Fig. 4: Parallel genetic selections reveal most mutations result in prey-specific effects.

a Selection schematic. Cells from the mutant library were plated in duplicate in four parallel selections on the Gram(−) bacterial species K. aerogenes and K. pneumoniae, and the Gram(+) species B. subtilis and M. luteus. Cells were grown for either 100 generations (B. subtilis, M. luteus, K. pneumonia selections) or 200 generations (K. aerogenes selection) before being sequenced by REMI-seq to quantify the relative abundance of every mutant remaining in the pool (Supplementary Figs. 3,4 and Supplementary Data 2). b Patterns of behaviour across the different bacteria for mutants with a growth phenotype show an overall pattern of prey specificity. z-scores of mutants that were identified as either advantaged (yellow = mean z > 1.5, >100 normalised reads in both selection endpoint replicates) or disadvantaged (blue = mean z < −1, >100 normalised reads in the starting library) in one or more selections are shown across all four different bacteria (Ml = M. luteus, Bs = B. subtilis, Kp = K. pneumoniae, Ka = K. aerogenes). c Mutations showing positive pleiotropy tend to be disadvantaged across multiple prey, and especially across the closely related prey species K. aerogenes and K. pneumoniae. The behaviour of mutants that were identified as positively pleiotropic (either advantaged on more than one prey or disadvantaged on more than one prey) with >100 normalised starting reads are shown. d Most mutations that affect growth show conditional specificity. The behaviour of mutants across all four bacterial prey showing conditional specificity (advantaged or disadvantaged on a single prey species only) with >100 normalised starting reads are shown. e Antagonistically pleiotropic mutations show little pattern. The behaviour of mutants that were identified as advantaged in a selection and disadvantaged in at least one other is shown across all four different bacteria. The majority of antagonistically pleiotropic mutants were advantaged in the M. luteus selection and disadvantaged on different prey.