Strain identifier

BacDive ID: 158186

Type strain: Yes

Species: Leucothrix pacifica

Strain Designation: XH122

Strain history: X.-H. Zhang XH122.

NCBI tax ID(s): 1247513 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 64782

BacDive-ID: 158186

DSM-Number: 25984

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Leucothrix pacifica XH122 is a mesophilic, Gram-negative bacterium that was isolated from surface seawater.

NCBI tax id

  • NCBI tax id: 1247513
  • Matching level: species

strain history

@refhistory
64782<- X.-H. Zhang, Ocean Univ. China, Dept. of Marine Biology, Qingdao, P. R. China; XH122
67770X.-H. Zhang XH122.

doi: 10.13145/bacdive158186.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Beggiatoales
  • family: Leucotrichaceae
  • genus: Leucothrix
  • species: Leucothrix pacifica
  • full scientific name: Leucothrix pacifica Zhang et al. 2015

@ref: 64782

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Thiotrichales

family: Thiotrichaceae

genus: Leucothrix

species: Leucothrix pacifica

full scientific name: Leucothrix pacifica Zhang et al. 2015

strain designation: XH122

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.997

Culture and growth conditions

culture temp

  • @ref: 67770
  • growth: positive
  • type: growth
  • temperature: 30
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69480no99.896
69481no100

observation

  • @ref: 67770
  • observation: quinones: Q-8

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountrylatitudelongitude
64782surface seawaterSouth Pacific GyreSouthwest Pacific Ocean-45.9667-163.183
67770Surface seawater from the South Pacific Gyre (163° 11' S 45° 58' E)

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_105060.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_473;96_20019;97_35394;98_52157;99_105060&stattab=map
  • Last taxonomy: Leucothrix pacifica
  • 16S sequence: JQ082190
  • Sequence Identity:
  • Total samples: 792
  • soil counts: 4
  • aquatic counts: 660
  • animal counts: 123
  • plant counts: 5

Safety information

risk assessment

  • @ref: 64782
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
64782Leucothrix pacifica strain XH122 16S ribosomal RNA gene, partial sequenceJX5012561445ena1247513
67770Leucothrix sp. U1371-101227-XH122 16S ribosomal RNA gene, partial sequenceJQ0821901447ena1171542

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Leucothrix pacifica strain JCM 183881247513.4wgspatric1247513
66792Leucothrix pacifica JCM 183882889727904draftimg1247513
67770Leucothrix pacifica JCM 18388GCA_003172875scaffoldncbi1247513

GC content

  • @ref: 64782
  • GC-content: 46.2
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.342no
gram-positiveno98.219no
anaerobicno97.942no
aerobicyes89.52no
halophileno62.722no
spore-formingno95.117no
thermophileno99.065no
glucose-utilyes90.132no
flagellatedno88.281no
glucose-fermentno86.051no

External links

@ref: 64782

culture collection no.: DSM 25984, JCM 18388

straininfo link

  • @ref: 111017
  • straininfo: 405777

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25896354Leucothrix pacifica sp. nov., isolated from seawater, and emended description of the genus Leucothrix.Zhang Z, Gao X, Wang L, Zhang XHInt J Syst Evol Microbiol10.1099/ijs.0.0002702015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Pacific Ocean, Phosphatidylethanolamines/chemistry, Phosphatidylglycerols/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thiotrichaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny30516460Leucothrix arctica sp. nov., isolated from Arctic seawater.Baek K, Choi A, Lee YM, Lee HK, Cho JCInt J Syst Evol Microbiol10.1099/ijsem.0.0030722018Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Thiotrichaceae/*classification/genetics, Ubiquinone/chemistryTranscriptome
Phylogeny31486761Leucothrix sargassi sp. nov., isolated from a marine alga [Sargassum natans (L.) Gaillon].Liu T, Zhang Y, Zhang X, Zhou L, Meng C, Zhou C, Jing C, Zhu W, Wang YInt J Syst Evol Microbiol10.1099/ijsem.0.0036942019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sargassum/*microbiology, Sequence Analysis, DNA, Thiotrichaceae/*classification/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
64782Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25984Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25984)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
111017Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID405777.1