Strain identifier

BacDive ID: 130665

Type strain: Yes

Species: Novosphingobium kunmingense

Strain Designation: 18-11HK

Strain history: <- F. Xie, Henan Key Laboratory of Microbial Eng., Zhengzhou, China; 18-11HK

NCBI tax ID(s): 1211806 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 21701

BacDive-ID: 130665

DSM-Number: 25975

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Novosphingobium kunmingense 18-11HK is a mesophilic, Gram-negative bacterium that was isolated from phosphate rock powder from a phosphate-mining field.

NCBI tax id

  • NCBI tax id: 1211806
  • Matching level: species

strain history

  • @ref: 21701
  • history: <- F. Xie, Henan Key Laboratory of Microbial Eng., Zhengzhou, China; 18-11HK

doi: 10.13145/bacdive130665.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Sphingomonadales
  • family: Erythrobacteraceae
  • genus: Novosphingobium
  • species: Novosphingobium kunmingense
  • full scientific name: Novosphingobium kunmingense Xie et al. 2014

@ref: 21701

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium kunmingense

full scientific name: Novosphingobium kunmingense Xie et al. 2014

strain designation: 18-11HK

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.946

multimedia

  • @ref: 21701
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_25975.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 21701
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 21701
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.992

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
21701-----+--------------+

Isolation, sampling and environmental information

isolation

  • @ref: 21701
  • sample type: phosphate rock powder from a phosphate-mining field
  • geographic location: Yunnan Province, suburb of Kunming
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

Cat1Cat2Cat3
#Engineered#Other#Mine
#Environmental#Terrestrial#Geologic

Safety information

risk assessment

  • @ref: 21701
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 21701
  • description: Novosphingobium kunmingense strain 18-11HK 16S ribosomal RNA gene, partial sequence
  • accession: JQ246446
  • length: 1453
  • database: ena
  • NCBI tax ID: 1211806

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium kunmingense CGMCC 1.12274GCA_002813245contigncbi1211806
66792Novosphingobium kunmingense strain CGMCC 1.122741211806.3wgspatric1211806
66792Novosphingobium kunmingense CGMCC 1.122742718217687draftimg1211806

GC content

  • @ref: 21701
  • GC-content: 65.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno94.025no
gram-positiveno96.897no
anaerobicno99.218no
aerobicyes93.874no
halophileno95.459no
spore-formingno94.745no
thermophileno95.574no
glucose-utilyes74.654yes
flagellatedno97.955no
glucose-fermentno91.362yes

External links

@ref: 21701

culture collection no.: DSM 25975, CGMCC 1.12274

straininfo link

  • @ref: 89173
  • straininfo: 398635

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny24737793Novosphingobium kunmingense sp. nov., isolated from a phosphate mine.Xie F, Quan S, Liu D, He W, Wang Y, Ma H, Chen G, Chao Y, Qian SInt J Syst Evol Microbiol10.1099/ijs.0.057273-02014Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Mining, Molecular Sequence Data, Nucleic Acid Hybridization, Phosphates/*chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryGenetics
Phylogeny27199143Novosphingobium naphthae sp. nov., from oil-contaminated soil.Chaudhary DK, Kim JInt J Syst Evol Microbiol10.1099/ijsem.0.0011642016Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, *Petroleum Pollution, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Spermidine/chemistry, Sphingomonadaceae/*classification/genetics/isolation & purification, Ubiquinone/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
21701Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-25975Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 25975)
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/gkaa1025Nucleic Acids Res. 49: D498-D508 202033211880
68369Automatically annotated from API 20NE
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
89173Reimer, 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-ID398635.1