C. S. Henry, J. F. Zinner, M. P. Cohoon, and R. L. Stevens, "iBsu1103: An Improved Genome-Scale MetabolicModel of B. subtilis Based on SEED Annotations," Preprint ANL/MCS-P1579-0209, February 2009. [pdf]
Background: Bacillus subtilis is an organism of interest because of its extensive industrial applications, its similarity to pathogenic organisms, and its role as the model organism for Gram positive, sporulating bacteria. In this work, we introduce a new genomescale
metabolic model of B. subtilis 168 called iBsu1101. This new model is based on the annotated B. subtilis 168 genome generated by the SEED, one of the most up-todate and accurate annotations of B. subtilis 168 available.
Results: The iBsu1101 model includes 1,444 reactions associated with 1,101 genes, making it the most complete model of B. subtilis available. The model also includes Gibbs free energy change (ΔrG’°) values for 1,383 (96%) of the model reactions estimated by using the group contribution method. This data was used with a novel reaction reversibility prediction method to identify 650 (45%) irreversible reactions in the model. The model was validated against an experimental dataset consisting of 1,500 distinct conditions and was optimized by using a novel method to improve model accuracy from 89.5% to 93.6%.
Conclusions: Basing the iBsu1101 model on the annotations generated by the SEED significantly improved the model completeness and accuracy compared with the previous model published by Oh et al. The enhanced accuracy of the iBsu1101 model also demonstrates the efficacy of our reaction directionality prediction method in accurately identifying irreversible reactions in the B. subtilis metabolism. The model optimization methodology was demonstrated to be effective in minimally adjusting model content to improve model accuracy.