iSep23 – Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228

Staphylococcus epidermidis is a Gram-positive, coagulase-negative (CoNS) bacterium that is carried asymptomatically on the skin and mucous membranes of virtually all human beings. It is a major cause of nosocomial infections and associated with invasive procedures (Méric et al., 2018). Virulent S. epidermidis strains contaminate indwelling medical devices, such as catheters or implants (Sabaté Brescó et al., 2017), showing pathogenicity traits, e.g., biofilm formation, cell toxicity, or methicillin resistance (Méric et al., 2018). Apart from that, even the low-virulent, low-biofilm forming strain of S. epidermidis ATCC 12228 was shown to form a biofilm under decreased oxygen conditions (Uribe-Alvarez et al., 2015). As a member of the skin and mucosal microbiome, S. epidermidis prevents the colonization of Staphylococcus aureus (Otto, 2011). Its well-studied metabolism and the ability to grow on known media make S. epidermidis a possible reconstruction candidate. A reconstruction of a genome-scale metabolic model (GEM) of S. epidermidis was created using CarveMe (Machado et al., 2018) and carefully refined in subsequent manual curation efforts, using the S. epidermidis ATCC 12228 strain sequence. The model was experimentally validated on multiple media under varying growth conditions, such as different carbon sources.