Strain identifier

BacDive ID: 132339

Type strain: Yes

Species: Novosphingobium endophyticum

Strain history: W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; EGI 60015.

NCBI tax ID(s): 1955250 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 24128

BacDive-ID: 132339

DSM-Number: 29948

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

description: Novosphingobium endophyticum DSM 29948 is a mesophilic, Gram-negative bacterium that was isolated from surface sterilized healthy roots of Chinese liquorice Glycyrrhiza uralensis.

NCBI tax id

  • NCBI tax id: 1955250
  • Matching level: species

strain history

@refhistory
24128<- W.-J. Li, YIM Yunnan Institute of Microbiology <- Y. Li, YIM <- L. Li, YIM
67770W.-J. Li; Yunnan Inst. of Microbiol., Yunnan Univ., China; EGI 60015.

doi: 10.13145/bacdive132339.20230509.8.1

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 endophyticum
  • full scientific name: Novosphingobium endophyticum Li et al. 2016

@ref: 24128

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Pseudomonadales

family: Erythrobacteraceae

genus: Novosphingobium

species: Novosphingobium endophyticum

full scientific name: Novosphingobium endophyticum Li et al. 2016

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.984

Culture and growth conditions

culture medium

  • @ref: 24128
  • name: R2A MEDIUM (DSMZ Medium 830)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/830
  • composition: Name: R2A MEDIUM (DSMZ Medium 830) Composition: Agar 15.0 g/l Casamino acids 0.5 g/l Starch 0.5 g/l Glucose 0.5 g/l Proteose peptone 0.5 g/l Yeast extract 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
24128positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.996

observation

  • @ref: 67770
  • observation: quinones: Q-10

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
24128surface sterilized healthy roots of Chinese liquorice Glycyrrhiza uralensisGlycyrrhiza uralensisXinjiang province, Yili CountyChinaCHNAsia
67770Healthy roots of Glycyrrhiza uralensis F. collected from Yili CountyGlycyrrhiza uralensisXinjiang Province, northwest ChinaChinaCHNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root (Rhizome)
#Host Body-Site#Plant#Sterilized plant part

taxonmaps

  • @ref: 69479
  • File name: preview.99_184426.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_20;96_795;97_15120;98_46773;99_184426&stattab=map
  • Last taxonomy: Novosphingobium endophyticum
  • 16S sequence: KP721487
  • Sequence Identity:
  • Total samples: 979
  • soil counts: 317
  • aquatic counts: 522
  • animal counts: 80
  • plant counts: 60

Safety information

risk assessment

  • @ref: 24128
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24128
  • description: Novosphingobium pentaromativorans strain EGI 60015 16S ribosomal RNA gene, partial sequence
  • accession: KP721487
  • length: 1492
  • database: ena
  • NCBI tax ID: 1955250

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Novosphingobium endophyticum CGMCC 1.15095GCA_014640675contigncbi1955250
66792Novosphingobium endophyticum strain CGMCC 1.150951955250.3wgspatric1955250

GC content

  • @ref: 24128
  • GC-content: 66.6
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes50.572no
gram-positiveno97.19no
anaerobicno98.649no
aerobicyes92.716no
halophileno91.57no
spore-formingno93.383no
glucose-utilyes90.181no
flagellatedno82.196no
thermophileno96.778yes
glucose-fermentno90.596no

External links

@ref: 24128

culture collection no.: DSM 29948, CGMCC 1.15095, KCTC 42486, EGI 600015, JCM 30707

straininfo link

  • @ref: 90685
  • straininfo: 405299

literature

  • topic: Phylogeny
  • Pubmed-ID: 26047607
  • title: Novosphingobium endophyticum sp. nov. isolated from roots of Glycyrrhiza uralensis.
  • authors: Li YQ, Li L, Chen W, Duan YQ, Nimaichand S, Guo JW, Gao R, Li WJ
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-015-1124-1
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycyrrhiza uralensis/*microbiology, Phylogeny, Plant Roots/*microbiology, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Species Specificity, Sphingomonadaceae/*classification/genetics/isolation & purification
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlcatalogue
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
24128Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29948Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29948)
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
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
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
90685Reimer, 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-ID405299.1