MIGRENE: The toolbox for microbial and individualized GEMs, reactobiome and community network modelling

MotivationUnderstanding microbial metabolism is crucial for evaluating shifts in human host-microbiome interactions during health and disease. However, the primary hurdle in the realm of constraint-based modeling and genome-scale metabolic models (GEMs) pertaining to host-microbiome interactions lies in the efficient utilization of metagenomic data for constructing GEMs that encompass unexplored and uncharacterized genomes. Challenges persist in effectively employing metagenomic data to address individualized microbial metabolism to investigate host-microbiome interactions. ResultTo tackle this issue, we have created a computational framework designed for personalized microbiome metabolism. This framework takes into account factors such as microbiome composition, metagenomic species profiles and microbial gene catalogues. Subsequently, it generates GEMs at microbial level and individualized microbiome metabolism, including reaction richness, reaction abundance, reactobiome, individualized reaction set enrichment (iRSE), and community models. Availability and implementationThe MIGRENE toolbox is freely available at our GitHub repository https://github.com/sysbiomelab/MIGRENE. Comprehensive tutorials on the GitHub were provided for each step of the workflow.