Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

ABSTRACT

Staphylococcus epidermidis, a commensal bacterium inhabiting collagen-rich areas, like human skin, has gained significance due to its probiotic potential in the nasal microbiome and as a leading cause of nosocomial infections. While infrequently leading to severe illnesses, S. epidermidis exerts a significant influence, particularly in its close association with implant-related infections and its role as a classic opportunistic biofilm former. Understanding its opportunistic nature is crucial for developing novel therapeutic strategies, addressing both its beneficial and pathogenic aspects, and alleviating the burdens it imposes on patients and healthcare systems. Here, we employ genome-scale metabolic modeling as a powerful tool to elucidate the lifestyle and capabilities of S. epidermidis. We created a comprehensive computational resource for understanding the organism’s growth conditions within diverse habitats by reconstructing and analyzing a manually curated and experimentally validated metabolic model. The final network, iSep23, incorporates 1,415 reactions, 1,051 metabolites, and 705 genes, adhering to established community standards and modeling guidelines. Benchmarking with the MEMOTE test suite yields a high score, highlighting the model’s high semantic quality. Following the FAIR data principles, iSep23 becomes a valuable and publicly accessible asset for subsequent studies. Growth simulations and carbon source utilization predictions align with experimental results, showcasing the model’s predictive power. This metabolic model advances our understanding of S. epidermidis as a commensal and potential probiotic and enhances insights into its opportunistic pathogenicity against other microorganisms.