Strain identifier

BacDive ID: 24187

Type strain: Yes

Species: Cryobacterium levicorallinum

Strain Designation: Hh34

Strain history: <- NBRC; NBRC 107883 <- CGMCC <- Y. Xin; Hh34

NCBI tax ID(s): 995038 (species)

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General

@ref: 20519

BacDive-ID: 24187

DSM-Number: 28143

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

description: Cryobacterium levicorallinum Hh34 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from ice in glacier.

NCBI tax id

  • NCBI tax id: 995038
  • Matching level: species

strain history

  • @ref: 20519
  • history: <- NBRC; NBRC 107883 <- CGMCC <- Y. Xin; Hh34

doi: 10.13145/bacdive24187.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Micrococcales
  • family: Microbacteriaceae
  • genus: Cryobacterium
  • species: Cryobacterium levicorallinum
  • full scientific name: Cryobacterium levicorallinum Liu et al. 2013

@ref: 20519

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Cryobacterium

species: Cryobacterium levicorallinum

full scientific name: Cryobacterium levicorallinum Liu et al. 2013

strain designation: Hh34

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
30890positive0.93 µm0.43 µmrod-shaped
69480positive100

colony morphology

  • @ref: 20519
  • incubation period: 3-7 days

pigmentation

  • @ref: 30890
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 20519
  • name: PP-MEDIUM (DSMZ Medium 513)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/513
  • composition: Name: PP-MEDIUM (DSMZ Medium 513) Composition: Agar 15.0 g/l Polypeptone 10.0 g/l Yeast extract 2.0 g/l MgSO4 x 7 H2O 1.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
20519positivegrowth10psychrophilic
30890positivegrowth0-18psychrophilic
30890positiveoptimum11psychrophilic

culture pH

  • @ref: 30890
  • ability: positive
  • type: growth
  • pH: 6.0-12.0
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30890
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.967

halophily

  • @ref: 30890
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

  • @ref: 30890
  • observation: aggregates in clumps

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3089030089acetate+carbon source
3089022599arabinose+carbon source
3089017057cellobiose+carbon source
3089028757fructose+carbon source
3089028260galactose+carbon source
3089024265gluconate+carbon source
3089017234glucose+carbon source
3089017754glycerol+carbon source
3089025115malate+carbon source
3089017306maltose+carbon source
3089029864mannitol+carbon source
3089037684mannose+carbon source
3089033942ribose+carbon source
3089030911sorbitol+carbon source
3089017992sucrose+carbon source
3089027082trehalose+carbon source
3089018222xylose+carbon source
3089017632nitrate+reduction

enzymes

  • @ref: 30890
  • value: catalase
  • activity: +
  • ec: 1.11.1.6

Isolation, sampling and environmental information

isolation

  • @ref: 20519
  • sample type: ice in glacier
  • geographic location: No.1 Glacier in Xingjiang Uygur Autonomous Region, north-west China
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Aquatic#Ice

Safety information

risk assessment

  • @ref: 20519
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20519
  • description: Cryobacterium levicorallinum strain Hh34 16S ribosomal RNA gene, partial sequence
  • accession: JF267312
  • length: 1478
  • database: ena
  • NCBI tax ID: 995038

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cryobacterium levicorallinum NBRC 107883GCA_007992355contigncbi995038
66792Cryobacterium levicorallinum Hh34GCA_004402405contigncbi995038
66792Cryobacterium levicorallinum strain Hh34995038.5wgspatric995038
66792Cryobacterium levicorallinum strain NBRC 107883995038.7wgspatric995038
66792Cryobacterium levicorallinum CGMCC 1.112112663762754draftimg995038

GC content

  • @ref: 20519
  • GC-content: 63.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes73.49no
flagellatedno94.396no
gram-positiveyes93.405yes
anaerobicno99.348yes
halophileno79.188no
spore-formingno89.492no
thermophileno97.89no
glucose-utilyes84.36yes
aerobicyes94.62yes
glucose-fermentno89.101no

External links

@ref: 20519

culture collection no.: DSM 28143, CGMCC 1.11211, NBRC 107883

straininfo link

  • @ref: 88140
  • straininfo: 402409

literature

  • topic: Phylogeny
  • Pubmed-ID: 23315411
  • title: Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.
  • authors: Liu Q, Liu H, Zhang J, Zhou Y, Xin Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.046896-0
  • year: 2013
  • mesh: Actinomycetales/*classification/genetics/metabolism, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Ice, Ice Cover/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogueID_cross_referencepubmedjournal
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
20519Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-28143Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28143)
30890Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172722028776041
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/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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
88140Reimer, 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-ID402409.1