pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes

Abstract

Abstract The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools leverage sequence homology from single genomes, this study introduces pan-Draft, a pan-reactome-based approach exploiting recurrent genetic evidence to determine the solid core structure of species-level GEMs. By comparing MAGs clustered at the species-level, pan-Draft addresses the issues due to the incompleteness and contamination of individual genomes, providing high-quality draft models and an accessory reactions catalog supporting the gapfilling step. This approach will improve our comprehension of metabolic functions of uncultured species.

Keywords

• Genome-scale metabolic model
• Metagenome-assembled genome
• Metagenomics
• Species-level models
• Metabolic network gapfilling
• Human gut microbiome