1887

Abstract

The genus includes only one species with validly published name, . The type strain YJ01 was isolated from soil in Korea, while XNB-1 was isolated from soil in China. Both strains share similar phenotypic and chemotaxonomic characteristics, including predominant menaquinone MK-8(H) and major polar lipids diphosphatidylglycerol and phosphatidylglycerol. Whole genome sequences revealed a DNA G+C content of 70.1 mol% for both strains and 100% similarity in their 16S rRNA gene sequences. Phylogenetic analysis showed they form a distinct cluster separate from other genera. Genomic comparisons showed average nucleotide identity and digital DNA–DNA hybridization values of 99.16 and 94.2%, respectively, indicating they represent a single species. Based on this genomic evidence, Jiang . 2020 is proposed to be a later heterotypic synonym of Lee and Whang 2020.

Funding
This study was supported by the:
  • National Natural Science Foundation of China (Award 32170007)
    • Principle Award Recipient: QingLiu
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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/content/journal/ijsem/10.1099/ijsem.0.006503
2024-08-27
2024-09-15
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References

  1. Lee JC, Whang KS. Segeticoccus rhizosphaerae gen. nov., sp. nov., an actinobacterium isolated from soil of a farming field. Int J Syst Evol Microbiol 2020; 70:1785–1792 [View Article] [PubMed]
    [Google Scholar]
  2. Oren A, Garrity GM. Notification that new names of prokaryotes, new combinations, and new taxonomic opinions have appeared in volume 70, part 3 of the IJSEM. Int J Syst Evol Microbiol 2020; 70:3583–3587 [View Article]
    [Google Scholar]
  3. Jiang W-K, Gao Q-Q, Zhang L, Sun G-J, Zhang M-L et al. Ornithinicoccus soli sp. nov., isolated from farmland soil. Int J Syst Evol Microbiol 2020; 70:1793–1799 [View Article] [PubMed]
    [Google Scholar]
  4. 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 [View Article]
    [Google Scholar]
  5. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  6. 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]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  8. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011; 28:2731–2739 [View Article] [PubMed]
    [Google Scholar]
  9. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
    [Google Scholar]
  10. 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]
  11. Nei M, Kumar S. Molecular Evolution and Phylogenetics New York: Oxford University Press; 2000
    [Google Scholar]
  12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  13. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  14. Na S-I, Kim YO, Yoon S-H, Ha S, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  15. 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]
  16. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
    [Google Scholar]
  17. Konstantinidis KT, Tiedje JM. Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. Curr Opin Microbiol 2007; 10:504–509 [View Article] [PubMed]
    [Google Scholar]
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