A structured evaluation of genome-scale constraint-based modeling tools for microbial consortia

• DOI: 10.1371/journal.pcbi.1011363
• Publication Date: 2023-08-14T17:28:19Z
• Authors: William T. Scott; Sara Benito-Vaque...; Johannes Zimmermann; Djordje Bajić; Almut Heinken; Maria Suarez-Diez; Peter J. Schaap
• Keywords: Plug-in

Harnessing the power of microbial consortia is integral to a diverse range sectors, from healthcare biotechnology environmental remediation. To fully realize this potential, it critical understand mechanisms behind interactions that structure and determine their functions. Constraint-based reconstruction analysis (COBRA) approaches, employing genome-scale metabolic models (GEMs), have emerged as state-of-the-art tool simulate behavior communities constituent genomes. In last decade, many tools been developed use COBRA approaches multi-species consortia, under either steady-state, dynamic, or spatiotemporally varying scenarios. Yet, these not systematically evaluated regarding software quality, most suitable application, predictive power. Hence, uncertain which users should apply system what are urgent directions developers take in future improve existing capacities. This study conducted systematic evaluation COBRA-based for using datasets two-member test cases. First, we performed qualitative assessment 24 published based on list FAIR (Findability, Accessibility, Interoperability, Reusability) features essential quality. Next, quantitatively tested predictions subset 14 against experimental data three different case studies: a) syngas fermentation by C. autoethanogenum kluyveri static tools, b) glucose/xylose with engineered E. coli S. cerevisiae dynamic c) Petri dish enterica incorporating spatiotemporal variation. Our results show performance levels best qualitatively assessed when examining categories tools. The differences mathematical formulation relation were also discussed. Ultimately, provide recommendations refining GEM modeling