Extended Data Fig. 3: Cd ornithine degradation and biosynthesis pathways.
From: Oxidative ornithine metabolism supports non-inflammatory C. difficile colonization
a, Annotated biosynthetic and degradative pathways of L-ornithine in Cd. b, R20291 WT exhibits increased growth yield in rich media (0.5X BHIS) supplemented with different concentrations of L-ornithine (mean ± s.e.m., n = 5/group; one-way ANOVA F(2,12)=16.80 with Tukey’s post hoc comparisons). c, 630 WT exhibits increased growth yield in fully defined amino acid basal defined media (BDM) when supplemented with 8 mM L-ornithine (mean ± s.e.m., n = 5/group, unpaired two-tailed t-test). d, In vitro competition between 630 WT and mutants in L-ornithine degradation (∆oraSE n = 4) or biosynthesis (∆argF, n = 4; ∆argM, n = 3). Strains were co-cultured for 24 hours in amino acid minimal media (CDDM) supplemented with additional 50 mM L-ornithine (mean ± s.e.m.; ANOVA with post hoc comparisons: F(2,7)=25.63,). A competitive index of 1 indicates equal abundance. e, In vitro competitive index between WT Cd and ∆oraSE in BDM supplemented with 8 mM L-ornithine or 8 mM L-arginine (mean ± s.e.m., n = 4/group; ANOVA with Dunnett’s post hoc comparisons using base medium as the control group: F(2,9)=3.553). Strains were co-cultured for 48 hours. For all panels, * P < 0.05, ** P < 0.01, *** P < 0.001. f, WT Cd (n = 6) and ∆oraSE (n = 7) grow equally well in rich media (0.5X BHIS). Supplementation with 0.5% or 0.25% (w/v) L-ornithine leads to increased growth yield in WT but not the ornithine aminomutase mutant (n = 7/group, mean ± s.e.m.). g, In gnotobiotic mice harboring a defined community of bacteria, the ∆oraSE mutant exhibits increased expression of genes in the oxidative ornithine locus (middle panel) but not the reductive locus (right) nor biosynthesis of arginine (argF) or glutamine (argM). For f and g, multiple unpaired t-tests with Benjamini, Krieger and Yekutieli two-stage step-up FDR correction.
