Figure 3: The microbiota influences the selective advantage of adaptive mutations.

Competitive fitness experiments of the emerging gatZ allele against the ancestral strain in (a) WT co-housed with Rag2^−/− mice (left panel, n=11) and Rag2^−/− co-housed with WT mice (right panel, n=11) and in (b) GF WT (left panel, n=7) and GF Rag2^−/− (right panel, n=7) mice. In a, mice co-housed in the same group are represented with the same shape (triangles, squares or diamonds). Advantage of gatZ over the ancestral, per hour was calculated as in Fig. 2c. (c) Selective advantage of the gatZ mutant, per hour, inferred from the slope of the linear regression of ln(gatZ/anc), over 3 days of in vivo competition against the ancestral in mice either WT, Rag2^−/−, WT co-housed, Rag2^−/− co-housed, GF WT and GF Rag2^−/−. The competitive advantages differed between Rag2^−/− and WT (ANOVA with Tukey’s post hoc test, P<10⁻³), but upon co-housing the advantage in Rag2^−/− mice (co-housed) increased (ANOVA with Tukey’s post hoc test, P=0.02) and became similar to WT animals (co-housed) (ANOVA with Tukey’s post hoc test, P>0.99). The advantage of the WT did not significantly change upon co-housing (ANOVA with Tukey’s post hoc test, P=0.3). In the absence of microbiota (GF), the selective effect of gatZ is similar in WT (circles) and Rag2^−/− (triangles) mice (ANOVA with Tukey’s post hoc test, P>0.99) and smaller than in WT mice harbouring microbiota (ANOVA with Tukey’s post hoc test, P<10⁻³). NS, not significant; P>0.05, *P<0.05, ***P<0.001.