Table 6

Comparison of experimental and in silico net specific growth rates (h-1).

Aerobic

Anaerobic


μexp

μIn silicoa

μIn silicoIIb

μexp

μIn silicoa

μIn silicoIIb


E. coli MG1655

0.56 ± 0.03

0.74 ± 0.00

0.82 ± 0.05

0.39 ± 0.01

0.52 ± 0.00

0.19 ± 0.00


E. coli W3110

0.54 ± 0.01

0.74 ± 0.00

0.82 ± 0.00

0.33 ± 0.01

0.52 ± 0.00

0.19 ± 0.00


E. coli EDL933

0.79 ± 0.08

0.74 ± 0.00

0.63 ± 0.00

0.56 ± 0.04

0.53 ± 0.00

0.56 ± 0.01


E. coli Sakai

0.80 ± 0.01

0.74 ± 0.00

0.63 ± 0.00

0.68 ± 0.01

0.53 ± 0.00

0.56 ± 0.00


E. coli CFT073

0.76 ± 0.01

0.71 ± 0.00

0.60 ± 0.00

0.40 ± 0.01

0.45 ± 0.00

0.42 ± 0.00


E. coli UTI89

0.55 ± 0.02

0.72 ± 0.01

0.61 ± 0.01

0.64 ± 0.01

0.45 ± 0.01

0.42 ± 0.01


E. coli core

-

0.71

0.71

-

0.45

0.37


E. coli pangenome

-

0.74

0.73

-

0.53

0.42


S. typhimurium LT2

0.86 ± 0.05

0.73 ± 0.00

-

0.54 ± 0.01

0.44 ± 0.00

-


aMaximum oxygen uptake rates (15 mmol/gDW/h) and glucose uptake rates for aerobic (10 mmol/gDW/h) and anaerobic (18.5 mmol/gDW/h) conditions were used for in silico batch simulations in this work were those previously determined for E. coli W3110 from batch culture in M9 minimal media [73]

bExperimentally determined glucose uptake rate values from this work used for in silico batch simulations for E. coli K-12 (15.5 for aerobic and 8.1 for anaerobic), EHEC (7.9 for aerobic and 19.2 for anaerobic) or UPEC (7.7 for aerobic and 17.5 for anaerobic). For the core and pangenome models the average experimentally determined glucose uptake rate values from this work was used (10.3 for aerobic and 14.9 for anaerobic).

Baumler et al. BMC Systems Biology 2011 5:182   doi:10.1186/1752-0509-5-182

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