Strain identifier

BacDive ID: 7304

Type strain: Yes

Species: Cryobacterium roopkundense

Strain Designation: Rug 17

Strain history: S. Shivaji RuGl7.

NCBI tax ID(s): 1001240 (species)

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General

@ref: 15539

BacDive-ID: 7304

DSM-Number: 21065

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

description: Cryobacterium roopkundense Rug 17 is an aerobe, psychrophilic, Gram-positive bacterium that was isolated from glacial lake.

NCBI tax id

  • NCBI tax id: 1001240
  • Matching level: species

strain history

@refhistory
15539<- S. Shivaji, CCMB; Rug 17
67770S. Shivaji RuGl7.

doi: 10.13145/bacdive7304.20230509.8.1

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 roopkundense
  • full scientific name: Cryobacterium roopkundense Reddy et al. 2010

@ref: 15539

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Microbacteriaceae

genus: Cryobacterium

species: Cryobacterium roopkundense

full scientific name: Cryobacterium roopkundense Reddy et al. 2010

strain designation: Rug 17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29373positive2.5 µm0.8 µmrod-shapedyes
69480positive100

pigmentation

  • @ref: 29373
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
29373positivegrowth0-18psychrophilic
29373positiveoptimum15-18psychrophilic
29373positiveoptimum16.5psychrophilic
60699positivegrowth8psychrophilic
67770positivegrowth15psychrophilic

culture pH

  • @ref: 29373
  • ability: positive
  • type: optimum
  • pH: 7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29373aerobe
60699aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.676

observation

  • @ref: 67770
  • observation: quinones: MK-10, MK-11, MK-12

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2937316947citrate+carbon source
2937315792malonate+carbon source
2937317632nitrate+reduction

enzymes

@refvalueactivityec
29373catalase+1.11.1.6
29373gelatinase+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
15539glacial lakeRoopkund, Himalayan regionIndiaINDAsia
60699Water,glacierHimalayan region,Lake RoopkundIndiaINDAsia
67770Soil at the periphery of the glacial Lake Roopkund in the Himalayan mountain rangeIndiaINDAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Glacier
#Environmental#Aquatic#Lake (large)

taxonmaps

  • @ref: 69479
  • File name: preview.99_3549.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_9;96_1847;97_2217;98_2721;99_3549&stattab=map
  • Last taxonomy: Cryobacterium
  • 16S sequence: EF467640
  • Sequence Identity:
  • Total samples: 2746
  • soil counts: 1037
  • aquatic counts: 1295
  • animal counts: 250
  • plant counts: 164

Safety information

risk assessment

  • @ref: 15539
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15539
  • description: Cryobacterium roopkundense strain RuGl7 16S ribosomal RNA gene, partial sequence
  • accession: EF467640
  • length: 1459
  • database: ena
  • NCBI tax ID: 1001240

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Cryobacterium roopkundense DSM 21065GCA_014200405contigncbi1001240
66792Cryobacterium roopkundense strain DSM 210651001240.6wgspatric1001240
66792Cryobacterium roopkundense DSM 210652844826561draftimg1001240
67770Cryobacterium roopkundense RuG17GCA_000764165contigncbi1001240

GC content

  • @ref: 15539
  • GC-content: 64.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes75.025no
flagellatedno91.677no
gram-positiveyes92.244no
anaerobicno99.444yes
aerobicyes96.149yes
halophileno84.904no
spore-formingno81.257no
thermophileno99.239no
glucose-utilyes88.61no
glucose-fermentno90.281no

External links

@ref: 15539

culture collection no.: DSM 21065, JCM 15131, CCUG 55701, CGMCC 1.10672

straininfo link

  • @ref: 76754
  • straininfo: 408828

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19661491Cryobacterium roopkundense sp. nov., a psychrophilic bacterium isolated from glacial soil.Reddy GSN, Pradhan S, Manorama R, Shivaji SInt J Syst Evol Microbiol10.1099/ijs.0.011775-02009Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, *Cold Temperature, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Genes, rRNA, Genotype, Ice Cover/*microbiology, India, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species SpecificityGenetics
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_referencepubmedjournal
15539Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21065)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21065
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
29373Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2578128776041
60699Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 55701)https://www.ccug.se/strain?id=55701
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/
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
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
76754Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID408828.1StrainInfo: A central database for resolving microbial strain identifiers