iSsus3744: A Genome-Scale Model-Guided Strategy for Rational Media Design for Cultivated Pork

Abstract

Cultivated meat production is currently limited by high production costs and an incomplete understanding of cellular metabolism in agriculturally relevant species. Genome-scale metabolic models (GEMs) have successfully guided media optimization in biopharmaceutical systems but have not been widely applied to cultivated meat. In this study, we present iSsus3744, the first genome-scale metabolic reconstruction for Sus scrofa and demonstrate its application for rational media design in cultivated pork production. iSsus3744 was reconstructed using HumanGEM and Recon3D as template models and further constrained using experimentally determined biomass composition and uptake and excretion fluxes from a Duroc porcine muscle satellite cell line. The final model comprised 3,744 genes, 8,854 metabolites, and 12,248 reactions distributed across eight cellular compartments. Flux balance analysis (FBA) and flux variability analysis (FVA) were used to identify amino acids limiting cellular growth and predict media supplementation strategies. Experimental validation demonstrated that model-guided amino acid supplementation significantly improved proliferation. Supplementation with phenylalanine reduced doubling time from 31.9 hours to 17.2 hours, representing a 46% reduction, while lysine, methionine, tyrosine, leucine, and valine also improved growth performance. These results demonstrate the potential of genome-scale metabolic modeling as a powerful platform for rational media optimization in cultivated meat systems. iSsus3744 provides a foundational resource for future integration of omics, transcriptional regulation, and isotope-assisted metabolic flux analysis to further accelerate serum-free media development and cultivated meat bioprocess optimization.