Fig. 2: A subset of Enterobacter strains kills E. coli and V. cholerae in a T6SS-1-dependent manner.

Survival of E. coli (a, d, e) or V. cholerae (a) was scored after co-incubation with wild-type (WT) or T6SS-1-/T6SS-2-negative (∆tssB or ∆tssB1 and/or ∆tssB2) Enterobacter commensals #10 and #11 (a, e) or a collection of E. cloacae complex strains (E. ludwigii, E. cloacae, and E. hormaechei) (d, e), as indicated on the Y-axis. Values are derived from three independent experiments and the bars represent the mean (±SD, as shown by the error bars). dl, detection limit, as indicated by the dashed line. Significant differences were determined using a two-sided Student’s t-test corrected for multiple comparisons (a, e) and a one-way ANOVA followed by Holm–Sidak’s multiple comparison test comparing each strain to the T6SS-deficient control commensal strain (#10∆tssB; value indicated by the dotted gray line) (d). *p < 0.05; **p < 0.01; ***p < 0.001; ns, not significant. b Absence of secreted Hcp protein in T6SS-1-negative Enterobacter mutants. The commensal Enterobacter strains #10 and #11 (WT) and their T6SS-1-deficient mutants (∆tssB/∆tssB1), were scored for secreted proteins, which were separated by SDS PAGE and stained using Coomassie blue. The arrow on the right indicates the migration position of the Hcp proteins (~17 kDa), compared to the 15 kDa ladder protein indicated on the left. Representative image (out of three independent experiments). c Core-genome-based phylogeny of E. cloacae complex strains and reclassified commensal isolates. The tree was rooted with the E. coli commensals #1, #2, and #5 as outgroup (gray triangle). The boxed Enterobacter strains were tested for interbacterial killing in panel (d). Details on the right of the tree (from left to right): First two columns: Summary heatmap of E. coli and V. cholerae survival, when challenged by the indicated strains as predators. Color scale from light (lowest survival) to dark (highest survival), according to the data provided in supplementary Fig. S5a and S5b. Middle column: Presence (closed circles) or absence (open circles) of the specific T6SS clusters. T6SS clusters were scored as present if at least 10 core T6SS genes were identified in the genome data (detailed information are provided in Supplementary Data file 5). Last column: Origin of isolates according to the legend at the bottom of the figure. Source data underlying all panels are provided in the Source data file.