1887

Abstract

Five strains of Gram-positive-staining, catalase-negative, coccus-shaped, chain-forming organisms isolated separately from the respiratory tracts of five animals in the Qinghai-Tibet Plateau of China were subjected to phenotypic and molecular taxonomic analyses. Comparative analysis of the 16S rRNA gene indicated that these singular organisms represent a new member of the genus , being phylogenetically closest to DSM 101995 (98.4 % similarity). The , and sequence analysis showed interspecies similarity values between HTS2 and DSM 101995, its closest phylogenetic relative based on 16S rRNA gene sequences, of 98.2, 78.8 and 93.7 %, respectively. A whole-genome phylogenetic tree built from 82 core genes of genomes from 16 species of the genus validated that HTS2 forms a distinct subline and exhibits specific phylogenetic affinity with DNA–DNA hybridization of HTS2 showed an estimated DNA reassociation value of 40.5 % with DSM 101995. On the basis of their phenotypic characteristics and phylogenetic findings, it is proposed that the five isolates be classified as representatives of a novel species of the genus , sp. nov. The type strain is HTS2 (=DSM 101997=CGMCC 1.15533). The genome of sp. nov. strain HTS2 contains 2195 genes with a size of 2 275 471 bp and a mean DNA G+C content of 41.3 mol%.

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2017-02-01
2020-01-27
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References

  1. Bai X, Xiong Y, Lu S, Jin D, Lai X et al. Streptococcus pantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii) in Hoh Xil National Nature Reserve, Qinghai, China. Int J Syst Evol Microbiol 2016;66:3281–3286[CrossRef]
    [Google Scholar]
  2. Niu L, Lu S, Hu S, Jin D, Lai X et al. Streptococcus halotolerans sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China. Int J Syst Evol Microbiol 2016;66:4211–4217 [CrossRef][PubMed]
    [Google Scholar]
  3. Niu L, Lu S, Hu S, Jin D, Lai X et al. Streptococcus marmotae sp. nov. isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China. Int J Syst Evol Microbiol 2016
    [Google Scholar]
  4. Okamoto M, Imai S, Miyanohara M, Saito W, Momoi Y et al. Streptococcus panodentis sp. nov. from the oral cavities of chimpanzees. Microbiol Immunol 2015;59:526–532 [CrossRef][PubMed]
    [Google Scholar]
  5. Vela AI, Casas-Díaz E, Lavín S, Domínguez L, Fernández-Garayzábal JF. Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits. Int J Syst Evol Microbiol 2015;65:2903–2907 [CrossRef][PubMed]
    [Google Scholar]
  6. Stone R. China. Race to contain plague in quake zone. Nature 2010;328:559
    [Google Scholar]
  7. Hu S, Jin D, Lu S, Liu S, Zhang J et al. Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana. Int J Syst Evol Microbiol 2015;65:1719–1725 [CrossRef][PubMed]
    [Google Scholar]
  8. Liu S, Jin D, Lan R, Wang Y, Meng Q et al. Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana. Int J Syst Evol Microbiol 2015;65:2130–2134 [CrossRef][PubMed]
    [Google Scholar]
  9. Facklam R, Elliott JA. Identification, classification, and clinical relevance of catalase-negative, gram-positive cocci, excluding the streptococci and enterococci. Clin Microbiol Rev 1995;8:479–495[PubMed]
    [Google Scholar]
  10. Austrian R. The Gram stain and the etiology of Lobar pneumonia, an historical note. Bacteriol Rev 1960;24:261–265[PubMed]
    [Google Scholar]
  11. Xu Y, Xu X, Lan R, Xiong Y, Ye C et al. An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7. PLoS One 2013;8:e64211 [CrossRef][PubMed]
    [Google Scholar]
  12. Vela AI, Fernández E, Lawson PA, Latre MV, Falsen E et al. Streptococcus entericus sp. nov., isolated from cattle intestine. Int J Syst Evol Microbiol 2002;52:665–669 [CrossRef][PubMed]
    [Google Scholar]
  13. Delgado S, Suárez A, Mayo B. Identification of dominant bacteria in feces and colonic mucosa from healthy Spanish adults by culturing and by 16S rDNA sequence analysis. Dig Dis Sci 2006;51:744–751 [CrossRef][PubMed]
    [Google Scholar]
  14. Jin D, Chen C, Li L, Lu S, Li Z et al. Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. BMC Microbiol 2013;13:141 [CrossRef][PubMed]
    [Google Scholar]
  15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013;30:2725–2729 [CrossRef][PubMed]
    [Google Scholar]
  17. Rasmussen SW. 2002; SEQtools, a software package for analysis of nucleotide and protein sequences. www.seqtools.dk
  18. Póntigo F, Moraga M, Flores SV. Molecular phylogeny and a taxonomic proposal for the genus Streptococcus. Genet Mol Res 2015;14:10905–10918 [CrossRef][PubMed]
    [Google Scholar]
  19. Saito M, Shinozaki-Kuwahara N, Hirasawa M, Takada K. Streptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin. Int J Syst Evol Microbiol 2016;66:1063–1067 [CrossRef][PubMed]
    [Google Scholar]
  20. Shinozaki-Kuwahara N, Saito M, Hirasawa M, Takada K. Streptococcus oriloxodontae sp. nov., isolated from the oral cavities of elephants. Int J Syst Evol Microbiol 2014;64:3755–3759 [CrossRef][PubMed]
    [Google Scholar]
  21. Glazunova OO, Raoult D, Roux V. Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus. Int J Syst Evol Microbiol 2009;59:2317–2322 [CrossRef][PubMed]
    [Google Scholar]
  22. Poyart C, Quesne G, Trieu-Cuot P. Taxonomic dissection of the Streptococcus bovis group by analysis of manganese-dependent superoxide dismutase gene (sodA) sequences: reclassification of 'Streptococcus infantarius subsp. Coli' as Streptococcus lutetiensis sp. nov. and of Streptococcus bovis biotype 11.2 as Streptococcus pasteurianus sp. nov. Int J Syst Evol Microbiol 2002;52:1247–1255 [CrossRef][PubMed]
    [Google Scholar]
  23. Drancourt M, Roux V, Fournier PE, Raoult D. rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. J Clin Microbiol 2004;42:497–504 [CrossRef][PubMed]
    [Google Scholar]
  24. Guimaraes AM, Santos AP, Sanmiguel P, Walter T, Timenetsky J et al. Complete genome sequence of Mycoplasma suis and insights into its biology and adaption to an erythrocyte niche. PLoS One 2011;6:e19574 [CrossRef][PubMed]
    [Google Scholar]
  25. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009;26:1641–1650 [CrossRef][PubMed]
    [Google Scholar]
  26. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012;28:3150–3152 [CrossRef][PubMed]
    [Google Scholar]
  27. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013;30:772–780 [CrossRef][PubMed]
    [Google Scholar]
  28. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012;61:1061–1067 [CrossRef][PubMed]
    [Google Scholar]
  29. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987;37:463–464[CrossRef]
    [Google Scholar]
  30. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P. Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 2010;60:249–266 [CrossRef][PubMed]
    [Google Scholar]
  31. Goodfellow M, Stainsby F, Davenport R, Chun J, Curtis T. Activated sludge foaming: the true extent of actinomycete diversity. Water Sci Technol 1998;37:511–519 [CrossRef]
    [Google Scholar]
  32. Auch AF, von Jan M, Klenk HP, Göker M. Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010;2:117–134 [CrossRef][PubMed]
    [Google Scholar]
  33. Colston SM, Fullmer MS, Beka L, Lamy B, Gogarten JP et al. Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. MBio 2014;5:e02136 [CrossRef][PubMed]
    [Google Scholar]
  34. Garrido-Sanz D, Meier-Kolthoff JP, Göker M, Martín M, Rivilla R et al. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex. PLoS One 2016;11:e0150183 [CrossRef][PubMed]
    [Google Scholar]
  35. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60 [CrossRef][PubMed]
    [Google Scholar]
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