sp. nov., a halophilic bacterium isolated from faeces of a Swinhoe's pheasant, Free

Abstract

A rod-shaped, Gram-stain-positive, motile and aerobic bacterium, designated LM2416, was isolated from faeces of living in Seoul Grand Park, Gyeonggi-do, Republic of Korea. Phylogenetic analyses based on 16S rRNA gene sequences indicated that strain LM2416 belonged to the genus , sharing high 16S rRNA gene sequence similarities to LMG 19488 (99.0 %), LMG 20964 (98.4 %), Hal 1 (98.3 %) and S1-20 (97.9 %). The isolate grew at 10–30 °C, pH 6–7 and 0–20 % (w/v) NaCl. Optimal growth was observed at 30 °C, pH 6–7 and 10 % (w/v) NaCl. The major fatty acid was anteiso-C. Polar lipids were composed of phosphatidylglycerol, diphosphatidylglycerol, three unknown phospholipids and two unknown aminophospholipids. The main menaquinone was MK-7. Strain LM2416 had alanine, lysine, glutamic acid, glycine and aspartic acid as cell-wall amino acids and ribose as a cell-wall sugar. The whole genome sequences of strain LM2416 and KCTC 3820 were sequenced by PacBio RS II sequencing. The genome sequence-based G+C content of strain LM2416 was 39.5 mol%. The orthologous average nucleotide identity value, showing genetic relatedness between strain LM2416 and KCTC 3820, was 78.3 %. Based on the phylogenetic, biochemical, chemotaxonomic and genotypic data presented in this study, strain LM2416 is considered to represent a novel species of the genus , for which the name is proposed. The type strain is LM2416 (=KCTC 33927=JCM 32144).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002650
2018-04-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/4/1190.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002650&mimeType=html&fmt=ahah

References

  1. Lei F-M, Qu Y-H, Lu J-L, Liu Y, Yin Z-H. Conservation on diversity and distribution patterns of endemic birds in China. Biodivers Conserv 2003; 12:239–254 [View Article]
    [Google Scholar]
  2. The IUCN red list of threatened species. Version 2017-2. www.iucnredlist.org
  3. Johnson S. 2018; Swinhoe's Pheasants. www.beautyofbirds.com/swinhoepheasants.html
  4. Heyndrickx M, Lebbe L, Kersters K, de Vos P, Forsyth G et al. Virgibacillus: a new genus to accommodate Bacillus pantothenticus (Proom and Knight 1950). Emended description of Virgibacillus pantothenticus. Int J Syst Bacteriol 1998; 48:99–106 [View Article]
    [Google Scholar]
  5. Yin X, Yang Y, Wang S, Zhang G. Virgibacillus oceani sp. nov. isolated from ocean sediment. Int J Syst Evol Microbiol 2015; 65:159–164 [View Article][PubMed]
    [Google Scholar]
  6. Zhang DC, Schumann P, Wu J, França L, Neuner K et al. Virgibacillus flavescens sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2016; 66:1138–1143 [View Article][PubMed]
    [Google Scholar]
  7. Daroonpunt R, Tanasupawat S, Kudo T, Ohkuma M, Itoh T. Virgibacillus kapii sp. nov., isolated from Thai shrimp paste (Ka-pi). Int J Syst Evol Microbiol 2016; 66:1832–1837 [View Article][PubMed]
    [Google Scholar]
  8. Sundararaman A, Srinivasan S, Lee JH, Lee SS. Virgibacillus jeotgali sp. nov., isolated from Myeolchi-jeotgal, a traditional Korean high-salt-fermented anchovy. Int J Syst Evol Microbiol 2016; 67:158–163 [View Article][PubMed]
    [Google Scholar]
  9. Heyrman J, Logan NA, Busse HJ, Balcaen A, Lebbe L et al. Virgibacillus carmonensis sp. nov., Virgibacillus necropolis sp. nov. and Virgibacillus picturae sp. nov., three novel species isolated from deteriorated mural paintings, transfer of the species of the genus Salibacillus to Virgibacillus, as Virgibacillus marismortui comb. nov. and Virgibacillus salexigens comb. nov., and emended description of the genus Virgibacillus. Int J Syst Evol Microbiol 2003; 53:501–511 [View Article][PubMed]
    [Google Scholar]
  10. Lane DJ. 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics New York, NY: John Wiley and Sons; 1991 pp. 115–175
    [Google Scholar]
  11. Yoon SH, Ha SM, 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]
  12. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  13. 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]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
    [Google Scholar]
  15. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool 1969; 18:1–32 [View Article]
    [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  17. Tittsler RP, Sandholzer LA. The use of semi-solid agar for the detection of bacterial motility. J Bacteriol 1936; 31:575–580[PubMed]
    [Google Scholar]
  18. MIDI Sherlock Microbial Identification System Operating Manual, Version 3.0 Newark, DE: MIDI, Inc; 1999
    [Google Scholar]
  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, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article][PubMed]
    [Google Scholar]
  21. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477[PubMed]
    [Google Scholar]
  22. Cummins CS, Harris H. The chemical composition of the cell wall in some gram-positive bacteria and its possible value as a taxonomic character. J Gen Microbiol 1956; 14:583–600 [View Article][PubMed]
    [Google Scholar]
  23. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2017; 68:461–466 [View Article][PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. Auch AF, von Jan M, Klenk HP, 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]
  27. Niederberger TD, Steven B, Charvet S, Barbier B, Whyte LG. Virgibacillus arcticus sp. nov., a moderately halophilic, endospore-forming bacterium from permafrost in the Canadian high Arctic. Int J Syst Evol Microbiol 2009; 59:2219–2225 [View Article][PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002650
Loading
/content/journal/ijsem/10.1099/ijsem.0.002650
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed