Standardizing biomass reactions and ensuring complete mass balance in genome-scale metabolic models

• DOI: 10.1093/bioinformatics/btx453
• Publication Date: 2017-07-12T11:20:01Z
• Authors: Siu H J Chan; Jingyi Cai; Lin Wang; Margaret N Simons...; Costas D Maranas
• Keywords: Python; Flux Balance Analysis

In a genome-scale metabolic model, the biomass produced is defined to have molecular weight (MW) of 1 g mmol-1. This critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, standard rarely verified in current practice chemical formulae components such as proteins, nucleic acids lipids are often represented by undefined side groups (e.g. X, R).We introduced systematic procedure checking ensuring complete mass balance model. We identified significant departures after examining 64 published models. The weights 34 differed 5-50%, while 8 discrepancies >50%. total 20 were manually curated. By maximizing original versus corrected reactions, flux analysis revealed >10% differences yields 12 curated Biomass MW accentuated community simulations they can cause errors composition. Microbes with underestimated MWs overpredicted whereas microbes overestimated underpredicted. observed composition disproportionately larger than estimate. propose presented reconstructions.The MALTAB Python scripts available Supplementary [e-mail] or [e-mail] data at Bioinformatics online.