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Open Access Research

iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations

Christopher S Henry1*, Jenifer F Zinner12, Matthew P Cohoon1 and Rick L Stevens12

Author Affiliations

1 Mathematics and Computer Science Department, Argonne National Laboratory, S. Cass Avenue, Argonne, IL 60439, USA

2 Computation Institute, The University of Chicago, S. Ellis Avenue, Chicago, IL 60637, USA

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Genome Biology 2009, 10:R69  doi:10.1186/gb-2009-10-6-r69

Published: 25 June 2009

Abstract

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 genome-scale metabolic model of B. subtilis 168 called iBsu1103. This new model is based on the annotated B. subtilis 168 genome generated by the SEED, one of the most up-to-date and accurate annotations of B. subtilis 168 available.

Results

The iBsu1103 model includes 1,437 reactions associated with 1,103 genes, making it the most complete model of B. subtilis available. The model also includes Gibbs free energy change (ΔrG'°) values for 1,403 (97%) of the model reactions estimated by using the group contribution method. These data were used with an improved reaction reversibility prediction method to identify 653 (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 an improved model optimization method to increase model accuracy from 89.7% to 93.1%.

Conclusions

Basing the iBsu1103 model on the annotations generated by the SEED significantly improved the model completeness and accuracy compared with the most recent previously published model. The enhanced accuracy of the iBsu1103 model also demonstrates the efficacy of the improved reaction directionality prediction method in accurately identifying irreversible reactions in the B. subtilis metabolism. The proposed improved model optimization methodology was also demonstrated to be effective in minimally adjusting model content to improve model accuracy.