Fig. 3: End-point population sequencing reveals a lifestyle associated pattern of mutations after evolution under intermittent antibiotic treatment.

Mutations identified by whole-population genome sequencing of control and AMK treated (5xMIC and 80xMIC) biofilm and planktonic populations of E. coli. The three populations corresponding to the three evolved lineages per lifestyle and treatment were sequenced after 10 cycles of treatment. The average depth of sequencing was x150. Mutations at higher frequency than 5% are detected by Breseq analysis. Red shading indicates the total frequency of all mutations in each gene within a population at cycle 10 of the experimental evolution and the number in each box corresponds to the exact frequency detected. Population 4, 5, 6 from the planktonic lifestyle did not survive after 3 cycles and thus could not be sequenced at cycle 10 (they are shaded in grey). We therefore sequenced the population corresponding to the last cycle before their respective extinction, but no mutation was detected at frequency of 5% or higher, with the exception of one fixed mutation in population P5 (see supplementary Data 2 and 3).