Additional file 2: Figure S2. of Metabolic modelling in a dynamic evolutionary framework predicts adaptive diversification of bacteria in a long-term evolution experiment

Diauxic growth in DM250 medium containing glucose and acetate at 10:90 ratio. Clone 6.5KS1 (red) exhibits a diauxic shift from glucose to acetate consumption much earlier than either the ancestor (green) or clone 6.5KL4 (blue). Curves show the average of three biological replicates. (PDF 113 kb

Additional file 6: Table S4. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Overlap between experimentally identified and computationally predicted essential genes. Lines 1–54 details genes that are predicted to be essential in all computationally tested media (100% essentiality score) and are also experimentally identified to be an essential gene under the BAB broth medium. Lines 55–78 details genes that are predicted to be essential in all computationally tested media (100% essentiality score) but not experimentally identified to be an essential gene under the BAB broth medium. The gene information was collected from http://www.genome.jp on October 18 2016. (DOCX 17 kb

Additional file 3: Table S3. of An integrated computational-experimental approach reveals Yersinia pestis genes essential across a narrow or a broad range of environmental conditions

Essential genes identified in different strains of Y. pestis by different methods. Genes in KIM10 identified in in vitro expansion of a himar1-derived transposon library grown on TB agar containing 2.5 mM CaCl2 and 25 μg/ml zeocin at 37 °C, then analysed using the Hidden Markov model (50). Genes in CO92 identified after in vitro growth in BAB broth at both 28 °C and 37 °C, then analysed using the DEM algorithm (14) (DOCX 48 kb