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Article: Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus
Title | Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus |
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Authors | |
Keywords | Streptococcus sinensis Genome Phylogenomic “Sinensis group” Illumina |
Issue Date | 2014 |
Publisher | Oxford University Press for Society for Molecular Biology and Evolution. The Journal's web site is located at http://gbe.oxfordjournals.org |
Citation | Genome Biology and Evolution, 2014, v. 6 n. 10, p. 2930-2943 How to Cite? |
Abstract | Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. |
Persistent Identifier | http://hdl.handle.net/10722/211868 |
ISSN | 2023 Impact Factor: 3.2 2023 SCImago Journal Rankings: 1.315 |
PubMed Central ID | |
ISI Accession Number ID |
DC Field | Value | Language |
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dc.contributor.author | Teng, JLL | - |
dc.contributor.author | Huang, Y | - |
dc.contributor.author | Tse, H | - |
dc.contributor.author | Chen, JHK | - |
dc.contributor.author | Tang, Y | - |
dc.contributor.author | Lau, SKP | - |
dc.contributor.author | Woo, PCY | - |
dc.date.accessioned | 2015-07-21T02:14:09Z | - |
dc.date.available | 2015-07-21T02:14:09Z | - |
dc.date.issued | 2014 | - |
dc.identifier.citation | Genome Biology and Evolution, 2014, v. 6 n. 10, p. 2930-2943 | - |
dc.identifier.issn | 1759-6653 | - |
dc.identifier.uri | http://hdl.handle.net/10722/211868 | - |
dc.description.abstract | Streptococcus sinensis is a recently discovered human pathogen isolated from blood cultures of patients with infective endocarditis. Its phylogenetic position, as well as those of its closely related species, remains inconclusive when single genes were used for phylogenetic analysis. For example, S. sinensis branched out from members of the anginosus, mitis, and sanguinis groups in the 16S ribosomal RNA gene phylogenetic tree, but it was clustered with members of the anginosus and sanguinis groups when groEL gene sequences used for analysis. In this study, we sequenced the draft genome of S. sinensis and used a polyphasic approach, including concatenated genes, whole genomes, and matrix-assisted laser desorption ionization-time of flight mass spectrometry to analyze the phylogeny of S. sinensis. The size of the S. sinensis draft genome is 2.06 Mb, with GC content of 42.2%. Phylogenetic analysis using 50 concatenated genes or whole genomes revealed that S. sinensis formed a distinct cluster with Streptococcus oligofermentans and Streptococcus cristatus, and these three streptococci were clustered with the “sanguinis group.” As for phylogenetic analysis using hierarchical cluster analysis of the mass spectra of streptococci, S. sinensis also formed a distinct cluster with S. oligofermentans and S. cristatus, but these three streptococci were clustered with the “mitis group.” On the basis of the findings, we propose a novel group, named “sinensis group,” to include S. sinensis, S. oligofermentans, and S. cristatus, in the Streptococcus genus. Our study also illustrates the power of phylogenomic analyses for resolving ambiguities in bacterial taxonomy. | - |
dc.language | eng | - |
dc.publisher | Oxford University Press for Society for Molecular Biology and Evolution. The Journal's web site is located at http://gbe.oxfordjournals.org | - |
dc.relation.ispartof | Genome Biology and Evolution | - |
dc.rights | This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License. | - |
dc.subject | Streptococcus sinensis | - |
dc.subject | Genome | - |
dc.subject | Phylogenomic | - |
dc.subject | “Sinensis group” | - |
dc.subject | Illumina | - |
dc.title | Phylogenomic and MALDI-TOF MS analysis of Streptococcus sinensis HKU4T reveals a distinct phylogenetic clade in the genus Streptococcus | - |
dc.type | Article | - |
dc.identifier.email | Teng, JLL: llteng@hku.hk | - |
dc.identifier.email | Tse, H: htse@hkucc.hku.hk | - |
dc.identifier.email | Chen, JHK: jonchk@hku.hk | - |
dc.identifier.email | Lau, SKP: skplau@hkucc.hku.hk | - |
dc.identifier.email | Woo, PCY: pcywoo@hkucc.hku.hk | - |
dc.identifier.authority | Teng, JLL=rp00277 | - |
dc.identifier.authority | Tse, H=rp00519 | - |
dc.identifier.authority | Lau, SKP=rp00486 | - |
dc.identifier.authority | Woo, PCY=rp00430 | - |
dc.description.nature | published_or_final_version | - |
dc.identifier.doi | 10.1093/gbe/evu232 | - |
dc.identifier.pmid | 25331233 | - |
dc.identifier.pmcid | PMC4224358 | - |
dc.identifier.scopus | eid_2-s2.0-84931386247 | - |
dc.identifier.hkuros | 245765 | - |
dc.identifier.volume | 6 | - |
dc.identifier.issue | 10 | - |
dc.identifier.spage | 2930 | - |
dc.identifier.epage | 2943 | - |
dc.identifier.isi | WOS:000346775800027 | - |
dc.publisher.place | United Kingdom | - |
dc.identifier.issnl | 1759-6653 | - |