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The significance of the difference between both strains was calculated using Student's t-test.
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For each strain, the distance between it and all other strains was calculated for each tree pair, and the sum of all distances is the measure of instability.
Third, the percentage of polytomous strains (of 76 S. Enteritidis strains) was calculated.
The core-genome size of the 67 S. mutans strains was calculated to be 1,373.
The ANI between strains was calculated using JSpecies software package v1.2.1 using default parameters [ 74].
The minimum inhibitory concentration on 90%% bacterial strains was calculated as MIC90.
The fitness of the competing strains was calculated as the selection coefficient S, as described [ 19].
Translation efficiency (TE) for each gene in the parental strains was calculated from RFP/mRNA.
The Pearson's correlation coefficient of the distance to the Ori for orthologous genes between strains was calculated.
Statistical significance of the pairwise comparisons between strains was calculated using a post hoc Tukey test with p < 0.05.
The corresponding lattice strains are calculated from the data shown in Figure 3.
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