1887

Abstract

Two Gramstaining-positive, catalase-negative, α-hemolytic, coccus-shaped organisms were isolated separately from the respiratory tracts of two Marmota himalayana animals from the Qinghai-Tibet Plateau, PR China. Morphological, biological, biochemical, and molecular genetic studies were performed on these two isolates (HTS9 and HTS12). Their biochemical characteristics, such as acid production from different sugars and enzymatic activities, indicated that they represented a member of the genus Streptococcus . They are most closely related to Streptococcus thoraltensis CIP 105518 based on sequence analysis of their 16S rRNA, groEL, sodA and rpoB genes, with similarities of 97.6, 89.9, 92.6 and 91.1 % the four genes respectively. The whole genome phylogenetic tree reconstructed using 372 core genes from 65 genomes of members of the genus Streptococcus validates that HTS9 forms a distinct subline and exhibits specific phylogenetic affinity with S. thoraltensis . In silico DNA–DNA hybridization of HTS9 showed a DNA reassociation value of 32.1 %, closest to that of S. thoraltensis CIP 105518. Based on their phenotypic characteristics and in particular the phylogenetic findings (DNA–DNA hybridization, three phylogenetic trees built from the partial 16S rRNA/housekeeping genes, and from 372 core genes of 65 genomes of members of the genus Streptococcus ), we propose with confidence that strains HTS9 and HTS12 should be classified as representing a novel species of the genus Streptococcus , Streptococcus halotolerans sp. nov. The type strain is HTS9 (=DSM 101996=CGMCC1.15532). Genome analysis of Streptococcus halotolerans sp. nov. shows that its genome is 1 823 556 bp long with a DNA G+C content of 39.9 mol% and contains 2068 genes.

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2016-10-01
2019-12-05
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References

  1. Auch A. F., von Jan M., Klenk H. P., Göker M..( 2010;). Digital DNA–DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. . Stand Genomic Sci 2: 117–134. [CrossRef] [PubMed]
    [Google Scholar]
  2. Austrian R..( 1960;). The Gram stain and the etiology of lobar pneumonia, an historical note. . Bacteriol Rev 24: 261–265.[PubMed]
    [Google Scholar]
  3. Colston S. M., Fullmer M. S., Beka L., Lamy B., Gogarten J. P., Graf J..( 2014;). Bioinformatic genome comparisons for taxonomic and phylogenetic assignments using Aeromonas as a test case. . MBio 5: e02136. [CrossRef] [PubMed]
    [Google Scholar]
  4. Delgado S., Suárez A., Mayo B..( 2006;). Identification of dominant bacteria in feces and colonic mucosa from healthy Spanish adults by culturing and by 16S rDNA sequence analysis. . Dig Dis Sci 51: 744–751. [CrossRef] [PubMed]
    [Google Scholar]
  5. Devriese L. A., Pot B., Vandamme P., Kersters K., Collins M. D., Alvarez N., Haesebrouck F., Hommez J..( 1997;). Streptococcus hyovaginalis sp. nov. and Streptococcus thoraltensis sp. nov., from the genital tract of sows. . Int J Syst Bacteriol 47: 1073–1077. [CrossRef] [PubMed]
    [Google Scholar]
  6. Devriese L. A., Vandamme P., Collins M. D., Alvarez N., Pot B., Hommez J., Butaye P., Haesebrouck F..( 1999;). Streptococcus pluranimalium sp. nov., from cattle and other animals. . Int J Syst Bacteriol 49: 1221–1226. [CrossRef] [PubMed]
    [Google Scholar]
  7. Drancourt M., Roux V., Fournier P. E., Raoult D..( 2004;). rpoB gene sequence-based identification of aerobic Gram-positive cocci of the genera Streptococcus, Enterococcus, Gemella, Abiotrophia, and Granulicatella. . J Clin Microbiol 42: 497–504. [CrossRef] [PubMed]
    [Google Scholar]
  8. Facklam R., Elliott J. A..( 1995;). Identification, classification, and clinical relevance of catalase-negative, Gram-positive cocci, excluding the Streptococci and Enterococci. . Clin Microbiol Rev 8: 479–495.[PubMed]
    [Google Scholar]
  9. Garrido-Sanz D., Meier-Kolthoff J. P., Göker M., Martín M., Rivilla R., Redondo-Nieto M..( 2016;). Genomic and genetic diversity within the Pseudomonas fluorescens Complex. . PLoS One 11: e0150183. [CrossRef] [PubMed]
    [Google Scholar]
  10. Glazunova O. O., Raoult D., Roux V..( 2009;). Partial sequence comparison of the rpoB, sodA, groEL and gyrB genes within the genus Streptococcus. . Int J Syst Evol Microbiol 59: 2317–2322. [CrossRef] [PubMed]
    [Google Scholar]
  11. Goh S. H., Potter S., Wood J. O., Hemmingsen S. M., Reynolds R. P., Chow A. W..( 1996;). HSP60 gene sequences as universal targets for microbial species identification: studies with coagulase-negative staphylococci. . J Clin Microbiol 34: 818–823.[PubMed]
    [Google Scholar]
  12. Goodfellow M., Stainsby F. M., Davenport R., Chun J., Curtis T..( 1998;). Activated sludge foaming: the true extent of actinomycete diversity. . Water Sci Technol 37: 511–519. [CrossRef]
    [Google Scholar]
  13. Guimaraes A. M., Santos A. P., SanMiguel P., Walter T., Timenetsky J., Messick J. B..( 2011;). Complete genome sequence of Mycoplasma suis and insights into its biology and adaption to an erythrocyte niche. . PLoS One 6: e19574. [CrossRef] [PubMed]
    [Google Scholar]
  14. Hu S., Jin D., Lu S., Liu S., Zhang J., Wang Y., Bai X., Xiong Y., Huang Y. et al.( 2015;). Helicobacter himalayensis sp. nov. isolated from gastric mucosa of Marmota himalayana. . Int J Syst Evol Microbiol 65: 1719–1725. [CrossRef] [PubMed]
    [Google Scholar]
  15. Huson D. H., Scornavacca C..( 2012;). Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. . Syst Biol 61: 1061–1067. [CrossRef] [PubMed]
    [Google Scholar]
  16. Jin D., Chen C., Li L., Lu S., Li Z., Zhou Z., Jing H., Xu Y., Du P. et al.( 2013;). Dynamics of fecal microbial communities in children with diarrhea of unknown etiology and genomic analysis of associated Streptococcus lutetiensis. . BMC Microbiol 13: 141. [CrossRef] [PubMed]
    [Google Scholar]
  17. Katoh K., Standley D. M..( 2013;). MAFFT multiple sequence alignment software version 7: improvements in performance and usability. . Mol Biol Evol 30: 772–780. [CrossRef] [PubMed]
    [Google Scholar]
  18. Kimura M..( 1980;). A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. . J Mol Evol 16: 111–120. [CrossRef] [PubMed]
    [Google Scholar]
  19. Liu S., Jin D., Lan R., Wang Y., Meng Q., Dai H., Lu S., Hu S., Xu J..( 2015;). Escherichia marmotae sp. nov., isolated from faeces of Marmota himalayana. . Int J Syst Evol Microbiol 65: 2130–2134. [CrossRef] [PubMed]
    [Google Scholar]
  20. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M..( 2013;). Genome sequence-based species delimitation with confidence intervals and improved distance functions. . BMC Bioinformatics 14: 60. [CrossRef] [PubMed]
    [Google Scholar]
  21. Póntigo F., Moraga M., Flores S. V..( 2015;). Molecular phylogeny and a taxonomic proposal for the genus Streptococcus. . Genet Mol Res 14: 10905–10918. [CrossRef] [PubMed]
    [Google Scholar]
  22. Poyart C., Quesne G., Trieu-Cuot P..( 2002;). 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 52: 1247–1255. [CrossRef] [PubMed]
    [Google Scholar]
  23. Price M. N., Dehal P. S., Arkin A. P..( 2009;). FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. . Mol Biol Evol 26: 1641–1650. [CrossRef] [PubMed]
    [Google Scholar]
  24. Rasmussen S. W..( 2002;). SEQtools, a software package for analysis of nucleotide and protein sequences. . http://www.seqtools.dk.
  25. Saito M., Shinozaki-Kuwahara N., Hirasawa M., Takada K..( 2016;). Streptococcus oricebi sp. nov., isolated from the oral cavity of tufted capuchin. . Int J Syst Evol Microbiol 66: 1063–1067. [CrossRef] [PubMed]
    [Google Scholar]
  26. Shinozaki-Kuwahara N., Saito M., Hirasawa M., Takada K..( 2014;). Streptococcus oriloxodontae sp. nov., isolated from the oral cavities of elephants. . Int J Syst Evol Microbiol 64: 3755–3759. [CrossRef] [PubMed]
    [Google Scholar]
  27. Stackebrandt E., Goebel B. M..( 1994;). Taxonomic note: a place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44: 846–849. [CrossRef]
    [Google Scholar]
  28. Stackebrandt E., Ebers J..( 2006;). Taxonomic parameters revisited: tarnished gold standards. . Microbiol Today 33: 152–155.
    [Google Scholar]
  29. Stone R..( 2010;). China. race to contain plague in quake zone. . Science 328: 559. [CrossRef] [PubMed]
    [Google Scholar]
  30. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S..( 2013;). mega6: molecular evolutionary genetics analysis version 6.0. . Mol Biol Evol 30: 2725–2729. [CrossRef] [PubMed]
    [Google Scholar]
  31. Vela A. I., Fernández E., Lawson P. A., Latre M. V., Falsen E., Domínguez L., Collins M. D., Fernández-Garayzábal J. F..( 2002;). Streptococcus entericus sp. nov., isolated from cattle intestine. . Int J Syst Evol Microbiol 52: 665–669. [CrossRef] [PubMed]
    [Google Scholar]
  32. Vela A. I., Casas-Díaz E., Lavín S., Domínguez L., Fernández-Garayzábal J. F..( 2015;). Streptococcus pharyngis sp. nov., a novel streptococcal species isolated from the respiratory tract of wild rabbits. . Int J Syst Evol Microbiol 65: 2903–2907. [CrossRef] [PubMed]
    [Google Scholar]
  33. Vela A. I., Mentaberre G., Lavín S., Domínguez L., Fernández-Garayzábal J. F..( 2016;). Streptococcus caprae sp. nov., isolated from Iberian ibex (Capra pyrenaica hispanica). . Int J Syst Evol Microbiol 66: 196–200. [CrossRef] [PubMed]
    [Google Scholar]
  34. Wayne L. G..( 1988;). International committee on systematic bacteriology: announcement of the report of the ad hoc committee on reconciliation of approaches to bacterial systematics. . Zentralbl Bakteriol Mikrobiol Hyg A 268: 433–434.[PubMed]
    [Google Scholar]
  35. Xu Y., Xu X., Lan R., Xiong Y., Ye C., Ren Z., Liu L., Zhao A., Wu L. F., Xu J..( 2013;). An O island 172 encoded RNA helicase regulates the motility of Escherichia coli O157:H7. . PLoS One 8: e64211.
    [Google Scholar]
  36. Yarza P., Richter M., Peplies J., Euzeby J., Amann R., Schleifer K. H., Ludwig W., Glöckner F. O., Rosselló-Móra R..( 2008;). The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. . Syst Appl Microbiol 31: 241–250. [CrossRef] [PubMed]
    [Google Scholar]
  37. Yarza P., Yilmaz P., Pruesse E., Glöckner F. O., Ludwig W., Schleifer K. H., Whitman W. B., Euzéby J., Amann R., Rosselló-Móra R..( 2014;). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. . Nat Rev Microbiol 12: 635–645. [CrossRef] [PubMed]
    [Google Scholar]
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