Fig. 7

Pangenomic analysis reveals gene features associated with E. coli in vivo mucosal colonization of the inflamed intestine. A Circle phylogram displays the pangenome of four in vivo “colonized” isolates (red) and three in vivo “disappeared” isolates (blue), showing gene cluster presence/absence (solid/light color in the layer) by isolate. In vitro defined AIEC and non-AIEC are denoted with pink and orange squares. Gene clusters with assigned KEGG functions are labelled with green, or gray for unknown. Yersiniabactin synthetase gene groups contained in core genomes are common to all the isolates and serve as a positive control. Selected group-specific gene clusters are highlighted to show that their distribution was confined to either “colonized” (red) or “disappeared” (blue) groups. B UpSet plot displays KEGG gene functions associated with E. coli strains in “colonized” or “disappeared” groups. Columns of the matrix show intersection patterns of KEGG functions: a single dot denotes non-shared functions within that isolate (singleton pattern), with linked dots showing numbers of functions shared and exclusive to those linked isolates (shared pattern 2 to 6 displayed; core pattern 7 not shown). The vertical bar shows frequency of functions exclusive to those isolate(s). The blue bar depicts number of functions present in all disappeared isolates and absent in colonized isolates, while red denotes number of functions detected in 2 to 3 colonized isolates and absent in all disappeared isolates. Arrows reveal the number of functions exclusively shared by AIEC strains. Three gene functions unique to two disappeared strains (see triangle-pointing pattern) are discussed in the main text. C Circle phylogram displays the pangenome of 7 E. coli isolates based on further exploration of KEGG unannotated gene clusters against COG database. D UpSet plot displays COG gene functions associated with specific “colonized” (red) or “disappeared” (blue) groups. The arrow reveals the number of COG functions exclusively shared by AIEC strains. E The list of selected KEGG functions displayed in phylogram and their associated isolate genomes displayed in UpSet plot. Red: functions specific for “colonized” isolates. Blue: functions specific for “disappeared” isolates. The full list of group-specific gene functions is contained in Table S1