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In recent decades, the incidence of non-infectious diseases, such as asthma, allergies, diabetes, and others has risen dramatically—a change Martin Blaser of New York University School of Medicine suspects might be due to the increased use of antibiotics, which not only kill pathogenic bacteria, but our bodies’ “friendly flora” as well. In a comment in this week’s Nature, Blaser laid out his approach to understanding the impact of antibiotics on microbiota in humans. The Scientist spoke with Blaser about his travels to the depths of our guts and the Peruvian Amazon to find the answers.