Within-species control reveals novel immune response genes in Caenorhabditis elegans

The nematode Caenorhabditis elegans is a simple model host for studying the interaction between bacterial pathogens and the metazoan innate immune system. In the last two decades, much focus has been given to studying intestinal infection in the worm by the clinical strain Pseudomonas aeruginosa PA14. Powerful genetic and molecular tools in both species facilitate the identification and analysis of bacterial virulence factors as well as host defense factors. However, findings from these studies are confounded by the use of the genetically, metabolically, and physiologically divergent E. coli OP50 as a food source and as the non-virulent control. Here we report the use of P. aeruginosa z11 strain as a preferable control for PA14 infection studies. We demonstrate that many aspects of worm behavior, health-span, longevity, food attraction, brood size, lifespan, and pathogen avoidance and survival are not affected in z11. We show that the use of z11 as a control for transcriptomics analysis can increase the discovery power. In particular, we identified three novel pathogenesis-related genes in C. elegans. Our findings accentuate the importance of choosing an appropriate control environment for host-pathogen studies.