Fig 3. Adding back a wild-type copy of the respective genes to the deletion mutant strains restores in vivo fitness.

Germ free animals were gavaged with 1:1 mixtures of each deletion mutant and the corresponding gene add-back strain in three or four mice. The abundance of each strain in the inoculum (I) and after recovery from fecal pellets (R) was estimated by qPCR at day 1, 9 and 21 post gavage (strains were barcoded). In contrast to the deletion mutants which were depleted over time from the fecal pellets, the add-back strains maintained their relative abundance (P values are indicated on top of each comparison). Each circle represents the measurement from one mouse. Statistical analysis by two-tailed unpaired t-test assuming unequal variance. NS, not significant.