1887

Abstract

and belong to the genus and show close phylogenetic relationships. In a previous study, and were proposed to be reclassified as later heterotypic synonyms of using high 16S rRNA gene sequence similarities (≥99.5 %) and DNA–DNA hybridization values (≥82 %). We determined high quality whole genome assemblies of the type strains of and , which were then compared with that of . Average nucleotide identity values among three genomes ranged from 91.4 to 92.3 % which are clearly below 95~96 %, the generally recognized cutoff value for bacterial species boundaries. On the basis of comparative genomic evidence, and should stand as separate species in the genus . We therefore suggest rejecting the previous proposal to combine these three species into a single species.

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2017-11-01
2019-12-11
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References

  1. 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 [CrossRef][PubMed]
    [Google Scholar]
  2. 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 [CrossRef][PubMed]
    [Google Scholar]
  3. Cai Y, Okada H, Mori H, Benno Y, Nakase T et al. Lactobacillus paralimentarius sp. nov., isolated from sourdough. Int J Syst Bacteriol 1999;49:1451–1455 [CrossRef][PubMed]
    [Google Scholar]
  4. Pang H, Kitahara M, Tan Z, Wang Y, Qin G et al. Reclassification of Lactobacillus kimchii and Lactobacillus bobalius as later subjective synonyms of Lactobacillus paralimentarius. Int J Syst Evol Microbiol 2012;62:2383–2387 [CrossRef][PubMed]
    [Google Scholar]
  5. Ziemke F, Höfle MG, Lalucat J, Rosselló-Mora R. Reclassification of Shewanella putrefaciens Owen's genomic group II as Shewanella baltica sp. nov. Int J Syst Bacteriol 1998;48:179–186 [CrossRef][PubMed]
    [Google Scholar]
  6. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 1989;39:224–229 [CrossRef]
    [Google Scholar]
  7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19:455–477 [CrossRef][PubMed]
    [Google Scholar]
  8. Lee I, Chalita M, Ha SM, Na SI, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017;67:2053–2057 [CrossRef][PubMed]
    [Google Scholar]
  9. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25:1043–1055 [CrossRef][PubMed]
    [Google Scholar]
  10. 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]
  11. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek doi:10.1007/s10482-017-0844-4 [CrossRef][PubMed]
    [Google Scholar]
  12. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014;64:316–324 [CrossRef][PubMed]
    [Google Scholar]
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