Systematic assessment of template-based genome-scale metabolic models created with the BiGG Integration Tool

Abstract

Genome-scale metabolic models (GEMs) are essential tools for in silico phenotype prediction and strain optimisation. The most straightforward GEMs reconstruction approach uses published models as templates to generate the initial draft, requiring further curation. Such an approach is used by BiGG Integration Tool (BIT), available for merlin users. This tool uses models from BiGG Models database as templates for the draft models. Moreover, BIT allows the selection between different template combinations. The main objective of this study is to assess the draft models generated using this tool and compare them BIT, comparing these to CarveMe models, both of which use the BiGG database, and curated models. For this, three organisms were selected, namely Streptococcus thermophilus, Xylella fastidiosa and Mycobacterium tuberculosis. The models’ variability was assessed using reactions and genes’ metabolic functions. This study concluded that models generated with BIT for each organism were differentiated, despite sharing a significant portion of metabolic functions. Furthermore, the template seems to influence the content of the models, though to a lower extent. When comparing each draft with curated models, BIT had better performances than CarveMe in all metrics. Hence, BIT can be considered a fast and reliable alternative for draft reconstruction for bacteria models.

Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets

“…In the context of genome-scale metabolic models (GEMs), various strategies have been explored in applying ML to improve the understanding of patterns and characteristics in complex biological data. For a few years now, approaches to the use of ML with GEMs have been made under three strategies: (1) fluxomics, (2) multimodal analysis, and (3) the generation of models based on constraints together with fluxomic data [ 164 , 165 ].…”