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

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Abstract

Motivation

In a genome-scale metabolic model, the biomass produced is defined to have a molecular weight (MW) of 1 g mmol−1. This is critical for correctly predicting growth yields, contrasting multiple models and more importantly modeling microbial communities. However, the standard is rarely verified in the current practice and the chemical formulae of biomass components such as proteins, nucleic acids and lipids are often represented by undefined side groups (e.g. X, R).

Results

We introduced a systematic procedure for checking the biomass weight and ensuring complete mass balance of a model. We identified significant departures after examining 64 published models. The biomass weights of 34 models differed by 5-50%, while 8 models have discrepancies >50%. In total 20 models were manually curated. By maximizing the original versus corrected biomass reactions, flux balance analysis revealed >10% differences in growth yields for 12 of the curated models. Biomass MW discrepancies are accentuated in microbial community simulations as they can cause significant and systematic errors in the community composition. Microbes with underestimated biomass MWs are overpredicted in the community whereas microbes with overestimated biomass weights are underpredicted. The observed departures in community composition are disproportionately larger than the discrepancies in the biomass weight estimate. We propose the presented procedure as a standard practice for metabolic reconstructions.

Availability and implementation

The MALTAB and Python scripts are available in the Supplementary Material.

Contact

costas@psu.edu or joshua.chan@connect.polyu.hk

Supplementary information

Supplementary data are available at Bioinformatics online.

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