Antibiotics save lives, but they also wipe out a lot of beneficial organisms that our bodies rely on, says Martin Blaser. João Canziani

We're in the midst of an extinction crisis, and it doesn't involve Siberian tigers. Microbiologist Martin Blaser of New York University School of Medicine says that many species of germs are disappearing from our bodies—and that's a problem.

In his new book, Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, Blaser argues that while antibiotics have saved countless lives, they're an assault on our microbiome. His experiments have linked the resulting extinctions to disorders from asthma to obesity. wired spoke to Blaser about the need to look at our bodies less as battlefields to be conquered and more as gardens to be tended.

You've studied the Helicobacter pylori bacterium, which causes ulcers and gastric cancer. That sounds like something you would want to wipe out.

H. pylori is responsible for 80 percent or more of stomach cancer cases. But as we were studying it, we kept finding it in healthy people all over the world. I began to think, "Well, if everybody has it, maybe it's not so bad."

What's so good about it?

Our research shows that people who have H. pylori are less likely to have childhood-onset asthma and hay fever.

If one species can have that effect, it's fascinating to think about what all the other species we harbor are doing. How many species are we talking about?

The average person probably has at least several thousand. But we don't really know. We're in the early days of discovery.

And where are all these germs?

Maybe everywhere. Each of the major skin zones—oily skin, moist skin, and dry skin—has its own predominant microbiota. The mouth is a very rich ecosystem: Each tooth has its own series of niches. The top of the tongue and the bottom of the tongue are different. Where the tooth goes into the gum, what's called the gingival crevice, that has a very rich microbiota—it's probably as bacterially dense as the colon. But obviously smaller volume.

So what do all these bacteria actually do for us?

They help us extract energy from food. We've outsourced the ability to make certain vitamins to our microbes. And then there's defense: The good guys help us fight off the bad guys. They can also affect the brain, because a lot of serotonin is made in the gut by neuroendocrine cells that are in conversation with the microbiota.

Where do the antibiotics come in then?

"Why don't we just give some antibiotics, because it can't hurt?" That's how people think—doctors and patients alike. But our data says it does hurt. So we're going to have to change our approach. If every time a baby takes a course of antibiotics, it's going to increase their chance of getting diabetes or Crohn's disease or obesity or asthma, maybe doctors will say, "Well, this is not without risk, so let's wait a day and see if your baby gets better."

My hypothesis is that every time someone takes antibiotics, a few species go to extinction in that person. I don't have proof of this. But we know that the popu­lation sizes of some of the organisms are pretty small. For 50 or 70 years, every­body thought that if you take an antibiotic it will have some short-term effects and then everything will bounce back to normal. But why should they bounce back? If certain less common organisms disappeared, we might not even know.

So how can we take fewer antibiotics but still use them when they'll save our lives?

We need better diagnostics so we can tell bacterial infections from viral ones. And if it's a bacterium, which one is it? We'd have to develop drugs for each. That's a sea change from the impetus over the past 70 years to create broad-spectrum antibiotics. We can either pay for the development of the diagnostics and the drugs, or we can pay for it at the clinic with the illnesses that are coming from this.

What about hand sanitizers?

I have a small photo gallery: When I see a hand sanitizer in a new place I take a picture of it. They're very important in hospitals, but what's the rationale for hand sanitizers everywhere? They don't have antibiotics in them, but they have antibacterials like triclosan. Triclosan is in our soaps and our deodorants, in our clothes, in our pizza cutters, in our staplers. It's everywhere. This is a germophobia that is unsupported.

What do you think of the probiotics sold in grocery stores?

In general they're safe—they don't seem to be associated with health problems. But with few exceptions, they haven't been tested in rigorous clinical studies. The future will hold a lot of probiotics, but we're going to have to discover what their specific activities are and when we need to use them. Maybe there will be particu­lar bacteria that are good to give to kids with asthma. Maybe if there's one that turns off Th1 immune cells, that will be a good probiotic for people with rheuma­toid arthritis. I think we'll be able to harness these microbes, just as we've har­nessed the microbes that make bread and beer for us.