and deadly threat — methicillin-resistant Staphylococcus aureus, or MRSA, a dangerous kind of staph that has been causing outbreaks of deadly pneumonia among the otherwise young and healthy, typically on the heels of the flu.

Unfortunately, we have no practical way to eradicate MRSA. About a third of us silently carry staph at any given time, and trying to eradicate MRSA or any other staph strain from a community of symptom-free carriers is difficult to impossible. Worse, the experts conclude, any widespread effort to do so is certain to breed greater drug resistance.

Flu shots don’t guarantee protection from MRSA pneumonia. It can piggyback on other kinds of viral respiratory infections. But protecting yourself and your children from the flu may be the best way to reduce your family’s risk.

Whether dealing with the flu, other “routine” infections or even the chickenpox, the message is the same: In a world abounding in harmless, even beneficial microbes, don’t embrace the tiny fraction that can make you ill.