1887

Abstract

The type strains of four subspecies of , subsp. , subsp. , subsp. and subsp. , and strain DRC1506, used as a starter culture for commercial kimchi production in Korea, were phylogenetically analyzed on the basis of their complete genome sequences. Although the type strains of the four subspecies and strain DRC1506 shared very high 16S rRNA gene sequence similarities (>99.72 %), the results of analysis of average nucleotide identity (ANI), DNA–DNA hybridization (DDH) and core-genome-based relatedness indicated that they could form five different phylogenetic lineages. The type strains of subsp. , subsp. and subsp. and DRC1506 shared higher ANI and DDH values than the thresholds (95–96 % and 70 %, respectively) generally accepted for different species delineation, whereas the type strain of subsp. (DSM 20241) shared lower ANI (<94.1 %) and DDH values (<57.0 %) with the other four lineage strains, indicating that DSM 20241 couldn be reclassified as representing a different species. Here, we report that DRC1506 represents a novel subspecies within the species for which the name subsp. subsp. nov. is proposed. The type strain is DRC1506 (=KCCM 43249=JCM 31787). In addition, subsp. is also reclassified as . sp. nov. (type strain DSM 20241=ATCC 9135=LMG 8159=NCIMB 6992).

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2017-07-01
2020-01-21
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References

  1. Chambel L, Chelo IM, Zé-Zé L, Pedro LG, Santos MA et al. Leuconostoc pseudoficulneum sp. nov., isolated from a ripe fig. Int J Syst Evol Microbiol 2006;56:1375–1381 [CrossRef][PubMed]
    [Google Scholar]
  2. De Bruyne K, Schillinger U, Caroline L, Boehringer B, Cleenwerck I et al. Leuconostoc holzapfelii sp. nov., isolated from Ethiopian coffee fermentation and assessment of sequence analysis of housekeeping genes for delineation of Leuconostoc species. Int J Syst Evol Microbiol 2007;57:2952–2959 [CrossRef][PubMed]
    [Google Scholar]
  3. Ehrmann MA, Freiding S, Vogel RF. Leuconostoc palmae sp. nov., a novel lactic acid bacterium isolated from palm wine. Int J Syst Evol Microbiol 2009;59:943–947 [CrossRef][PubMed]
    [Google Scholar]
  4. Gu CT, Wang F, Li CY, Liu F, Huo GC. Leuconostoc mesenteroides subsp. suionicum subsp. nov. Int J Syst Evol Microbiol 2012;62:1548–1551 [CrossRef][PubMed]
    [Google Scholar]
  5. Lee SH, Park MS, Jung JY, Jeon CO. Leuconostoc miyukkimchii sp. nov., isolated from brown algae (Undaria pinnatifida) kimchi. Int J Syst Evol Microbiol 2012;62:1098–1103 [CrossRef][PubMed]
    [Google Scholar]
  6. Garvie EI. Leuconostoc mesenteroides subsp. cremoris (Knudsen and Sørensen) comb. nov. and Leuconostoc mesenteroides subsp. dextranicum (Beijerinck) comb. nov. Int J Syst Evol Microbiol 1983;33:118–119
    [Google Scholar]
  7. Jung JY, Lee SH, Jin HM, Hahn Y, Madsen EL et al. Metatranscriptomic analysis of lactic acid bacterial gene expression during kimchi fermentation. Int J Food Microbiol 2013;163:171–179 [CrossRef][PubMed]
    [Google Scholar]
  8. Jung JY, Lee SH, Jeon CO. Kimchi microflora: history, current status, and perspectives for industrial kimchi production. Appl Microbiol Biotechnol 2014;98:2385–2393 [CrossRef][PubMed]
    [Google Scholar]
  9. Jung JY, Lee SH, Lee HJ, Seo HY, Park WS et al. Effects of Leuconostoc mesenteroides starter cultures on microbial communities and metabolites during kimchi fermentation. Int J Food Microbiol 2012;153:378–387 [CrossRef][PubMed]
    [Google Scholar]
  10. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005;187:6258–6264 [CrossRef][PubMed]
    [Google Scholar]
  11. 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 [CrossRef][PubMed]
    [Google Scholar]
  12. Zangenah S, Abbasi N, Andersson AF, Bergman P. Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans. Sci Rep 2016;6:22919 [CrossRef][PubMed]
    [Google Scholar]
  13. Jung JY, Chun BH, Moon JY, Yeo SH, Jeon CO. Complete genome sequence of Bacillus methylotrophicus JJ-D34 isolated from Deonjang, a Korean traditional fermented soybean paste. J Biotechnol 2016;219:36–37 [CrossRef][PubMed]
    [Google Scholar]
  14. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007;3:e56 [CrossRef][PubMed]
    [Google Scholar]
  15. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980;16:111–120 [CrossRef][PubMed]
    [Google Scholar]
  16. Felsenstein J. PHYLIP (Phylogeny Inference Package), Version 3.6a Seattle: Department of Genome Sciences, University of Washington, Seattle, WA, USA; 2002
    [Google Scholar]
  17. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  18. Lee I, Kim YO, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016;66:1100–1103 [CrossRef]
    [Google Scholar]
  19. 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]
  20. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009;10:421 [CrossRef][PubMed]
    [Google Scholar]
  21. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016;6:24373 [CrossRef][PubMed]
    [Google Scholar]
  22. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  23. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  24. 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 [CrossRef][PubMed]
    [Google Scholar]
  25. Rosselló-Móra R, Amann R. Past and future species definitions for Bacteria and Archaea. Syst Appl Microbiol 2015;38:209–216 [CrossRef][PubMed]
    [Google Scholar]
  26. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001;25:39–67 [CrossRef][PubMed]
    [Google Scholar]
  27. Garvie EI. Hybridization between the deoxyribonucleic acids of some strains of heterofermentative lactic acid bacteria. Int J Syst Bacteriol 1976;26:116–122 [CrossRef]
    [Google Scholar]
  28. Farrow JAE, Facklam RR, Collins MD. Nucleic acid homologies of some vancomycin-resistant Leuconostocs and description of Leuconostoc citreum sp. nov. and Leuconostoc pseudomesenteroides sp. nov. Int J Syst Bacteriol 1989;39:279–283 [CrossRef]
    [Google Scholar]
  29. Smibert RM, Krieg NR. Phenotypic characterization. In Gerhardt P. (editor) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp.607–654
    [Google Scholar]
  30. Hitchener BJ, Egan AF, Rogers PJ. Characteristics of lactic acid bacteria isolated from vacuum-packaged beef. J Appl Bacteriol 1982;52:31–37 [CrossRef][PubMed]
    [Google Scholar]
  31. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  32. Schumann P. Peptidoglycan structure. Methods Microbiol 2011;38:101–129[CrossRef]
    [Google Scholar]
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