Stephen Lory’s entire scientific career has been devoted to the study of Pseudomonas aeruginosa, a bacterium that is widely distributed in the environment and an important human pathogen. During his postdoctoral studies at Harvard, he studied the secretion of protein toxins from P. aeruginosa, which he continued in his laboratory at the University of Washington, leading to the discovery of the type II secretion system. Here he also became interested in microbial genomics and participated in a project that resulted in the sequencing of the first P. aeruginosa. He developed the first microarray for P. aeruginosa, which allowed researchers to define its transcriptome in a wide range of environments. After moving to Harvard in 2000, he was one of the first researchers in the field of cyclic nucleotide signalling. His current work uses deep sequencing as a tool to understand bacterial evolution and the role of small regulatory RNAs in regulating gene expression. He is an active reviewer of manuscripts and grants for the NIH and the Cystic Fibrosis Foundation and has published over 140 articles in peer-reviewed journals.