1887

Abstract

A Gram-stain-negative, rod-shaped, non-flagellated, non-gliding, aerobic bacterial strain, designated LPB0138, was isolated from a marine spoon worm (). The strain LPB0138 contains a circular chromosome of 3.43 Mb with a DNA G+C content of 30.4 mol%. The genome includes 2987 protein-coding genes and two copies of rRNA operons. The 16S rRNA gene sequence analysis showed that the isolate occurred within a clade containing only members of the family . The highest sequence similarity was observed with the genus (93.0–94.3 %), but the phylogenetic leaf of the new isolate did not belong to any of the genera known in the family . The low sequence similarity and the phylogenetic tree topology implied the novel generic status of the new isolate. The phenotypic properties of the strain LPB0138 also differentiated this isolate from its neighbour genera by showing a distinctive fatty acid composition, unique polar lipids profile, and low DNA G+C content. The LPB0138 strain contained menaquinone 6 as the isoprenoid quinone; iso-C G, iso-C, iso-C 3-OH, and iso-C 3-OH as the major fatty acids; and phosphatidylethanolamine, unidentified aminophospholipids, unidentified aminolipids, and unidentified lipids as the major polar lipids. Based on the polyphasic taxonomic data obtained, the LPB0138 strain is considered to represent a novel species in a novel genus of the family for which the name gen. nov., sp. nov. was proposed. The type strain is LPB0138 (=KACC 18889;=JCM 31563).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003966
2020-01-14
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/3/1751.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003966&mimeType=html&fmt=ahah

References

  1. Validation of the publication of new names and new combinations previously effectively published outside the IJSB, list no. 41. Int J Syst Evol Microbiol 1992; 42:327–329
    [Google Scholar]
  2. Bernardet JF, Segers P, Vancanneyt M, Berthe F, Kersters K et al. Cutting a Gordian knot: emended classification and description of the genus Flavobacterium, emended description of the family Flavobacteriaceae, and proposal of Flavobacterium hydatis nom. nov. (basonym, Cytophaga aquatilis STROHL and Tait 1978). Int J Syst Bacteriol 1996; 46:128–148 [View Article]
    [Google Scholar]
  3. Bernardet JF, Nakagawa Y, Holmes B. Subcommittee on the taxonomy of Flavobacterium 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
    [Google Scholar]
  4. 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]
    [Google Scholar]
  5. Bernardet JF. Flavobacteriaceae . In Whitman WB, Rainey F, Kämpfer P, Trujillo M, Chun J. (editors) Bergey's Manual of Systematics of Archaea and Bacteria 2015
    [Google Scholar]
  6. Shin S-K, Kim E, Choi S, Yi H. Cochleicola gelatinilyticus gen. nov., sp. nov., isolated from a marine gastropod, Reichia luteostoma . J Microbiol Biotechnol 2016; 26:1439–1445 [View Article]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. Jeon YS, Lee K, Park SC, Kim BS, Cho YJ et al. EzEditor: a versatile sequence alignment editor for both rRNA- and protein-coding genes. Int J Syst Evol Microbiol 2014; 64:689–691 [View Article]
    [Google Scholar]
  9. 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]
    [Google Scholar]
  10. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012; 61:539–542 [View Article]
    [Google Scholar]
  11. Angiuoli SV, Gussman A, Klimke W, Cochrane G, Field D et al. Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation. OMICS 2008; 12:137–141 [View Article]
    [Google Scholar]
  12. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005; 187:6258–6264 [View Article]
    [Google Scholar]
  13. Rodríguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species: culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe Magazine 2014111–118
    [Google Scholar]
  14. Rodriguez-R LM, Konstantinidis KT. The Enveomics Collection: a Toolbox for Specialized Analyses of Microbial Genomes and Metagenomes 2016
    [Google Scholar]
  15. Bowman JP. Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 2000; 50:1861–1868 [View Article]
    [Google Scholar]
  16. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 2014; 37:342–350
    [Google Scholar]
  17. da Costa MS, Albuquerque L, Nobre MF, Wait R. The extraction and identification of respiratory lipoquinones of prokaryotes and their use in taxonomy. Methods Microbiol 2011; 38:197–206
    [Google Scholar]
  18. 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]
  19. da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol 2011; 38:165–181
    [Google Scholar]
  20. Choi DH, Cho BC. Lutibacter litoralis gen. nov., sp. nov., a marine bacterium of the family Flavobacteriaceae isolated from tidal flat sediment. Int J Syst Evol Microbiol 2006; 56:771–776 [View Article]
    [Google Scholar]
  21. Kim Y-O, Park S, Nam B-H, Jung Y-T, Kim D-G et al. Description of Lutimonas halocynthiae sp. nov., isolated from a golden sea squirt (Halocynthia aurantium), reclassification of Aestuariicola saemankumensis as Lutimonas saemankumensis comb. nov. and emended description of the genus Lutimonas . Int J Syst Evol Microbiol 2014; 64:1984–1990 [View Article]
    [Google Scholar]
  22. Park SC, Baik KS, Kim D, Seong CN. Maritimimonas rapanae gen. nov., sp. nov., isolated from gut microflora of the veined rapa whelk, Rapana venosa . Int J Syst Evol Microbiol 2009; 59:2824–2829 [View Article]
    [Google Scholar]
  23. Jung YT, Kim JH, Kang SJ, Oh TK, Yoon JH. Namhaeicola litoreus gen. nov., sp. nov., a member of the family Flavobacteriaceae isolated from seawater. Int J Syst Evol Microbiol 2012; 62:2163–2168 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003966
Loading
/content/journal/ijsem/10.1099/ijsem.0.003966
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