1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 67, Issue 7

A proposal of subsp. subsp. nov. and reclassification of subsp. (Gu ., 2012) as sp. nov. based on complete genome sequences Free

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).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genome , Leuconotoc mesenteroides subsp. jonggajibkimchii , Leuconotoc mesenteroides subsp. suionicum , reclassification and taxonomy
© 2017 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.001930
2017-07-01
2024-04-24
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/67/7/2225.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.001930&mimeType=html&fmt=ahah

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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  10. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  14. Nawrocki EP, Eddy SR. Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput Biol 2007; 3:e56 [View Article][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 [View Article][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 [View Article][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 [View Article]
     [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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  21. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article][PubMed]
     [Google Scholar]
  22. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][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 [View Article][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 [View Article][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 [View Article][PubMed]
     [Google Scholar]
  26. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001; 25:39–67 [View Article][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 [View Article]
     [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 [View Article]
     [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 [View Article][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]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.001930
Loading
A proposal of Leuconostoc mesenteroides subsp. jonggajibkimchii subsp. nov. and reclassification of Leuconostoc mesenteroides subsp. suionicum (Gu et al., 2012) as Leuconostoc suionicum sp. nov. based on complete genome sequences
Int J Syst Evol Microbiol 67, 2225 (2017); https://doi.org/10.1099/ijsem.0.001930
/content/journal/ijsem/10.1099/ijsem.0.001930
/content/journal/ijsem/10.1099/ijsem.0.001930
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

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