Fig. 1: Rational design of the WISH-barcoded S. Typhimurium mutant pool.

a Overview of the five mouse models used in this study, showing microbiota composition, colonization resistance, and when gut inflammation typically occurs. b Schematic representation of the wild-type isogenic standardized hybrid (WISH)-tag³⁴. c The composition of the inoculum pool, as detailed in the main text, included a control wild type and mutants, seven wild-type strains for Shannon evenness score calculation, wild-type dilution standards to assess the limit of detection, and the carbohydrate mutants. d A schematic illustration shows the cytosolic genes selected for the mutant pool. Within each pathway, only the designated gene is highlighted, while each circle represents an enzymatic step in the degradation of the corresponding carbohydrate. Refer to Supplementary Data 12 for abbreviations. e Mouse infection protocol and sampling procedures for the germ-free (GF) and streptomycin (Str)-pretreated C57BL/6J and 129S6/SvEvTac mouse models. f Mouse infection protocol and sampling procedures for the gnotobiotic low complex microbiota (LCM) and oligo mouse microbiota (OligoMM¹²) model. Abbreviations: cc, cecal contents.