1887

Abstract

Five novel lactic acid bacterial strains, isolated from Chinese traditional pickle juice, were characterised by a polyphasic approach, including 16S rRNA gene sequence analysis, gene sequence analysis, gene sequence analysis, determination of DNA G+C content, average nucleotide identity (ANI) analysis, DNA–DNA hybridisation (DDH), fatty acid methyl ester (FAME) analysis and an analysis of phenotypic features. Strains 241-2-2, 63-4 and 190-7 were closely related to the type strains of , , , , , , and , having 99.1–99.9 % 16S rRNA gene sequence similarities. Strain 94-2 was distantly related to the type strains of , and , having 95.2–96.1 % 16S rRNA gene sequence similarities. Strain 85-4 was distantly related to the type strains of , , , , , , , and , having 95.7–97.8 % 16S rRNA gene sequence similarities. Less than 91.5 % ANI and 45.3 % DDH values between strains 241-2-2, 63-4, 190-7, 94-2, 85-4 and type strains of phylogenetically related species showed that they represent five new species within the genus . Based upon the data of polyphasic characterisation obtained in the present study, five novel species, sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., are proposed and the type strains are 241-2-2 (=NCIMB 15185=CCM 8921=LMG 31181), 63-4 (=NCIMB 15178=CCM 8922), 190-7 (=NCIMB 15200=CCM 8949), 94-2 (=NCIMB 15180=CCM 8920=LMG 31180) and 85-4 (=NCIMB 15179=CCM 8923=LMG 31183), respectively.

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003608
2019-10-01
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/3191.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003608&mimeType=html&fmt=ahah

References

  1. Schleifer KH, Kilpper-Balz R. Transfer of Streptococcus faecalis and Streptococcus faecium to the genus Enterococcus nom. rev. as Enterococcus faecalis comb. nov. and Enterococcus faecium comb. nov. Int J Syst Bacteriol 1984; 34:31–34 [View Article]
    [Google Scholar]
  2. Ludwig W, Schleifer KH, Whitman WB. Taxonomic outline of the phylum Firmicutes . In De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology New York: Springer; 2009 pp. 15–17
    [Google Scholar]
  3. Jin D, Yang J, Lu S, Lai XH, Xiong Y et al. Enterococcus wangshanyuanii sp. nov., isolated from faeces of yaks (Bos grunniens). Int J Syst Evol Microbiol 2017; 67:5216–5221 [View Article][PubMed]
    [Google Scholar]
  4. 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 [View Article][PubMed]
    [Google Scholar]
  5. Harada T, Dang VC, Nguyen DP, Nguyen TA, Sakamoto M et al. Enterococcus saigonensis sp. nov., isolated from retail chicken meat and liver. Int J Syst Evol Microbiol 2016; 66:3779–3785
    [Google Scholar]
  6. Sukontasing S, Tanasupawat S, Moonmangmee S, Lee JS, Suzuki K. Enterococcus camelliae sp. nov., isolated from fermented tea leaves in Thailand. Int J Syst Evol Microbiol 2007; 57:2151–2154 [View Article][PubMed]
    [Google Scholar]
  7. Fortina MG, Ricci G, Mora D, Manachini PL. Molecular analysis of artisanal Italian cheeses reveals Enterococcus italicus sp. nov. Int J Syst Evol Microbiol 2004; 54:1717–1721 [View Article][PubMed]
    [Google Scholar]
  8. Morandi S, Cremonesi P, Povolo M, Brasca M. Enterococcus lactis sp. nov., from Italian raw milk cheeses. Int J Syst Evol Microbiol 2012; 62:1992–1996 [View Article][PubMed]
    [Google Scholar]
  9. Lucena-Padrós H, González JM, Caballero-Guerrero B, Ruiz-Barba JL, Maldonado-Barragán A. Enterococcus olivae sp. nov., isolated from Spanish-style green-olive fermentations. Int J Syst Evol Microbiol 2014; 64:2534–2539 [View Article][PubMed]
    [Google Scholar]
  10. Tanasupawat S, Sukontasing S, Lee JS. Enterococcus thailandicus sp. nov., isolated from fermented sausage ('mum') in Thailand. Int J Syst Evol Microbiol 2008; 58:1630–1634 [View Article][PubMed]
    [Google Scholar]
  11. Li CY, Tian F, Zhao YD, Gu CT. Enterococcus xiangfangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2014; 64:1012–1017 [View Article][PubMed]
    [Google Scholar]
  12. Miyamoto M, Seto Y, Hao DH, Teshima T, Sun YB et al. Lactobacillus harbinensis sp. nov., consisted of strains isolated from traditional fermented vegetables 'Suan cai' in Harbin, Northeastern China and Lactobacillus perolens DSM 12745. Syst Appl Microbiol 2005; 28:688–694 [View Article][PubMed]
    [Google Scholar]
  13. Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus heilongjiangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2013; 63:4094–4099 [View Article][PubMed]
    [Google Scholar]
  14. An D, Cai S, Dong X. Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int J Syst Evol Microbiol 2006; 56:2043–2048 [View Article][PubMed]
    [Google Scholar]
  15. 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 [View Article][PubMed]
    [Google Scholar]
  16. 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 [View Article][PubMed]
    [Google Scholar]
  17. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article][PubMed]
    [Google Scholar]
  18. Kishino H, Hasegawa M. Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoidea. J Mol Evol 1989; 29:170–179 [View Article][PubMed]
    [Google Scholar]
  19. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  20. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article][PubMed]
    [Google Scholar]
  21. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
    [Google Scholar]
  22. Kim M, Oh HS, Park SC, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
    [Google Scholar]
  23. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article][PubMed]
    [Google Scholar]
  24. Aziz RK, Bartels D, Best AA, Dejongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article][PubMed]
    [Google Scholar]
  25. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article][PubMed]
    [Google Scholar]
  26. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article][PubMed]
    [Google Scholar]
  27. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article][PubMed]
    [Google Scholar]
  28. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  29. 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]
  30. Mattarelli P, Holzapfel W, Franz CM, Endo A, Felis GE et al. Recommended minimal standards for description of new taxa of the genera Bifidobacterium, Lactobacillus and related genera. Int J Syst Evol Microbiol 2014; 64:1434–1451 [View Article][PubMed]
    [Google Scholar]
  31. Krieg NR, Padgett PJ. Phenotypic and physiological characterization methods. Methods Microbiol 2011; 38:15–60
    [Google Scholar]
  32. Miyashita M, Yukphan P, Chaipitakchonlatarn W, Malimas T, Sugimoto M et al. Lactobacillus plajomi sp. nov. and Lactobacillus modestisalitolerans sp. nov., isolated from traditional fermented foods. Int J Syst Evol Microbiol 2015; 65:2485–2490 [View Article][PubMed]
    [Google Scholar]
  33. Hasegawa T, Takizawa M, Tanida S. A rapid analysis for chemical grouping of aerobic actinomycetes. J Gen Appl Microbiol 1983; 29:319–322 [View Article]
    [Google Scholar]
  34. Tak EJ, Kim HS, Lee JY, Kang W, Hyun DW et al. Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula . Int J Syst Evol Microbiol 2017; 67:3398–3402 [View Article][PubMed]
    [Google Scholar]
  35. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE, USA: Microbial ID Inc; 1990
    [Google Scholar]
  36. Svec P, Vancanneyt M, Koort J, Naser SM, Hoste B et al. Enterococcus devriesei sp. nov., associated with animal sources. Int J Syst Evol Microbiol 2005; 55:2479–2484 [View Article][PubMed]
    [Google Scholar]
  37. Rahkila R, Johansson P, Säde E, Björkroth J. Identification of enterococci from broiler products and a broiler processing plant and description of Enterococcus viikkiensis sp. nov. Appl Environ Microbiol 2011; 77:1196–1203 [View Article][PubMed]
    [Google Scholar]
  38. Collins MD, Facklam RR, Farrow JAE, Williamson R. Enterococcus raffinosus sp. nov., Enterococcus solitarius sp. nov. and Enterococcus pseudoavium sp. nov. FEMS Microbiol Lett 1989; 57:283–288 [View Article][PubMed]
    [Google Scholar]
  39. Collins MD, Jones D, Farrow JAE, Kilpper-Balz R, Schleifer KH. Enterococcus avium nom. rev., comb. nov.; E. casseliflavus nom. rev., comb. nov.; E. durans nom. rev., comb. nov.; E. gallinarum comb. nov.; and E. malodoratus sp. nov. Int J Syst Bacteriol 1984; 34:220–223 [View Article]
    [Google Scholar]
  40. Tyrrell GJ, Turnbull L, Teixeira LM, Lefebvre J, Carvalho MGS et al. Enterococcus gilvus sp. nov. and Enterococcus pallens sp. nov. isolated from human clinical specimens. J Clin Microbiol 2002; 40:1140–1145 [View Article][PubMed]
    [Google Scholar]
  41. Law-Brown J, Meyers PR. Enterococcus phoeniculicola sp. nov., a novel member of the enterococci isolated from the uropygial gland of the Red-billed Woodhoopoe, Phoeniculus purpureus . Int J Syst Evol Microbiol 2003; 53:683–685 [View Article][PubMed]
    [Google Scholar]
  42. Niemi RM, Ollinkangas T, Paulin L, Svec P, Vandamme P et al. Enterococcus rivorum sp. nov., from water of pristine brooks. Int J Syst Evol Microbiol 2012; 62:2169–2173 [View Article][PubMed]
    [Google Scholar]
  43. Collins MD, Rodrigues UM, Pigott NE, Facklam RR. Enterococcus dispar sp. nov. a new Enterococcus species from human sources. Lett Appl Microbiol 1991; 12:95–98 [View Article][PubMed]
    [Google Scholar]
  44. Naser SM, Vancanneyt M, De Graef E, Devriese LA, Snauwaert C et al. Enterococcus canintestini sp. nov., from faecal samples of healthy dogs. Int J Syst Evol Microbiol 2005; 55:2177–2182 [View Article][PubMed]
    [Google Scholar]
  45. Harada T, Dang VC, Nguyen DP, Nguyen TA, Sakamoto M et al. Enterococcus saigonensis sp. nov., isolated from retail chicken meat and liver. Int J Syst Evol Microbiol 2016; 66:3779–3785 [View Article][PubMed]
    [Google Scholar]
  46. Kim JY, Shin NR, Na HK, Hyun DW, Whon TW et al. Enterococcus diestrammenae sp. nov., isolated from the gut of Diestrammena coreana . Int J Syst Evol Microbiol 2013; 63:4540–4545 [View Article][PubMed]
    [Google Scholar]
  47. De Vaux A, Laguerre G, Diviès C, Prévost H. Enterococcus asini sp. nov. isolated from the caecum of donkeys (Equus asinus). Int J Syst Bacteriol 1998; 48 Pt 2:383–387 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003608
Loading
/content/journal/ijsem/10.1099/ijsem.0.003608
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF
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