1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 68, Issue 6

Isolation and characterization of sp. nov. from (Himalayan marmot) respiratory tract Free

Abstract

Two bacterial strains were individually isolated from respiratory tracts; the animals were from the Tibet–Qinghai Plateau, PR China. The isolates were Gram-stain-positive, catalase-negative, coccus-shaped, chain-forming organisms. Analysis of 16S rRNA gene sequences indicated that the type strain HTS25 shared 98.0, 97.4, 97.2 and 97.1 % similarity with , , and respectively. Sequence analysis of the and genes indicated that HTS25 was closely related to (similarities of 94.7 and 91.4 % respectively). Analysis of sequences showed interspecies similarity of 84.8 % between HTS25 and . A whole-genome phylogenetic tree reconstructed from 81 core genes from the genomes of 17 members of the genus was used to validate that HTS25 forms a distinct subline from other recognized species of the genus . DNA–DNA hybridization of HTS25 showed a maximum estimated DNA reassociation value of 32.1 % to CCUG 65085. On the basis of the results of phenotypic and phylogenetic analyses, we propose that the two isolates be classified as representing a novel species of the genus , named sp. nov. The type strain is HTS25 (=DSM 101998=CGMCC 1.15531). The genome of sp. nov. strain HTS25 (2 067 971 bp) contains 2001 genes with an average DNA G+C content of 42.7 mol%.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): 16S rRNA , Marmota himalayana , respiratory tract , Streptococcus respiraculi and Tibet-Qinghai Plateau
© 2018 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002806
2018-06-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/6/2082.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002806&mimeType=html&fmt=ahah

References

  1. 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 [View Article][PubMed]
     [Google Scholar]
  2. 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 [View Article][PubMed]
     [Google Scholar]
  3. 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 [View Article][PubMed]
     [Google Scholar]
  4. Niu L, Lu S, Hu S, Jin D, Lai X et al. Streptococcus marmotae sp. nov., isolated from the respiratory tract of Marmota himalayana . Int J Syst Evol Microbiol 2016; 66:4315–4322 [View Article][PubMed]
     [Google Scholar]
  5. Niu L, Lu S, Lai XH, Hu S, Chen C et al. Streptococcus himalayensis sp. nov., isolated from the respiratory tract of Marmota himalayana . Int J Syst Evol Microbiol 2017; 67:256–261 [View Article][PubMed]
     [Google Scholar]
  6. Zamora L, Pérez-Sancho M, Fernández-Garayzábal JF, Orden JA, Domínguez-Bernal G et al. Streptococcus ovuberis sp. nov., isolated from a subcutaneous abscess in the udder of a sheep. Int J Syst Evol Microbiol 2017; 67:4340–4344 [View Article][PubMed]
     [Google Scholar]
  7. Palakawong Na Ayudthaya S, Hilderink LJ, Oost JV, Vos WM, Plugge CM. Streptococcus caviae sp. nov., isolated from guinea pig faecal samples. Int J Syst Evol Microbiol 2017; 67:1551–1556 [View Article][PubMed]
     [Google Scholar]
  8. 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 [View Article]
     [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 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  15. 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 [View Article][PubMed]
     [Google Scholar]
  16. Rasmussen SW. SEQtools, a software package for analysis of nucleotide and protein sequences; 2002 www.seqtools.dk
  17. 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 [View Article][PubMed]
     [Google Scholar]
  18. Póntigo F, Moraga M, Flores SV. Molecular phylogeny and a taxonomic proposal for the genus Streptococcus . Genet Mol Res 2015; 14:10905–10918 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  21. 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 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. 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 [View Article][PubMed]
     [Google Scholar]
  24. 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 [View Article][PubMed]
     [Google Scholar]
  25. Berlin K, Koren S, Chin CS, Drake JP, Landolin JM et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 2015; 33:623–630 [View Article][PubMed]
     [Google Scholar]
  26. 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 [View Article][PubMed]
     [Google Scholar]
  27. 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 [View Article][PubMed]
     [Google Scholar]
  28. 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 [View Article][PubMed]
     [Google Scholar]
  29. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
     [Google Scholar]
  30. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. 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 [View Article][PubMed]
     [Google Scholar]
  33. Goodfellow M, Stainsby FM, 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]
  34. 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 [View Article][PubMed]
     [Google Scholar]
  35. 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 [View Article][PubMed]
     [Google Scholar]
  36. 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 [View Article][PubMed]
     [Google Scholar]
  37. 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 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002806
Loading
Isolation and characterization of Streptococcus respiraculi sp. nov. from Marmota himalayana (Himalayan marmot) respiratory tract
Int J Syst Evol Microbiol 68, 2082 (2018); https://doi.org/10.1099/ijsem.0.002806
/content/journal/ijsem/10.1099/ijsem.0.002806
/content/journal/ijsem/10.1099/ijsem.0.002806
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error