Personalization and evaluation of human whole-body metabolic models and community microbiome models using Persephone.

Persephone is a pipeline that personalizes and evaluates human whole-body metabolic models and community microbiome models, running on 100 metagenomic samples in several days to a week on a single computer.

• Why it matters: Human metabolism and gut microbiome co-metabolism are hard to study in vivo, and WBMs require specialized modeling expertise that can be a barrier for beginners.
• What they did: Persephone builds community microbiome models from raw sequencing or taxonomy-assigned read tables, uses physiological and metabolomic data to personalize WBMs, integrates microbiome and WBMs, optimizes user-defined reactions, and provides statistical analysis and visualization.
• The result: By saving intermediate outputs and logging all model and data changes and warnings, Persephone enables standardized, beginner-accessible workflows for studying human–microbiome co-metabolism and testing physiological parameter effects like weight.

AI summary of the abstract · may contain errors · not medical advice · read the paper.