1887

Abstract

The taxonomic position of four phenotypically closely related strains isolated from faecal samples of yaks (Bos grunniens) collected from the Qinghai-Tibetan plateau, China, was determined by a polyphasic approach. The strains were non-spore-forming, non-motile Gram-stain-positive, ovoid cocci, occurring predominantly in pairs and short chains or in irregular clusters. The 16S rRNA gene of strain MN05 was related phylogenetically to those of Enterococcus haemoperoxidus , Enterococcus rotai , Enterococcus quebecensis , Enterococcus plantarum , Enterococcus crotali , Enterococcus moraviensis , Enterococcus silesiacus , Enterococcus caccae , Enterococcus termitis , Enterococcus ureasiticus and Enterococcus ureilyticus , all belonging to the Enterococcus faecalis species group. The sequence similarities of three selected genes of MN05 to those of the type strains of phylogenetically related species were measured, with values within the range of 99.2–99.5 % (16S rRNA gene), 90.0–97.3 % (rpoA) and 80.0–85.3 % (pheS), respectively. The genome of MN05 (3 842 361 bp) contained 4299 genes with a DNA G+C content of 37.5 mol%. A whole-genome phylogenetic tree based on 808 core genes confirmed that MN05 belongs to a distinct lineage, well separated from all recognized species of the Enterococcus faecalis species group. DNA–DNA hybridization in silico showed that MN05 displayed less than 70 % DNA–DNA relatedness with the other 13 species of the Enterococcus faecalis species group. Moreover, their phenotypic features distinguished the four strains from the other species of the Enterococcus faecalis species group. Based upon these data obtained from the polyphasic characterization performed in the present study, a novel species of the genus Enterococcus , Enterococcus wangshanyuanii sp. nov., is proposed, with the type strain MN05 (=DSM 104047=CGMCC 1.15942).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002447
2017-10-26
2019-08-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/12/5216.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002447&mimeType=html&fmt=ahah

References

  1. Franz CM, Holzapfel WH, Stiles ME. Enterococci at the crossroads of food safety?. Int J Food Microbiol 1999; 47: 1– 24 [CrossRef] [PubMed]
    [Google Scholar]
  2. Fisher K, Phillips C. The ecology, epidemiology and virulence of Enterococcus. Microbiology 2009; 155: 1749– 1757 [CrossRef] [PubMed]
    [Google Scholar]
  3. Hugas M, Garriga M, Aymerich MT. Functionality of enterococci in meat products. Int J Food Microbiol 2003; 88: 223– 233 [CrossRef] [PubMed]
    [Google Scholar]
  4. Köhler W. The present state of species within the genera Streptococcus and Enterococcus. Int J Med Microbiol 2007; 297: 133– 150 [CrossRef] [PubMed]
    [Google Scholar]
  5. Parte AC. LPSN–list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42: D613– D616 [CrossRef] [PubMed]
    [Google Scholar]
  6. 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]
  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. 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]
  9. Niu L, Lu S, Lai XH, Hu S, Chen C et al. Streptococcus himalayensis sp. nov., a new streptococcal species isolated from the respiratory tract of Marmota himalayana in Qinghai-Tibet Plateau of China. Int J Syst Evol Microbiol 2017; 67: 256– 261 [Crossref]
    [Google Scholar]
  10. 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 [CrossRef] [PubMed]
    [Google Scholar]
  11. 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). Int J Syst Evol Microbiol 2016; 66: 3281– 3286 [CrossRef] [PubMed]
    [Google Scholar]
  12. Meng X, Lu S, Lai XH, Wang Y, Wen Y et al. Actinomyces liubingyangii sp. nov. isolated from the vulture Gypaetus barbatus. Int J Syst Evol Microbiol 2017; 67: 1873– 1879 [CrossRef] [PubMed]
    [Google Scholar]
  13. Meng X, Lu S, Wang Y, Lai XH, Wen Y et al. Actinomyces vulturis sp. nov., isolated from Gyps himalayensis. Int J Syst Evol Microbiol 2017; 67: 1720– 1726 [CrossRef] [PubMed]
    [Google Scholar]
  14. Bai X, Zhao A, Lan R, Xin Y, Xie H et al. Shiga toxin-producing Escherichia coli in yaks (Bos grunniens) from the Qinghai-Tibetan Plateau, China. PLoS One 2013; 8: e65537 [CrossRef] [PubMed]
    [Google Scholar]
  15. 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]
  16. 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]
  17. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67: 1613– 1617 [CrossRef] [PubMed]
    [Google Scholar]
  18. McLaughlin RW, Shewmaker PL, Whitney AM, Humrighouse BW, Lauer AC et al. Enterococcus crotali sp. nov., isolated from faecal material of a timber rattlesnake. Int J Syst Evol Microbiol 2017; 67: 1984– 1989 [CrossRef] [PubMed]
    [Google Scholar]
  19. Thompson JD, Higgins DG, Gibson TJ. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994; 22: 4673– 4680 [CrossRef] [PubMed]
    [Google Scholar]
  20. 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]
  21. Naser SM, Thompson FL, Hoste B, Gevers D, Dawyndt P et al. Application of multilocus sequence analysis (MLSA) for rapid identification of Enterococcus species based on rpoA and pheS genes. Microbiology 2005; 151: 2141– 2150 [CrossRef] [PubMed]
    [Google Scholar]
  22. Svec P, Vandamme P, Bryndová H, Holochová P, Kosina M et al. Enterococcus plantarum sp. nov., isolated from plants. Int J Syst Evol Microbiol 2012; 62: 1499– 1505 [CrossRef] [PubMed]
    [Google Scholar]
  23. Houf K, On SL, Coenye T, Mast J, van Hoof J et al. Arcobacter cibarius sp. nov., isolated from broiler carcasses. Int J Syst Evol Microbiol 2005; 55: 713– 717 [CrossRef] [PubMed]
    [Google Scholar]
  24. 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]
  25. Austrian R. The Gram stain and the etiology of lobar pneumonia, an historical note. Bacteriol Rev 1960; 24: 261– 265 [PubMed]
    [Google Scholar]
  26. 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]
  27. 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 [CrossRef] [PubMed]
    [Google Scholar]
  28. Vilella AJ, Severin J, Ureta-Vidal A, Heng L, Durbin R et al. EnsemblCompara GeneTrees: complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009; 19: 327– 335 [CrossRef] [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 [CrossRef] [PubMed]
    [Google Scholar]
  30. Wayne LG. International Committee on Systematic Bacteriology: announcement of the report of the ad hoc Committee on reconciliation of approaches to bacterial systematics. Zentralblatt fur Bakteriologie, Mikrobiologie, und Hygiene Series A, Medical Microbiology, Infectious Diseases, Virology, parasitology 1988; 268: 433– 434 [Crossref]
    [Google Scholar]
  31. 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
    [Google Scholar]
  32. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33: 152– 155
    [Google Scholar]
  33. 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]
  34. 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: e02136-14 [CrossRef] [PubMed]
    [Google Scholar]
  35. 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]
  36. 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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002447
Loading
/content/journal/ijsem/10.1099/ijsem.0.002447
Loading

Data & Media loading...

Supplementary File 1

PDF

Most Cited This Month

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