{"doi":"10.1089/omi.2019.0005","title":"Analyses of Livestock-Associated\n                    <i>Staphylococcus aureus</i>\n                    Pan-Genomes Suggest Virulence Is Not Primary Interest in Evolution of Its Genome","abstract":"<jats:title>Abstract</jats:title>\n                  <jats:p>\n                    <jats:italic toggle=\"yes\">Staphylococcus aureus</jats:italic>\n                    is not only part of normal flora but also an opportunistic pathogen relevant to microbial genomics, public health, and veterinary medicine. In addition to being a well-known human pathogen,\n                    <jats:italic toggle=\"yes\">S. aureus</jats:italic>\n                    causes various infections in economically important livestock animals such as cows, sheep, goats, and pigs. There are very few studies that have examined the pan-genome of\n                    <jats:italic toggle=\"yes\">S. aureus</jats:italic>\n                    or the host-specific strains' pan-genomes. We report on livestock-associated\n                    <jats:italic toggle=\"yes\">S. aureus'</jats:italic>\n                    (LA-\n                    <jats:italic toggle=\"yes\">SA</jats:italic>\n                    ) pan-genome and suggest that virulence is not the primary interest in evolution of its genome. LA-\n                    <jats:italic toggle=\"yes\">SA</jats:italic>\n                    ' complete genomes were retrieved from the NCBI and pan-genome was constructed by high-speed Roary pipeline. The pan-genome size was 4637 clusters, whereas 42.46% of the pan-genome was associated with the core genome. We found 1268 genes were associated with the strain-unique genome, and the remaining 1432 cluster with the accessory genome. COG (clusters of orthologous group of proteins) analysis of the core genes revealed 34% of clusters related to metabolism responsible for amino acid and inorganic ion transport (COG categories E and P), followed by carbohydrate metabolism (category G). Virulent gene analysis revealed the core genes responsible for antiphagocytosis and iron uptake. The fluidity of pan-genome was calculated as 0.082 ± 0.025. Importantly, the positive selection analysis suggested a slower rate of evolution among the LA-\n                    <jats:italic toggle=\"yes\">SA</jats:italic>\n                    genomes. We call for comparative microbial and pan-genome research between human and LA\n                    <jats:italic toggle=\"yes\">-SA</jats:italic>\n                    that can help further understand the evolution of virulence and thus inform future microbial diagnostics and drug discovery.\n                  </jats:p>","journal":"OMICS: A Journal of Integrative Biology","year":2019,"id":35474,"datarank":0.57907178511536,"base_score":2.639057329615259,"endowment":2.639057329615259,"self_citation_contribution":0.3958585994422889,"citation_network_contribution":0.183213185673071,"self_endowment_contribution":0.3958585994422889,"citer_contribution":0.183213185673071,"corpus_percentile":null,"corpus_rank":null,"citation_count":13,"citer_count":13,"citers_with_citation_signal":8,"citers_with_endowment":8,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":null,"is_data_producer":false,"deposit_databanks":null,"is_oa":false,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":null,"fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":181602,"name":"Natesan Sivakumar","orcid":null,"position":1,"is_corresponding":false},{"id":181603,"name":"Kannan Jayakumar","orcid":null,"position":2,"is_corresponding":false},{"id":181601,"name":"Relangi Tulasi Rao","orcid":null,"position":0,"is_corresponding":false}],"reference_count":0,"raw_metadata":{"has_enrichment":true,"base_score":2.639057329615259,"endowment":2.639057329615259,"datacite_reuse_total":0,"file_count":0,"downloads":0,"views":0,"has_version_chain":false,"is_dataset":false,"is_oa":false,"pmid":"31009331","pmcid":null,"openalex_id":"https://openalex.org/W2941201441","authors":[],"funders":[],"total_grants":0,"fwci":0.6835,"citation_percentile":0.68613163,"influential_citations":0,"citation_trend":[{"year":2019,"count":1},{"year":2020,"count":2},{"year":2021,"count":1},{"year":2022,"count":4},{"year":2024,"count":4},{"year":2026,"count":1}],"oa_status":"closed","license":"https://journals.sagepub.com/page/policies/text-and-data-mining-license","oa_locations":[{"url":"https://journals.sagepub.com/doi/full-xml/10.1089/omi.2019.0005","host_type":"publisher"},{"url":"https://journals.sagepub.com/doi/pdf/10.1089/omi.2019.0005","host_type":"publisher"},{"url":"https://doi.org/10.1089/omi.2019.0005","host_type":"journal"},{"url":"https://pubmed.ncbi.nlm.nih.gov/31009331","host_type":"repository"}],"fields_of_study":["Genomics and Phylogenetic Studies","Bacteriophages and microbial interactions","Medicine","Biology","Environmental Science","Computational Biology","Drug Discovery","Genome, Bacterial","Genomics","Staphylococcus aureus","Virulence"],"mesh_terms":["Staphylococcus aureus","Virulence","Genome, Bacterial","Computational Biology","Genomics","Drug Discovery"],"keywords":["Genome","Virulence","Biology","Comparative genomics","Gene","Genetics","Genome evolution","Genomics","Staphylococcus aureus","Bacteria","Bioinformatics","drug discovery","Microbial Evolution","Microbial Genomics","Pan-genome","Livestock-associated"],"sdg_mappings":[{"sdg_number":0,"sdg_label":"Good health and well-being"}],"linked_datasets":[],"clinical_trials":[],"software_tools":[],"database_accessions":[],"source":"live","citation_network_status":"fetched"},"created_at":"2026-06-10T04:11:41.428810Z","pmid":null,"pmcid":null,"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":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}