Strain identifier

BacDive ID: 7489

Type strain: Yes

Species: Salinibacterium xinjiangense

Strain Designation: 0543

Strain history: D.-C. Zhang and P.-J. Zhou 0543.

NCBI tax ID(s): 386302 (species)

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

@ref: 16248

BacDive-ID: 7489

DSM-Number: 22272

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-positive, rod-shaped

description: Salinibacterium xinjiangense 0543 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from The China No.1 glacier.

NCBI tax id

  • NCBI tax id: 386302
  • Matching level: species

strain history

@refhistory
16248<- JCM/RIKEN; JCM 13926 <- D. Zhang and P. Zhou, CGMCC; 0543
67770D.-C. Zhang and P.-J. Zhou 0543.

doi: 10.13145/bacdive7489.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Salinibacterium
  • species: Salinibacterium xinjiangense
  • full scientific name: Salinibacterium xinjiangense Zhang et al. 2008

@ref: 16248

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Salinibacterium

species: Salinibacterium xinjiangense

full scientific name: Salinibacterium xinjiangense Zhang et al. 2008

strain designation: 0543

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32626positive1.4-2.3 µm0.5-0.8 µmrod-shapedno
69480positive100

pigmentation

  • @ref: 32626
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16248
  • name: RICH MEDIUM (DSMZ Medium 736)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/736
  • composition: Name: RICH MEDIUM (DSMZ Medium 736) Composition: Agar 20.0 g/l Bacto peptone 10.0 g/l Yeast extract 5.0 g/l Malt extract 5.0 g/l Casamino acids 5.0 g/l Glycerol 2.0 g/l Meat extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Tween 80 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
16248positivegrowth20psychrophilic
32626positivegrowth04-23psychrophilic
32626positiveoptimum18-19psychrophilic
67770positivegrowth10psychrophilic

culture pH

@refabilitytypepHPH range
32626positivegrowth05-09alkaliphile
32626positiveoptimum06-08

Physiology and metabolism

oxygen tolerance

  • @ref: 32626
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32626no
69481no100
69480no99.989

halophily

@refsaltgrowthtested relationconcentration
32626NaClpositivegrowth0-14 %
32626NaClpositiveoptimum0-14 %

observation

@refobservation
32626aggregates in chains
67770quinones: MK-10 (54%), MK-11 (29%), MK-9 (7%), MK-12 (5%), MK-8 (4%)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3262622599arabinose+carbon source
3262617057cellobiose+carbon source
3262628757fructose+carbon source
3262628260galactose+carbon source
3262617234glucose+carbon source
3262617306maltose+carbon source
3262637684mannose+carbon source
3262628053melibiose+carbon source
3262617992sucrose+carbon source
3262617632nitrate+reduction

enzymes

  • @ref: 32626
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16248The China No.1 glacierXinjiang Uygur Autonomous RegionChinaCHNAsia
67770The China No. 1 glacierXinjiang Uygur Autonomous RegionChinaCHNAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Glacier

Safety information

risk assessment

  • @ref: 16248
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16248
  • description: Salinibacterium xinjiangense strain 0543 16S ribosomal RNA gene, partial sequence
  • accession: DQ515964
  • length: 1409
  • database: ena
  • NCBI tax ID: 386302

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Salinibacterium xinjiangense CGMCC 1.5381GCA_014645015scaffoldncbi386302
66792Salinibacterium xinjiangense strain CGMCC 1.5381386302.6wgspatric386302
67770Salinibacterium xinjiangense CGMCC 1.05381GCA_900230175scaffoldncbi386302

GC content

@refGC-contentmethod
1624863.5
6777063.5thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno97.688yes
gram-positiveyes95.054yes
anaerobicno99.338yes
aerobicyes95.272yes
halophileno88.984no
spore-formingno94.008yes
glucose-utilyes87.971yes
thermophileno98.87yes
motileno89.398no
glucose-fermentno92.916no

External links

@ref: 16248

culture collection no.: DSM 22272, CGMCC 1.5381, JCM 13926

straininfo link

  • @ref: 76935
  • straininfo: 312489

literature

  • topic: Phylogeny
  • Pubmed-ID: 19060050
  • title: Salinibacterium xinjiangense sp. nov., a psychrophilic bacterium isolated from the China No. 1 glacier.
  • authors: Zhang DC, Liu HC, Xin YH, Yu Y, Zhou PJ, Zhou YG
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65802-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/isolation & purification/*physiology, China, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16248Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22272)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22272
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32626Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2883728776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
76935Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID312489.1StrainInfo: A central database for resolving microbial strain identifiers