Skip to content
1887

Abstract

DHUNG17 was compared with XHP0097 to examine the taxonomic relationship between the two type strains. The 16S rRNA gene sequence of DHUNG17 shared high similarity (99.9 %) to that of XHP0097. The results of phylogenetic analyses based on 16S rRNA gene sequences indicated that the two strains formed a tight cluster within the genus . The average amino acid identity, average nucleotide identity and digital DNA–DNA hybridization values between DHUNG17 and XHP0097 were below 99.0, 99.1 and 92.2±1.7 %, respectively, all of which were greater than the species delineation threshold for AAI (95.5 %), ANI (95–96 %) and dDDH (70 %), strongly indicating that the two strains represented a single species. Based on the combined phylogenetic, genomic and phenotypic characterization presented here, we propose as a later heterotypic synonym of .

Funding
This study was supported by the:
  • the National Natural Science Foundation of China (Award 42073077)
    • Principle Award Recipient: YuliWei
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006446
2024-07-24
2025-07-14
Loading full text...

Full text loading...

References

  1. Takeuchi M, Hamana K, Hiraishi A. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int J Syst Evol Microbiol 2001; 51:1405–1417 [View Article] [PubMed]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  3. Kim B-S, Lim YW, Chun J. Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58:2415–2419 [View Article] [PubMed]
    [Google Scholar]
  4. Gao Z-Y, Xue H-P, Wang L, Yao Y, Zhang D-F et al. Sphingopyxis jiangsuensis sp. nov. isolated from the surface water of the Yellow Sea. Curr Microbiol 2022; 79:214 [View Article] [PubMed]
    [Google Scholar]
  5. Baik KS, Choe HN, Park SC, Hwang YM, Kim EM et al. Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis. Int J Syst Evol Microbiol 2013; 63:1297–1303 [View Article]
    [Google Scholar]
  6. Kampfer P. Sphingopyxis witflariensis sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2002; 52:2029–2034 [View Article]
    [Google Scholar]
  7. Srinivasan S, Kim MK, Sathiyaraj G, Veena V, Mahalakshmi M et al. Sphingopyxis panaciterrulae sp. nov., isolated from soil of a ginseng field. Int J Syst Evol Microbiol 2010; 60:2358–2363 [View Article]
    [Google Scholar]
  8. Oren A, Göker M. Validation list no.209. list of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2023; 73:5709
    [Google Scholar]
  9. Chhetri G, Kim I, Seo T. Sphingopyxis lutea sp. nov., a novel moderately halotolerant bacterium isolated from pebbles. Arch Microbiol 2022; 204:406 [View Article] [PubMed]
    [Google Scholar]
  10. Oren A, Göker M. Validation list No. 213. list of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2023; 73:5997
    [Google Scholar]
  11. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol 2023; 73:005585 [View Article]
    [Google Scholar]
  12. Yoon S-H, Ha S-M, 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 [View Article] [PubMed]
    [Google Scholar]
  13. 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]
  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. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  16. Yoon S-H, Ha S-M, 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]
  17. 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]
  18. Auch AF, Klenk HP, Göker M. Standard operating procedure for calculating genome-to-genome distances based on high-scoring segment pairs. Stand Genomic Sci 2010; 2:142–148 [View Article] [PubMed]
    [Google Scholar]
  19. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006446
Loading
/content/journal/ijsem/10.1099/ijsem.0.006446
Loading

Data & Media loading...

Supplements

Supplementary material 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