1887

Abstract

Fourteen Gram-stain-positive bacterial strains were isolated from Chinese traditional pickle and yogurt. The strains were characterised using a polyphasic taxonomic approach, including 16S rRNA gene sequence analysis, gene sequence analysis, gene sequence analysis, determination of DNA G+C content, determination of average nucleotide identity, fatty acid methyl ester analysis and an analysis of phenotypic features. The data demonstrated that the fourteen strains represented nine novel species belonging to the genus , strains 54-2, 54-5, 33-7, 116-2, 184-8, 204-8, 8-1(1), 256-3 and M1575 were designated as the type strains. Strain 54-2 was phylogenetically related to the type strains of and , having 96.5 and 91.6 % 16S rRNA gene sequence similarities, less than 74.6 % gene sequence similarities, less than 81.6 % gene sequence similarities and less than 72.5 % ANI values. Strain 54-5 was phylogenetically related to the type strains of and , exhibiting 99.1 and 97.3 % 16S rRNA gene sequence similarities, less than 83.1 % gene sequence similarities, less than 93.1 % gene sequence similarities and less than 79.9 % ANI values. Strains 33-7, 116-2, 184-8, 204-8, 8-1(1), 256-3 and M1575 were phylogenetically related to the type strains of , , , , , , and , sharing 95.6–100 % 16S rRNA gene sequence similarities, less than 91.6 % gene sequence similarities, less than 98.2 % gene sequence similarities and less than 89.4 % ANI values. Based upon the data of polyphasic characterisation obtained in the present study, nine novel species, sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov., sp. nov. and sp. nov., are proposed and the type strains are 54-2 (=NCIMB 15154=CCM 8896=KCTC 21120=LMG 31058), 54-5 (=NCIMB 15151=CCM 8894), 33-7 (=NCIMB 15153=CCM 8936=KCTC 21118=LMG 31166), 116-2 (=NCIMB 15158=CCM 8899=KCTC 21124=LMG 31051), 184-8 (=NCIMB 15152=CCM 8895=KCTC 21131=LMG 31050), 204-8 (=NCIMB 15159=CCM 8900=KCTC 21133=LMG 31054), 8-1(1) (=NCIMB 15156=CCM 8898=KCTC 21115=LMG 31047), 256-3 (=NCIMB 15160=CCM 8901=LMG 31048) and M1575 (=NCIMB 15149=CCM 8892=LMG 31045), respectively.

Keyword(s): Lactobacillus , pickle and yogurt
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003609
2019-10-01
2024-04-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/10/3178.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003609&mimeType=html&fmt=ahah

References

  1. 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]
  2. Skerman VBD, Sneath PHA, Mcgowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
    [Google Scholar]
  3. Hammes WP, Hertel C. Genus Lactobacillus Beijerink, 1901. In De Vos P, Garrity GM, Jones D, Krieg NR, Ludwig W et al. (editors) Bergey’s Manual of Systematic Bacteriology, 2nd ed. vol. 3 Berlin: Springer; 2009 pp. 465–510
    [Google Scholar]
  4. 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]
  5. Gu CT, Wang F, Li CY, Liu F, Huo GC. Lactobacillus xiangfangensis sp. nov., isolated from Chinese pickle. Int J Syst Evol Microbiol 2012; 62:860–863 [View Article][PubMed]
    [Google Scholar]
  6. 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]
  7. Gu CT, Li CY, Yang LJ, Huo GC. Lactobacillus mudanjiangensis sp. nov., Lactobacillus songhuajiangensis sp. nov. and Lactobacillus nenjiangensis sp. nov., isolated from Chinese traditional pickle and sourdough. Int J Syst Evol Microbiol 2013; 63:4698–4706 [View Article][PubMed]
    [Google Scholar]
  8. Zhao W, Gu CT. Lactobacillus hulanensis sp. nov., isolated from suancai, a traditional Chinese pickle. Int J Syst Evol Microbiol 2019; 69:2147–2152 [View Article][PubMed]
    [Google Scholar]
  9. Long GY, Gu CT. Lactobacillus jixianensis sp. nov., Lactobacillus baoqingensis sp. nov., Lactobacillus jiayinensis sp. nov., Lactobacillus zhaoyuanensis sp. nov., Lactobacillus lindianensis sp. nov., Lactobacillus huananensis sp. nov., Lactobacillus tangyuanensis sp. nov., Lactobacillus fuyuanensis sp. nov., Lactobacillus tongjiangensis sp. nov., Lactobacillus fujinensis sp. nov. and Lactobacillus mulengensis sp. nov., isolated from Chinese traditional pickle. Int J Syst Evol Microbiol 2019 [View Article][PubMed]
    [Google Scholar]
  10. Fu ML, Gu CT. Lactobacillus huachuanensis sp. nov., isolated from Chinese traditional pickle. Int J Syst Evol Microbiol 2019 [View Article][PubMed]
    [Google Scholar]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. Naser SM, Dawyndt P, Hoste B, Gevers D, Vandemeulebroecke K et al. Identification of lactobacilli by pheS and rpoA gene sequence analyses. Int J Syst Evol Microbiol 2007; 57:2777–2789 [View Article][PubMed]
    [Google Scholar]
  19. 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]
  20. 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]
  21. 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]
  22. 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]
  23. 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]
  24. 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]
  25. 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]
  26. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  27. 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]
  28. Krieg NR, Padgett PJ. Phenotypic and physiological characterization methods. Methods Microbiol 2011; 38:15–60
    [Google Scholar]
  29. 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]
  30. 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]
  31. 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]
  32. 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]
  33. Endo A, Okada S. Lactobacillus composti sp. nov., a lactic acid bacterium isolated from a compost of distilled shochu residue. Int J Syst Evol Microbiol 2007; 57:870–872 [View Article][PubMed]
    [Google Scholar]
  34. Kawasaki S, Kurosawa K, Miyazaki M, Yagi C, Kitajima Y et al. Lactobacillus floricola sp. nov., lactic acid bacteria isolated from mountain flowers. Int J Syst Evol Microbiol 2011; 61:1356–1359 [View Article][PubMed]
    [Google Scholar]
  35. Back W. Elevation of Pediococcus cerevisiae subsp. dextrinicus coster and white to species status [Pediococcus dextrinicus (coster and white) comb. nov.]. Int J Syst Bacteriol 1978; 28:523–527 [View Article]
    [Google Scholar]
  36. Tong H, Dong X. Lactobacillus concavus sp. nov., isolated from the walls of a distilled spirit fermenting cellar in China. Int J Syst Evol Microbiol 2005; 55:2199–2202 [View Article][PubMed]
    [Google Scholar]
  37. Chenoll E, Carmen Macián M, Aznar R. Lactobacillus tucceti sp. nov., a new lactic acid bacterium isolated from sausage. Syst Appl Microbiol 2006; 29:389–395 [View Article][PubMed]
    [Google Scholar]
  38. Kashiwagi T, Suzuki T, Kamakura T. Lactobacillus nodensis sp. nov., isolated from rice bran. Int J Syst Evol Microbiol 2009; 59:83–86 [View Article][PubMed]
    [Google Scholar]
  39. Ehrmann MA, Kröckel L, Lick S, Radmann P, Bantleon A et al. Lactobacillus insicii sp. nov., isolated from fermented raw meat. Int J Syst Evol Microbiol 2016; 66:236–242 [View Article][PubMed]
    [Google Scholar]
  40. Jung MY, Lee SH, Lee M, Song JH, Chang JY. Lactobacillus allii sp. nov. isolated from scallion kimchi. Int J Syst Evol Microbiol 2017; 67:4936–4942 [View Article][PubMed]
    [Google Scholar]
  41. Chiba M, Itabashi T, Hirai K, Sakamoto M, Ohkuma M et al. Lactobacillus metriopterae sp. nov., a novel lactic acid bacterium isolated from the gut of grasshopper Metrioptera engelhardti . Int J Syst Evol Microbiol 2018; 68:1484–1489 [View Article][PubMed]
    [Google Scholar]
  42. Kim HJ, Lee HJ, Lim B, Kim E, Kim HY et al. Lactobacillus terrae sp. nov., a novel species isolated from soil samples in the Republic of Korea. Int J Syst Evol Microbiol 2018; 68:2906–2911 [View Article][PubMed]
    [Google Scholar]
  43. Kröckel L, Schillinger U, Franz CM, Bantleon A, Ludwig W. Lactobacillus versmoldensis sp. nov., isolated from raw fermented sausage. Int J Syst Evol Microbiol 2003; 53:513–517 [View Article][PubMed]
    [Google Scholar]
  44. Irisawa T, Tanaka N, Kitahara M, Sakamoto M, Ohkuma M et al. Lactobacillus furfuricola sp. nov., isolated from Nukadoko, rice bran paste for Japanese pickles. Int J Syst Evol Microbiol 2014; 64:2902–2906 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003609
Loading
/content/journal/ijsem/10.1099/ijsem.0.003609
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