Strain identifier

BacDive ID: 7306

Type strain: Yes

Species: Cryobacterium luteum

Strain Designation: Hh15

Strain history: CGMCC 1.11210 <-- Y. Xin Hh15.

NCBI tax ID(s): 1424661 (species)

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General

@ref: 18238

BacDive-ID: 7306

DSM-Number: 26476

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

description: Cryobacterium luteum Hh15 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from glacier ice.

NCBI tax id

  • NCBI tax id: 1424661
  • Matching level: species

strain history

@refhistory
18238<- NBRC <- CGMCC <- Y. Xin, CAS; Hh15
67770CGMCC 1.11210 <-- Y. Xin Hh15.

doi: 10.13145/bacdive7306.20230509.8.1

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 luteum
  • full scientific name: Cryobacterium luteum Liu et al. 2012

@ref: 18238

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Cryobacterium

species: Cryobacterium luteum

full scientific name: Cryobacterium luteum Liu et al. 2012 emend. Nouioui et al. 2018

strain designation: Hh15

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapeconfidence
30337positive0.93 µm0.44 µmrod-shaped
69480positive100

colony morphology

  • @ref: 18238
  • incubation period: 3-7 days

pigmentation

  • @ref: 30337
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 18238
  • 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
18238positivegrowth10psychrophilic
30337positivegrowth0-20psychrophilic
67770positivegrowth10psychrophilic

culture pH

  • @ref: 30337
  • ability: positive
  • type: growth
  • pH: 5.5-12
  • PH range: alkaliphile

Physiology and metabolism

oxygen tolerance

  • @ref: 30337
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.982

halophily

  • @ref: 30337
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-3 %

observation

  • @ref: 67770
  • observation: quinones: MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3033717057cellobiose+carbon source
3033728757fructose+carbon source
3033717234glucose+carbon source
3033717754glycerol+carbon source
3033717306maltose+carbon source
3033729864mannitol+carbon source
3033737684mannose+carbon source
3033733942ribose+carbon source
3033730911sorbitol+carbon source
3033717992sucrose+carbon source
3033727082trehalose+carbon source
3033718222xylose+carbon source
303374853esculin+hydrolysis
3033717632nitrate+reduction

enzymes

@refvalueactivityec
30337acid phosphatase+3.1.3.2
30337catalase+1.11.1.6

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
18238glacier iceGlacier in Xinjiang Uyghur Autonomous RegionChinaCHNAsia
67770Ice of the No. 1 glacierXingjiang Uygur Autonomous Region, north-west ChinaChinaCHNAsia

isolation source categories

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

Safety information

risk assessment

  • @ref: 18238
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 18238
  • description: Cryobacterium luteum strain Hh15 16S ribosomal RNA gene, partial sequence
  • accession: HQ845193
  • length: 1475
  • database: ena
  • NCBI tax ID: 1424661

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cryobacterium luteum Hh15GCA_004402515contigncbi1424661
66792Cryobacterium luteum strain CGMCC 1.112101424661.3wgspatric1424661
66792Cryobacterium luteum strain Hh151424661.5wgspatric1424661
66792Cryobacterium luteum CGMCC 1.112102667527407draftimg1424661
67770Cryobacterium luteum CGMCC 1.11210GCA_900110125scaffoldncbi1424661

GC content

@refGC-contentmethod
1823863.7
6777065.1genome sequence analysis
6777063.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes74.892no
gram-positiveyes94.179yes
anaerobicno99.623yes
halophileno85.5no
spore-formingno90.696no
glucose-utilyes87.07yes
thermophileno98.487yes
aerobicyes95.025yes
flagellatedno93.102no
glucose-fermentno87.939no

External links

@ref: 18238

culture collection no.: DSM 26476, CGMCC 1.11210, NBRC 107880, JCM 18569

straininfo link

  • @ref: 76756
  • straininfo: 397105

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny21784961Cryobacterium flavum sp. nov. and Cryobacterium luteum sp. nov., isolated from glacier ice.Liu Q, Liu H, Wen Y, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.033738-02011Actinomycetales/*classification/genetics/*isolation & purification/metabolism, China, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Ice Cover/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
Phylogeny23315411Cryobacterium levicorallinum sp. nov., a psychrophilic bacterium isolated from glacier ice.Liu Q, Liu H, Zhang J, Zhou Y, Xin YInt J Syst Evol Microbiol10.1099/ijs.0.046896-02013Actinomycetales/*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, DNAGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
18238Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26476)https://www.dsmz.de/collection/catalogue/details/culture/DSM-26476
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
30337Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2667828776041
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)
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
76756Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397105.1StrainInfo: A central database for resolving microbial strain identifiers