In Missing Microbes: How the Overuse of Antibiotics Is Fueling Our Modern Plagues, Blaser, director of the Human Microbiome Program at NYU, calls for significant changes to the way that we coexist with microbiota (the microscopic organisms that live within us).

The loss of the “invisible zoo inside of us” may be linked to a host of chronic illnesses on the rise, an idea that’s still widely considered to be almost heretical. How is your research being received?

The very good news is that our work is getting a great reception after being in the wilderness for many years. As a scientist, what you want to do is to make a difference and for your ideas to be converted into action. That’s one of the reasons I wrote the book; there are costs to antibiotics.

Do you think doctors might resent their patients questioning treatment that includes antibiotics?

All the incentives are to prescribe, and the patient thinks if they’re not given an antibiotic, they’re at risk. I want to change the dialogue. The doctor will say, “According to the latest research... there is an increased risk for asthma or obesity.” The doctor will be more cautious and the patient will be more cautious. It can be done if we change our culture.

You suggest a more targeted approach for the treatment of bacterial infections, but how far in the future is that likely to be?

I’m writing the book so it’ll come sooner. We have the ability to figure out whether a pathogen is a bacteria or a virus, but the diagnostics are too expensive. A lot of technology is there or soon will be. We have to make it less expensive. We have to change the economics, especially in the treatment of children.

Are the health care and political environments conducive to these necessary changes?

The longer we continue with the status quo, the worse it’s going to be. I’m sounding an alarm, just as 50 years ago Rachel Carson sounded the alarm. I think we have to change our medical priorities. In the name of cost savings, we’re cutting down the time the doctor can spend with a parent or child. A cheap fix now may lead to lifelong consequences. Reimbursement has the wrong priorities—too much for tests, and not enough for evaluation and thought.

Could you expand a little on the possible link between antibiotic overuse and autism?

I go back to the theory that the microbes in our body are not accidental, they’re there for a reason. My hypothesis is that there’s a developmental cascade; this is how our microbiome is organizing during the time the baby is growing, and it’s involved in the developmental pathways toward adult metabolism, immunity, and cognition.

Do you still think we’ll find ways to reintroduce the microbiota that we’ve destroyed?

You can’t lose ancient organisms without consequences. Sometimes that’s good—there’s less stomach cancer. Sometimes it’s bad—there’s more acid reflux and asthma. Both are linked to H. pylori. I think in the future doctors are going to be giving it back to kids and then, at a certain age, eradicate it so they can get the early life benefit but not the late-life cost.