1887

Abstract

A Gram-negative, facultatively anaerobic bacterium, designated SAP-6, was isolated from sap extracted from in Mt. Halla in Jeju, Republic of Korea and its precise taxonomic status was determined by a polyphasic approach. Cells were non-sporulating, motile, short rods and showed growth at 4–37 °C, pH 6.0–8.0 and 0–4% NaCl. Phylogenomic analysis based on 92 core gene sequences showed that strain SAP-6 belonged to the family and formed a distinct clade between members of the genera and with gene support index of 89. The closest phylogenetic neighbours were DSM 19580 (97.3% 16S rRNA gene sequence similarity) and HS1 (96.8%), with the average amino acid identity values of 75.3% and 74.0%, respectively. The major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylglycerol and an unidentified aminophospholipid. The major isoprenoid quinones were Q-7 and Q-8. The predominant fatty acids were C, C cyclo and summed feature 3. The DNA G+C content was 57.0%. On the basis of data presented here, strain SAP-6 (=KCTC 52622=DSM 104038) represents a novel species of a new genus in the family , for which the name gen. nov., sp. nov. is proposed.

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2021-02-02
2021-02-26
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References

  1. Na S-I, Kim YO, Yoon S-H, Ha S-M, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56: 280 285 [CrossRef] [PubMed]
    [Google Scholar]
  2. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9: 111 118 [CrossRef]
    [Google Scholar]
  3. 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 [CrossRef] [PubMed]
    [Google Scholar]
  4. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14: 60 [CrossRef] [PubMed]
    [Google Scholar]
  5. Kang HS, Yang HL, Lee SD. Nitratireductor kimnyeongensis sp. nov., isolated from seaweed. Int J Syst Evol Microbiol 2009; 59: 1036 1039 [CrossRef] [PubMed]
    [Google Scholar]
  6. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 24: 4876 4882
    [Google Scholar]
  7. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368 376 [CrossRef] [PubMed]
    [Google Scholar]
  8. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20: 406 416 [CrossRef]
    [Google Scholar]
  9. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406 425 [CrossRef] [PubMed]
    [Google Scholar]
  10. Felsenstein J. PHYLIP (phylogeny inference package) version 3.6a Seattle, USA: Distributed by the author. Department of Genome Sciences, University of Washington,; 2002
    [Google Scholar]
  11. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism New York: Academic Press; 1969 pp 21 132
    [Google Scholar]
  12. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783 791 [CrossRef] [PubMed]
    [Google Scholar]
  13. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16: 313 340 [CrossRef]
    [Google Scholar]
  14. Lee SD. Pigmentiphaga aceris sp. nov., isolated from tree sap. Int J Syst Evol Microbiol 2017; 67: 3198 3202 [CrossRef] [PubMed]
    [Google Scholar]
  15. Kroppenstedt RM. Fatty acid and menaquinone analysis of actinomycetes and related organisms. In Goodfellow M, Minnikin DE. (editors) Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp 173 199
    [Google Scholar]
  16. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2: 233 241 [CrossRef]
    [Google Scholar]
  17. Minnikin DE, PATEL PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of Nocardia and related bacteria. Int J Syst Bacteriol 1977; 27: 104 117 [CrossRef]
    [Google Scholar]
  18. Dale C, Maudlin I. Sodalis gen. nov. and Sodalis glossinidius sp. nov., a microaerophilic secondary endosymbiont of the tsetse fly Glossina morsitans morsitans . Int J Syst Bacteriol 1999; 49 Pt 1: 267 275 [CrossRef] [PubMed]
    [Google Scholar]
  19. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68: 2393 2411 [CrossRef] [PubMed]
    [Google Scholar]
  20. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2020; 70: 4432 4450 [CrossRef] [PubMed]
    [Google Scholar]
  21. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106: 12196 19131 [CrossRef] [PubMed]
    [Google Scholar]
  22. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9: 75 [CrossRef] [PubMed]
    [Google Scholar]
  23. Verbarg S, Frühling A, Cousin S, Brambilla E, Gronow S et al. Biostraticola tofi gen. nov., spec. nov., a novel member of the family Enterobacteriaceae . Curr Microbiol 2008; 56: 603 608 [CrossRef] [PubMed]
    [Google Scholar]
  24. Chari A, Oakeson KF, Enomoto S, Jackson DG, Fisher MA et al. Phenotypic characterization of Sodalis praecaptivus sp. nov., a close non-insect-associated member of the Sodalis-allied lineage of insect endosymbionts. Int J Syst Evol Microbiol 2015; 65: 1400 1405 [CrossRef] [PubMed]
    [Google Scholar]
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