PPubMed25 Jun 2009Cited 169×

<i> i </i> Bsu1103: a new genome-scale metabolic model of <i> Bacillus subtilis </i> based on SEED annotations

Christopher S Henry, Jenifer F Zinner, Matthew P Cohoon, Rick L Stevens

Abstract

'Rick L Stevens'] A new and validated genome-scale metabolic model of Bacillus subtilis 168, iBsu1103, is presented that has significantly improved completeness and accuracy.

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iBsu1103 is a new, validated genome-scale metabolic model of Bacillus subtilis 168 with improved completeness and 93% prediction accuracy.

What’s new

i.Construction of the iBsu1103 model using SEED annotations covering 1,104 genes and 1,405 reactions
ii.Identification and addition of 73 open‑problem transport reactions to cover Biolog nutrient data
iii.Development of a modified GrowMatch optimization workflow with new reconciliation steps
iv.Improvement of model prediction accuracy from 89.7% to 93.1% across 1,500 experimental conditions
v.Comparison with the previous Oh et al. model, highlighting 628 exclusive reactions and functional enhancements

How they did it

The authors extracted the annotated B. subtilis 168 genome from the SEED, mapped functional roles to reactions, and assembled a core model. They then applied a four‑step modified GrowMatch procedure—gap filling, gap‑filling reconciliation, gap generation, and gap‑generation reconciliation—to correct false predictions. Model performance was evaluated against 1,500 experimental data points from Biolog phenotyping and gene essentiality studies.

What they found

Core model contains 1,405 reactions and 1,104 genes (1,103 after optimization)
Added 73 transport reactions for nutrients lacking gene annotations
Optimized model accuracy increased from 89.7% (1,344/1,500) to 93.1% (1,398/1,500)
35 new reactions added, 2 irreversible reactions made reversible, 21 reversible made irreversible, and 3 reactions removed
Metabolizes 95 carbon, 42 nitrogen, 45 phosphate, and 2 sulfate sources as observed in Biolog assays

Caveats

✕Only 51% of proven nutrient transport genes are present, requiring manual addition of transport reactions
✕Remaining false predictions (e.g., 116 false negatives and 39 false positives before optimization) indicate incomplete coverage
✕Reversibility assignments rely on thermodynamic estimates that may be over‑ or under‑estimated

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