Decoding the mechanisms of bacterial life and death

Bacteria do not live in flasks: they navigate physical barriers, compete with neighboring microbes, and constantly fend off viral predators like phages and immunological predators like macrophages, all while trying to infect and colonize us. The Gitai lab is organized around both sides of this struggle: bacteria as formidable invaders of mammalian hosts, and bacteria as targets of phages, antibiotics, and the immune system.

We treat this symmetry not as two separate research programs but as a single ecological lens. The same principles that make bacteria effective pathogens, including their physical organization, mechanical sensing, and remarkable single-cell individuality, also determine how they survive being hunted. Rather than being bound to a single model organism or a favorite technique, we use pressing therapeutic problems like antibiotic resistance as a compass: the most urgent clinical challenges tend to point directly at the most important unsolved questions in basic microbiology.

Following that compass has led us to pioneer mechano-microbiology, develop M3-Seq and Duet-Seq for single-cell transcriptomics, uncover new principles of phage-bacteria conflict, and discover antibiotics with novel mechanisms of action that evade resistance entirely. We bring whatever tools the question demands, such as quantitative imaging, machine learning, and 3D hydrogel environments that actually resemble where bacteria live, because mapping the rules of bacterial survival is ultimately how you learn to defeat them.