Fig. 6: Mutants sensitive to host-specific factors can be compensated by co-culture.

a The volcano plot shows genome-wide fitness changes from a dTn-Seq experiment comparing growth in droplets with either glucose or alpha-1-acid glycoprotein as the main carbon source. Validated genes nagB, SP_1674, nanE, and nagA are circled in red. b While ΔnanE (orange) grows similarly to wt (blue) in glucose, there is a growth defect for the mutant (green) compared with wt (red) when AGP is the sole carbon source. c Individual and mixed culturing combined with bacterial cell enumeration on agar plates containing antibiotics enabling differentiation between the wt and mt were used to determine relative fitness of the mt. While mutants grow just as well as the wt when glucose is the main carbon source (orange bars), they grow significantly slower than the wt when grown independently (green bars). However, their fitness is significantly improved when grown in the presence of the wt (blue bars), indicating that wt is providing “community support” (each growth experiment was performed at least four times, significance was determined through a one-way ANOVA with Bonferroni correction for multiple testing). d Volcano plot comparing growth in droplets in the absence and presence of elastase. e Deletion mutant ΔmscL (green) has reduced survival in two different concentrations of elastase compared with wt (orange) when cultured as single strains. However, ΔmscL survival in elastase is improved, and indistinguishable from wt, when the mutant is cultured in the presence of the wt. “Percent survival” was calculated relative to an untreated control (each experiment was performed at least three times and significance was determined through a two-way ANOVA). All error bars are standard error of the mean; ns = not significant, * < 0.05, ** < 0.005, *** < 0.0005, **** < 0.0001. Source data are available in the Source Data file.