We study the responses of microbial communities and isolated microbes to external stress 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, chemotherapeutic agents and other stressors. Understanding how these extracellular stressors affect our microbiome will provide critical biological insight into the development of dysbiosis, disease, and antibiotic resistance. Relying on recent advances in high-throughput DNA and RNA sequencing, we are studying the effects of antimicrobial agents on these highly complex microbial communities to identify microbial mechanisms that lead to improved antimicrobial tolerance and the development of resistance.