{"doi":"10.1038/s41540-019-0122-3","title":"An integrated computational and experimental study to investigate Staphylococcus aureus metabolism","abstract":"Staphylococcus aureus is a metabolically versatile pathogen that colonizes nearly all organs of the human body. A detailed and comprehensive knowledge of staphylococcal metabolism is essential to understand its pathogenesis. To this end, we have reconstructed and experimentally validated an updated and enhanced genome-scale metabolic model of S. aureus USA300_FPR3757. The model combined genome annotation data, reaction stoichiometry, and regulation information from biochemical databases and previous strain-specific models. Reactions in the model were checked and fixed to ensure chemical balance and thermodynamic consistency. To further refine the model, growth assessment of 1920 nonessential mutants from the Nebraska Transposon Mutant Library was performed, and metabolite excretion profiles of important mutants in carbon and nitrogen metabolism were determined. The growth and no-growth inconsistencies between the model predictions and in vivo essentiality data were resolved using extensive manual curation based on optimization-based reconciliation algorithms. Upon intensive curation and refinements, the model contains 863 metabolic genes, 1379 metabolites (including 1159 unique metabolites), and 1545 reactions including transport and exchange reactions. To improve the accuracy and predictability of the model to environmental changes, condition-specific regulation information curated from the existing knowledgebase was incorporated. These critical additions improved the model performance significantly in capturing gene essentiality, substrate utilization, and metabolite production capabilities and increased the ability to generate model-based discoveries of therapeutic significance. Use of this highly curated model will enhance the functional utility of omics data, and therefore, serve as a resource to support future investigations of S. aureus and to augment staphylococcal research worldwide.","journal":"npj Systems Biology and Applications","year":2020,"id":75308,"datarank":0.777030600665584,"base_score":3.258096538021482,"endowment":3.258096538021482,"self_citation_contribution":0.4887144807032224,"citation_network_contribution":0.2883161199623616,"self_endowment_contribution":0.4887144807032224,"citer_contribution":0.2883161199623616,"corpus_percentile":74.11619091823316,"corpus_rank":3347,"citation_count":25,"citer_count":17,"citers_with_citation_signal":11,"citers_with_endowment":11,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.8952,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":29.1667,"fair_percentile":43.01436869458881,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":393120,"name":"Vinai C. Thomas","orcid":"0000-0002-7886-0727","position":1,"is_corresponding":false},{"id":394220,"name":"Matthew Van Beek","orcid":null,"position":2,"is_corresponding":false},{"id":393121,"name":"Jongsam Ahn","orcid":"0000-0002-6696-9549","position":3,"is_corresponding":false},{"id":393122,"name":"Abdulelah A. Alqarzaee","orcid":"0000-0003-0000-9040","position":4,"is_corresponding":false},{"id":393123,"name":"Chunyi Zhou","orcid":"0000-0003-1278-5901","position":5,"is_corresponding":false},{"id":393124,"name":"Paul D. Fey","orcid":"0000-0003-0939-6884","position":6,"is_corresponding":false},{"id":350687,"name":"Kenneth W. Bayles","orcid":"0000-0001-9521-3540","position":7,"is_corresponding":false},{"id":393125,"name":"Rajib Saha","orcid":"0000-0002-2974-0243","position":8,"is_corresponding":false},{"id":393119,"name":"Mohammad Mazharul Islam","orcid":"0000-0002-9745-0344","position":0,"is_corresponding":true}],"reference_count":98,"raw_metadata":null,"created_at":"2026-07-18T21:46:33.313355Z","pmid":"32001720","pmcid":"PMC6992624","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":11.1111,"fair_a":25.0,"fair_i":100.0,"fair_r":41.6667,"fair_zscore":-0.2091,"fair_rationale":{"fair_score":29.17,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":11.11,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"The paper does not provide any persistent identifier string for its own dataset; the model is only mentioned as available in SBML format in Dataset 1 without a DOI or accession.","anchors":["RDA-F1-01D — FAIR Data Maturity Model: 'Data is identified by a persistent identifier' (priorit","RDA-F1-02D — FAIR Data Maturity Model: 'Data is identified by a globally unique identifier'","FsF-F1-02D — F-UJI/FAIRsFAIR: 'Data is assigned a persistent identifier'"],"scored":true,"signal":null},{"key":"f_repository_named","label":"Named repository","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":null,"grounded":false,"rationale":"No repository is named as the holder; the data are stated to be in the article and supplementary files, not in a curated repository.","anchors":["RDA-F4-01M — FAIR Data Maturity Model: metadata is offered so it can be harvested and indexed (","NIH DMS Policy Element 4 (NOT-OD-21-014) — name the repository where data will be archived","NSTC Desirable Characteristics of Data Repositories (2022) — 'Long-Term Sustainability', 'Reten"],"scored":true,"signal":null},{"key":"f_data_availability_statement","label":"Data-availability statement","kind":"llm","weight":2.0,"fraction":0.0,"verdict":"no","evidence":"All data generated or analysed during this study are included in this published article and its supplementary information files.","grounded":false,"rationale":"The statement points to the article and supplementary files (Colavizza category 2) rather than to a repository record. 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