SICKO: Systematic Imaging of Killing Organisms.

are an important model system for research on host-microbe interaction. Their rapid life cycle, short lifespan, and transparent body structure allow simple quantification of microbial load and the influence of microbial exposure on host survival. host-microbe interaction studies typically examine group survival and infection severity at fixed timepoints. Here we present an imaging pipeline, Systematic Imaging of Killing Organisms (SICKO), that allows longitudinal characterization of microbes colonizing isolated , enabling dynamic tracking of tissue colonization and host survival in the same animals. Using SICKO, we show that or gut colonization dramatically shortens lifespan and that immunodeficient animals lacking are more susceptible to colonization but display similar colony growth relative to wild type. SICKO opens new avenues for detailed research into bacterial pathogenesis, the benefits of probiotics, and the role of the microbiome in host health.