1887

Abstract

Three novel strains, designated as HMF5036, HMF5335 and HMF5405, were isolated from freshwater, rusty iron and forsythia flower, in Yong-in, Republic of Korea, respectively. They were Gram-stain-negative, facultatively anaerobic, non-motile, reddish-pigmented and rod-shaped bacteria. The predominant fatty acids of three strains were C 5 and summed feature 3 (comprising C 7 and/or C 6). They were found to contain MK-7 as the predominant menaquinone. The major polar lipids are phosphatidylethanolamine, an unidentified aminophospholipid and an unidentified lipid. Strains HMF5036, HMF5335 and HMF5405 exhibited the highest 16S rRNA gene sequence similarities of 91.8, 92.6 and 93.6 % to BUZ 2 and less than 88.7 % to other members of the family . Similarity values among the three isolates ranged from 94.9 to 96.6 %. Phylogenetic analysis based on the 16S rRNA gene sequences of the three isolates revealed that they formed a distinct clade within the family . The genome sizes of strains HMF5036, HMF5335 and HMF5405 were 6.8, 6.4 and 7.8 Mbp, and their DNA G+C contents were 54.9, 54.0 and 52.1 mol%, respectively. The average nucleotide identity, digital DNA–DNA hybridization and amino acid identity values between three isolates and BUZ 2 were 73.8–82.2, 19.6–25.4 and 75.0–87.5 %, respectively. These values were lower than the recommended threshold values for species delimitation. Based on the results of the phenotypic, genotypic, chemotaxonomic and phylogenetic investigations, three novel species, sp. nov., sp. nov. and sp. nov. are proposed. The type strains are HMF5036 (=KCTC 82476=NBRC 115092), HMF5335 (=KCTC 82477=NBRC 115093) and HMF5405 (=KCTC 82478=NBRC 115094), respectively.

Keyword(s): Fibrella , forsythia , freshwater and rusty iron
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2022-05-13
2022-05-29
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References

  1. Larkin JM, Borrall R. NOTES: Spirosomaceae, a New Family to Contain the Genera Spirosoma Migula 1894, Flectobacillus Larkin et al. 1977, and Runella Larkin and Williams 1978. Int J Syst Bacteriol 1978; 28:595–596 [View Article]
    [Google Scholar]
  2. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:2083 [View Article] [PubMed]
    [Google Scholar]
  3. Filippini M, Svercel M, Laczko E, Kaech A, Ziegler U et al. Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008. Int J Syst Evol Microbiol 2011; 61:184–189 [View Article] [PubMed]
    [Google Scholar]
  4. Kang H, Cha I, Kim H, Joh K. Saliniradius amylolyticus gen. nov., sp. nov., isolated from solar saltern sediment. Int J Syst Evol Microbiol 2020; 70:267–273 [View Article]
    [Google Scholar]
  5. 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]
  6. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article] [PubMed]
    [Google Scholar]
  7. 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]
  8. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  9. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Systematic Zoology 1971; 20:406 [View Article]
    [Google Scholar]
  10. 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]
  11. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  12. 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]
  13. Brown AE. Benson’s Microbiological Application Laboratory Manual in General Microbiology, 10th ed. New York: McGraw-Hill; 2007
    [Google Scholar]
  14. Alexander SK, Strete D. Microbiology: A Photographic Atlas for the Laboratory Benjamin Cummings; 2001
    [Google Scholar]
  15. CLSI Performance standards for antimicrobial disk susceptibility testing: approved standard. CLSI document M02-A11, 11th ed. PA: Clinical and Laboratory Standards Institute; 2012
    [Google Scholar]
  16. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium and Cytophaga-like bacteria of the International Committee on Systematics of Prokaryotes Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article]
    [Google Scholar]
  17. Rainey F, Oren A. Taxonomy of Prokaryotes Amsterdam: Elsevier;
    [Google Scholar]
  18. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids. MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
  19. 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 [View Article]
    [Google Scholar]
  20. Collins MD. Analysis of isoprenoid quinones. In Gottschalk G. eds Methods in Microbiology, 18 New York: Acad Press; 1985 pp 329–366
    [Google Scholar]
  21. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  22. Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R et al. Galaxy: a web-based genome analysis tool for experimentalists. Curr Protoc Mol Biol 2010; Chapter 19:Unit [View Article] [PubMed]
    [Google Scholar]
  23. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
    [Google Scholar]
  24. Bushnell B. BBMap: a Fast, Accurate, Splice-aware Aligner (no.LBNL-7065E) Berkeley, CA (United States): Lawrence Berkeley National Lab. (LBNL); 2014
    [Google Scholar]
  25. 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] [PubMed]
    [Google Scholar]
  26. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  27. 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 [View Article] [PubMed]
    [Google Scholar]
  28. Lee I, Ouk Kim Y, 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] [PubMed]
    [Google Scholar]
  29. 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]
  30. 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]
  31. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
    [Google Scholar]
  32. Luo C, Rodriguez-R LM, Konstantinidis KT. MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 2014; 42:e73 [View Article] [PubMed]
    [Google Scholar]
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