Extended Data Fig. 5: Input compositions and phenotypic validations for barcoded consortium infections with strains carrying mutations in Shigella T3SS effecto s.
(a, b) BO and AO enteroids (a) and BO and AO colonoids (b) were infected with a mixed barcoded consortium comprising two wt (tagA, tagB), two ΔmxiD (tagC, tagD) and two mutant (tagE, tagF) strains at MOI 40 for 6 h. Mut refers to the specific mutant as indicated on x-axis. Graphs depict the composition of barcoded Shigella consortia used as input inoculums for experiments in Fig. 3j–m. The relative abundance of each tag in the input consortia is plotted as percentage of the total population. Note that no strain is consistently over- or underrepresented. Shown are data for two independently generated consortia for each infection. See Fig. 3j–m for the corresponding relative tag abundances in the intracellular population and Colonization Index scores. (c–f) BO and AO enteroids (ID 22-2jej) (c) and BO and AO colonoids (ID 22-4col) (e) were infected with a mixed barcoded consortium comprising two wt (tagA, tagB), two ΔmxiD (tagC, tagD) and two ΔipaA (tagE, tagF) strains at MOI 40 for 6 h. Shown is the quantification of relative tag abundance, normalized against the corresponding input. For each geometry, infections were executed with four independently generated consortia. Significance determined by two-sided paired t-test for each specific mutant between the normalized output and the normalized input abundances (see Methods). ***p < 0.001. (d–f) Bar graph showing the Colonization Index for each mutant in BO (dark grey) and AO (light grey) enteroid 22-2jej infections (derived from data in c and calculated as 1-(wt/mut); sample size as in c) and BO (dark grey) and AO (light grey) colonoid 22-4col infections (derived from data in e and calculated as 1-(wt/mut); sample size as in e). wt is shown as 0. Data shown as Mean +/- SD.
