Strain identifier

BacDive ID: 11234

Type strain: Yes

Species: Nocardiopsis ganjiahuensis

Strain history: CGMCC 4.3500 <-- X. Zhang et al. HBUM 20038.

NCBI tax ID(s): 1237500 (strain), 239984 (species)

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General

@ref: 12258

BacDive-ID: 11234

DSM-Number: 45031

keywords: genome sequence, 16S sequence, Bacteria, aerobe, spore-forming, mesophilic, Gram-positive

description: Nocardiopsis ganjiahuensis DSM 45031 is an aerobe, spore-forming, mesophilic bacterium that was isolated from soil of saline.

NCBI tax id

NCBI tax idMatching level
239984species
1237500strain

strain history

@refhistory
12258<- Z. Liping; HBUM 20038 <- C.-L. Jiang
67770CGMCC 4.3500 <-- X. Zhang et al. HBUM 20038.

doi: 10.13145/bacdive11234.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/actinomycetota
  • domain: Bacteria
  • phylum: Actinomycetota
  • class: Actinomycetes
  • order: Streptosporangiales
  • family: Nocardiopsidaceae
  • genus: Nocardiopsis
  • species: Nocardiopsis ganjiahuensis
  • full scientific name: Nocardiopsis ganjiahuensis Zhang et al. 2008

@ref: 12258

domain: Bacteria

phylum: Actinobacteria

class: Actinobacteria

order: Actinomycetales

family: Nocardiopsaceae

genus: Nocardiopsis

species: Nocardiopsis ganjiahuensis

full scientific name: Nocardiopsis ganjiahuensis Zhang et al. 2008

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidence
32218positiveno
69480positive100

pigmentation

  • @ref: 32218
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
12258GYP GLUCOSE-YEAST-PEPTONE MEDIUM (DSMZ Medium 852)yeshttps://mediadive.dsmz.de/medium/852Name: GYP GLUCOSE-YEAST-PEPTONE MEDIUM (DSMZ Medium 852) Composition: Glucose 20.0 g/l Yeast extract 10.0 g/l Peptone 10.0 g/l Na-acetate 10.0 g/l Agar 10.0 g/l MgSO4 x 7 H2O 0.2 g/l MnSO4 x 4 H2O 0.01 g/l FeSO4 x 7 H2O 0.01 g/l NaCl 0.01 g/l Distilled water
12258BOGORIELLA MEDIUM (DSMZ Medium 785)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium785.pdf

culture temp

@refgrowthtypetemperaturerange
12258positivegrowth28mesophilic
32218positivegrowth10-32
32218positiveoptimum30mesophilic
67770positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
32218positivegrowth8.5-13alkaliphile
32218positiveoptimum9

Physiology and metabolism

oxygen tolerance

  • @ref: 32218
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
32218yes
69481yes100
69480yes100

halophily

  • @ref: 32218
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-5 %

observation

  • @ref: 67770
  • observation: quinones: MK-10(H2), MK-10(H4), MK-10(H6)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3221822599arabinose+carbon source
3221817754glycerol+carbon source
3221817268myo-inositol+carbon source
3221826546rhamnose+carbon source
3221818222xylose+carbon source
3221817632nitrate+reduction

enzymes

  • @ref: 32218
  • value: urease
  • activity: +
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
12258soil of salineGanjia Lake of Xinjiang ProvinceChinaCHNAsia
67770Alkaline soilChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Condition#Saline

taxonmaps

  • @ref: 69479
  • File name: preview.99_6587.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_152;96_659;97_762;98_1213;99_6587&stattab=map
  • Last taxonomy: Nocardiopsis
  • 16S sequence: AY336513
  • Sequence Identity:
  • Total samples: 43
  • soil counts: 7
  • aquatic counts: 2
  • animal counts: 34

Safety information

risk assessment

  • @ref: 12258
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 12258
  • description: Nocardiopsis ganjiahuensis strain HBUM 20038 16S ribosomal RNA gene, partial sequence
  • accession: AY336513
  • length: 1434
  • database: ena
  • NCBI tax ID: 239984

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Nocardiopsis ganjiahuensis DSM 450311237500.3wgspatric1237500
66792Nocardiopsis ganjiahuensis DSM 450312554235030draftimg1237500
67770Nocardiopsis ganjiahuensis DSM 45031GCA_000341085contigncbi1237500

GC content

@refGC-contentmethod
1225871.12
3221871.1
6777071.1high performance liquid chromatography (HPLC)
6777071genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingyes100no
motileno93.021no
gram-positiveyes92.889yes
anaerobicno99.341no
aerobicyes94.26no
halophileyes69.957no
spore-formingyes92.196yes
thermophileno98.624yes
glucose-utilyes86.891no
flagellatedno97.759yes
glucose-fermentno91.764no

External links

@ref: 12258

culture collection no.: DSM 45031, CGMCC 4.3500, HBUM 20038, JCM 15475

straininfo link

  • @ref: 80469
  • straininfo: 297498

literature

  • topic: Phylogeny
  • Pubmed-ID: 18175709
  • title: Nocardiopsis ganjiahuensis sp. nov., isolated from a soil from Ganjiahu, China.
  • authors: Zhang X, Zhang LP, Yang R, Shi N, Lu Z, Chen WX, Jiang CL, Xu LH
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.65145-0
  • year: 2008
  • mesh: Actinomycetales/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, China, DNA, Bacterial/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Species Specificity
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
12258Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45031)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45031
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
32218Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2846028776041
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/
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
80469Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297498.1StrainInfo: A central database for resolving microbial strain identifiers