Figure 2. Selection for carbohydrate utilization and acid tolerance in EcN mono-colonized mice.

A) Growth curves of strains expressing fragments enriched in the functional selections on minimal media supplemented with different carbon sources. *P < 6×10⁻³, Student’s t-test comparing time taken to reach OD₆₀₀=0.25 between WT and MD04. B) Annotations of select metagenomic fragments enriched in the functional selections. C) Growth curves of 3 biologically-replicate EcN strains expressing the gadX DNA insert (MD04) or EcN carrying empty vector (WT) after a 30 minute pulse in acidic (pH 2.5) or neutral (pH 7.0) conditions. * P < 0.001, Student’s t-test for the time needed to return to the maximum optical density prior to the pulse between MD04 fragments and WT, Bonferroni correction for multiple comparisons. D) Growth of WT EcN on 1% raffinose minimal media pre-conditioned by EcN strains carrying MD01 or MD02, or by WT EcN, or on unconditioned 1% raffinose minimal M9 media (left). No growth was observed in uninoculated conditioned media (right). * P < 0.001, Student’s t-test on the K parameter of logistic models fit to the data using the growthcurver R package, Bonferroni correction for multiple comparisons. The shaded regions represent the standard deviation of 8 experimental replicates. See also Figure S2, Figure S4, and Table S6.