ArticleGenome biology and evolution2019
Resolving Phylogenetic Relationships for Streptococcus mitis and Streptococcus oralis through Core- and Pan-Genome Analyses.
Article in Genome biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed.
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- Genomic relatedness and clinical significance ofMicrobial genomics · 2021Trial
- Topic Application of the ProbioticFrontiers in cellular and infection microbiology · 2020Trial
- The Oral Microbiome of King Richard III of England.American journal of biological anthropology · 2026Article
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- Rare Postoperative Pelvic Lymphocyst Infection byInternational medical case reports journal · 2026Article
- Genomic and functional insights into commensal streptococci with anti-pneumococcal activity.BMC genomics · 2025Article
- The research on the identification, taxonomy, and comparative genomics analysis of nineFrontiers in microbiology · 2025Article
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- Site-tropism of streptococci in the oral microbiome.Molecular oral microbiology · 2022Article
- Analysis of phylogenetic markers for classification of a hydrogen peroxide producing Streptococcus oralis isolated from saliva by a newly devised differential medium.Journal of microbiology (Seoul, Korea) · 2022Article
- Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.Microbiome · 2022Article
- Mechanisms underlying interactions between two abundant oral commensal bacteria.The ISME journal · 2022Article
- DNA isolation methods for Nanopore sequencing of theMicrobial genomics · 2022Article
- TAGOPSIN: collating taxa-specific gene and protein functional and structural information.BMC bioinformatics · 2021Article
- Complete Genome Sequence of Streptococcus oralis 34.Microbiology resource announcements · 2021Article
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- Epidural abscess related toBMJ case reports · 2021Article
- Identification and Monitoring ofJournal of microbiology and biotechnology · 2021Article
- A New Species-Specific Typing Method for Salivarius Group Streptococci Based on the Dephospho-Coenzyme A Kinase (Frontiers in cellular and infection microbiology · 2021Article
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3 authors.
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Abstract
Taxonomic and phylogenetic relationships of Streptococcus mitis and Streptococcus oralis have been difficult to establish biochemically and genetically. We used core-genome analyses of S. mitis and S. oralis, as well as the closely related species Streptococcus pneumoniae and Streptococcus parasanguinis, to clarify the phylogenetic relationships between S. mitis and S. oralis, as well as within subclades of S. oralis. All S. mitis (n = 67), S. oralis (n = 89), S. parasanguinis (n = 27), and 27 S. pneumoniae genome assemblies were downloaded from NCBI and reannotated. All genes were delineated into homologous clusters and maximum-likelihood phylogenies built from putatively nonrecombinant core gene sets. Population structure was determined using Bayesian genome clustering, and patristic distance was calculated between populations. Population-specific gene content was assessed using a phylogenetic-based genome-wide association approach. Streptococcus mitis and S. oralis formed distinct clades, but species mixing suggests taxonomic misassignment. Patristic distance between populations suggests that S. oralis subsp. dentisani is a distinct species, whereas S. oralis subsp. tigurinus and subsp. oralis are supported as subspecies, and that S. mitis comprises two subspecies. None of the genes within the pan-genomes of S. mitis and S. oralis could be statistically correlated with either, and the dispensable genomes showed extensive variation among isolates. These are likely important factors contributing to established overlap in biochemical characteristics for these taxa. Based on core-genome analysis, the substructure of S. oralis and S. mitis should be redefined, and species assignments within S. oralis and S. mitis should be made based on whole-genome analysis to be robust to misassignment.
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