ArticlePLoS computational biology2019
A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 61 citations in OpenAlex.
- Fermentative growth decreases the iron demand of Staphylococcus aureus.Journal of inorganic biochemistry · 2026Article
- From Single Organisms to Communities: Modeling Methanotrophs and Their Satellites.Microorganisms · 2025Review
- Reconstruction and application of a genome-scale metabolic model for Streptococcus suis.BMC genomics · 2025Article
- The mutational landscape of Staphylococcus aureus during colonisation.Nature communications · 2025Article
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- Bacterial single-cell RNA sequencing captures biofilm transcriptional heterogeneity and differential responses to immune pressure.Nature communications · 2024Article
- Pan-genome-scale metabolic modeling ofmSystems · 2024Article
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- Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling.PLoS pathogens · 2024Article
- Genome-scale model ofMicrobiology spectrum · 2024Article
- Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections.NPJ systems biology and applications · 2024Article
- Metabolic modeling predicts unique drug targets inmSystems · 2023Article
- Applications of genome-scale metabolic models to investigate microbial metabolic adaptations in response to genetic or environmental perturbations.Briefings in bioinformatics · 2023Review
- Robustness and Complexity of Directed and Weighted Metabolic Hypergraphs.Entropy (Basel, Switzerland) · 2023Article
- Elucidating the CodY regulon inmSystems · 2023Article
- High-quality genome-scale metabolic network reconstruction of probiotic bacterium Escherichia coli Nissle 1917.BMC bioinformatics · 2022Article
- Article
- Adaptive laboratory evolution and independent component analysis disentangle complex vancomycin adaptation trajectories.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Genome-Scale Metabolic Modelling Approach to Understand the Metabolism of the Opportunistic Human PathogenMetabolites · 2022Article
- NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome.Frontiers in bioinformatics · 2022Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
Abstract
S. aureus is classified as a serious threat pathogen and is a priority that guides the discovery and development of new antibiotics. Despite growing knowledge of S. aureus metabolic capabilities, our understanding of its systems-level responses to different media types remains incomplete. Here, we develop a manually reconstructed genome-scale model (GEM-PRO) of metabolism with 3D protein structures for S. aureus USA300 str. JE2 containing 854 genes, 1,440 reactions, 1,327 metabolites and 673 3-dimensional protein structures. Computations were in 85% agreement with gene essentiality data from random barcode transposon site sequencing (RB-TnSeq) and 68% agreement with experimental physiological data. Comparisons of computational predictions with experimental observations highlight: 1) cases of non-essential biomass precursors; 2) metabolic genes subject to transcriptional regulation involved in Staphyloxanthin biosynthesis; 3) the essentiality of purine and amino acid biosynthesis in synthetic physiological media; and 4) a switch to aerobic fermentation upon exposure to extracellular glucose elucidated as a result of integrating time-course of quantitative exo-metabolomics data. An up-to-date GEM-PRO thus serves as a knowledge-based platform to elucidate S. aureus' metabolic response to its environment.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.