Figure 2. Comparison of P. aeruginosa fitness determinants in vitro and in vivo.

(A) After characterizing a mock output population that was subjected to experimental conditions, but not administered to flies, we compared genes depleted in that group (n=379) to the output population recovered from flies (n=372). Eighty-five genes were depleted only in vitro; 78 genes were depleted only in vivo. Genes that were negatively selected in vivo, but not in vitro were termed putative “colonization-specific factors.” Nearly 300 genes were negatively selected both while the library was administered to flies (in vitro) and during passage through the fly (in vivo). (B) Genes depleted specifically during administration of the library tended to be categorized as contributing to secondary structure (COG category Q), nucleotide metabolism and transport (F), lipid metabolism (I), and energy production and conversion (C), whereas genes depleted specifically in the fly were tended to be categorized as contributing to transcription, translation, signal transduction, replication and repair, cell motility, and amino acid metabolism and transport. COG categories B (chromatin structure and dynamics), W (extracellular structures), Z (cytoskeleton), and mobile elements were not represented among these genes specifically depleted in either condition. COG = Clusters of Orthologous Groups. Full lists of genes can be found in Tables S2–S5 in reference ²¹.