We study the responses of microbial communities and isolated microbes to external stressors such as antimicrobial agents. This work is particularly pressing because unlike at any other time in human history, we are currently exposed to a wide array of natural and artificial antimicrobial agents in the form of antibiotics, chemical disinfectants, and chemotherapeutic agents among others. Our goals are to improve the efficiency of current antibiotics while protecting the beneficial bacteria that are part of our microbiome.