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

Nature Protocols, Published online: 05 November 2026; doi:10.1038/s41596-026-01437-8

This protocol for using Persephone, an automated pipeline for evaluation and personalization of human whole-body metabolic models, combines them with community microbiome models to enable investigation of human and human gut microbiome co-metabolism.