1887

Abstract

A Gram-stain-positive bacterial strain, 395-6.2, was isolated from traditional pickle in Heilongjiang Province, PR China. The bacterium was characterised by a polyphasic approach, including 16S rRNA gene sequence analysis, gene sequence analysis, gene sequence analysis, fatty acid methyl ester (FAME) analysis, determination of DNA G+C content, average nucleotide identity (ANI) analysis, DNA–DNA hybridisation (DDH) and an analysis of phenotypic features. Analysis of the 16S rRNA gene sequence showed that strain 395-6.2 was phylogenetically related to , , , , , , , , , , , , , and . Strain 395-6.2 exhibited 95.7–99.4 % 16S rRNA gene sequence similarities, 85.0–94.0 %  gene sequence similarities, 94.2–98.0 %  gene sequence similarities to type strains of phylogenetically related species. ANI and DDH values between strain 395-6.2 and type strains of phylogenetically related species were 77.9–87.1 % and 22.5–33.5 %, respectively. Based upon the data obtained in the present study, a novel species, sp. nov., is proposed and the type strain is 395-6.2 (=CCM 8927=NCIMB 15188=LMG 31179).

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2019-09-01
2022-01-22
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References

  1. Park KY, Kim BK. Lactic acid bacteria in vegetable fermentations. In Lahtinen S, Ouwehand AC, Salminen S, Von Wright A. (editors) Lactic Acid Bacteria: Microbiological and Functional Aspects, 4th ed. Boca Raton: CRC Press Taylor and Francis Group; 2012 pp. 187–211
    [Google Scholar]
  2. Huys G, Daniel HM, De Vuyst L. Taxonomy and biodiversity of sourdough yeasts and lactic acid bacteria. In Gobbetti M, Gänzle M. (editors) Handbook on Sourdough Biotechnology Boston: Springer; 2013 pp. 105–154
    [Google Scholar]
  3. Liu W, Pang H, Zhang H, Cai Y. Biodiversity of lactic acid bacteria. In Zhang H, Cai Y. (editors) Lactic Acid Bacteria: Fundamentals and Practice Dordrecht: Springer; 2014 pp. 103–203
    [Google Scholar]
  4. Fontana C, Fadda S, Cocconcelli PS, Vignolo G. Lactic acid bacteria in meat fermentations. In Lahtinen S, Ouwehand AC, Salminen S, Von Wright A. (editors) Lactic Acid Bacteria: Microbiological and Functional Aspects, 4th ed. Boca Raton: CRC Press Taylor and Francis Group; 2012 pp. 247–264
    [Google Scholar]
  5. Zhao W, Gu CT. Lactobacillus hulanensis sp. nov., isolated from suancai, a traditional Chinese pickle. Int J Syst Evol Microbiol 2019 DOI [View Article][PubMed]
    [Google Scholar]
  6. Liou JS, Huang CH, Wang CL, Lee AY, Mori K et al. Lactobacillus suantsaii sp. nov., isolated from suan-tsai, a traditional Taiwanese fermented mustard green. Int J Syst Evol Microbiol 2019; 69:1484–1489 [View Article][PubMed]
    [Google Scholar]
  7. Guu JR, Wang LT, Hamada M, Wang C, Lin RW et al. Lactobacillus bambusae sp. nov., isolated from traditional fermented ma bamboo shoots in Taiwan. Int J Syst Evol Microbiol 2018; 68:2424–2430 [View Article][PubMed]
    [Google Scholar]
  8. 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]
  9. Mao Y, Chen M, Horvath P. Lactobacillus herbarum sp. nov., a species related to Lactobacillus plantarum . Int J Syst Evol Microbiol 2015; 65:4682–4688 [View Article][PubMed]
    [Google Scholar]
  10. 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]
  11. 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]
  12. 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]
  13. Krieg NR, Padgett PJ. Phenotypic and physiological characterization methods. Methods Microbiol 2011; 38:15–60
    [Google Scholar]
  14. 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]
  15. 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]
  16. 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]
  17. 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]
  18. 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]
  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 [View Article][PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. Rzhetsky A, Nei M. A simple method for estimating and testing minimum evolution trees. Mol Biol Evol 1992; 9:945–967
    [Google Scholar]
  23. 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]
  24. 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]
  25. 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]
  26. 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]
  27. 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]
  28. 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]
  29. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007; 35:W182–W185 [View Article][PubMed]
    [Google Scholar]
  30. 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]
  31. 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]
  32. 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]
  33. 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]
  34. 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]
  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. Kandler O, Weiss N. Genus Lactobacillus beijerinck 1901, 212AL . In Sneath PHA, Mair NS, Sharpe ME, Holt JG. (editors) Bergey’s Manual of Systematic Bacteriology vol. 2 Baltimore: Williams & Wilkins; 1986 pp. 1209–1234
    [Google Scholar]
  37. Chang CH, Chen YS, Lee TT, Chang YC, Yu B. Lactobacillus formosensis sp. nov., a lactic acid bacterium isolated from fermented soybean meal. Int J Syst Evol Microbiol 2015; 65:101–106 [View Article][PubMed]
    [Google Scholar]
  38. Chao SH, Kudo Y, Tsai YC, Watanabe K. Lactobacillus futsaii sp. nov., isolated from fu-tsai and suan-tsai, traditional Taiwanese fermented mustard products. Int J Syst Evol Microbiol 2012; 62:489–494 [View Article][PubMed]
    [Google Scholar]
  39. Scheirlinck I, van der Meulen R, van Schoor A, Huys G, Vandamme P et al. Lactobacillus crustorum sp. nov., isolated from two traditional Belgian wheat sourdoughs. Int J Syst Evol Microbiol 2007; 57:1461–1467 [View Article][PubMed]
    [Google Scholar]
  40. Heo J, Saitou S, Tamura T, Cho H, Kim JS et al. Lactobacilus nuruki sp. nov., isolated from Nuruk, a Korean fermentation starter. Int J Syst Evol Microbiol 2018; 68:3273–3278 [View Article][PubMed]
    [Google Scholar]
  41. Chen YS, Wang LT, Liao YJ, Lan YS, Chang CH et al. Lactobacillus musae sp. nov., a novel lactic acid bacterium isolated from banana fruits. Int J Syst Evol Microbiol 2017; 67:5144–5149 [View Article][PubMed]
    [Google Scholar]
  42. Valcheva R, Ferchichi MF, Korakli M, Ivanova I, Gänzle MG et al. Lactobacillus nantensis sp. nov., isolated from French wheat sourdough. Int J Syst Evol Microbiol 2006; 56:587–591 [View Article][PubMed]
    [Google Scholar]
  43. Ehrmann MA, Müller MR, Vogel RF. Molecular analysis of sourdough reveals Lactobacillus mindensis sp. nov. Int J Syst Evol Microbiol 2003; 53:7–13 [View Article][PubMed]
    [Google Scholar]
  44. Kim J, Kim JY, Kim MS, Roh SW, Bae JW. Lactobacillus kimchiensis sp. nov., isolated from a fermented food. Int J Syst Evol Microbiol 2013; 63:1355–1359 [View Article][PubMed]
    [Google Scholar]
  45. Zhang Z, Hou Q, Wang Y, Li W, Zhao H et al. Lactobacillus zhachilii sp. nov., a lactic acid bacterium isolated from Zha-Chili. Int J Syst Evol Microbiol 2019 [View Article][PubMed]
    [Google Scholar]
  46. Mañes-Lázaro R, Ferrer S, Rodas AM, Urdiain M, Pardo I. Lactobacillus bobalius sp. nov., a lactic acid bacterium isolated from Spanish Bobal grape must. Int J Syst Evol Microbiol 2008; 58:2699–2703 [View Article][PubMed]
    [Google Scholar]
  47. Yoon JH, Kang SS, Mheen TI, Ahn JS, Lee HJ et al. Lactobacillus kimchii sp. nov., a new species from kimchi. Int J Syst Evol Microbiol 2000; 50:1789–1795 [View Article][PubMed]
    [Google Scholar]
  48. Cai Y, Okada H, Mori H, Benno Y, Nakase T. Lactobacillus paralimentarius sp. nov., isolated from sourdough. Int J Syst Bacteriol 1999; 49:1451–1455 [View Article][PubMed]
    [Google Scholar]
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