Strain identifier

BacDive ID: 130258

Type strain: Yes

Species: Diaphorobacter ruginosibacter

Strain Designation: BN30

Strain history: <- G. H. Wei, Northwest A&F Univ., Yangling, Shaanxi, China; BN30 <- X. L. Wei

NCBI tax ID(s): 1715720 (species)

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

@ref: 21575

BacDive-ID: 130258

DSM-Number: 27467

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

description: Diaphorobacter ruginosibacter BN30 is a mesophilic, Gram-negative bacterium that was isolated from root nodule of soybean.

NCBI tax id

  • NCBI tax id: 1715720
  • Matching level: species

strain history

  • @ref: 21575
  • history: <- G. H. Wei, Northwest A&F Univ., Yangling, Shaanxi, China; BN30 <- X. L. Wei

doi: 10.13145/bacdive130258.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Diaphorobacter
  • species: Diaphorobacter ruginosibacter
  • full scientific name: Diaphorobacter ruginosibacter Wei et al. 2015

@ref: 21575

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Diaphorobacter

species: Diaphorobacter ruginosibacter

full scientific name: Diaphorobacter ruginosibacter Wei et al. 2015

strain designation: BN30

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 100

multimedia

  • @ref: 21575
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_27467.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 21575
  • name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1a
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

  • @ref: 21575
  • growth: positive
  • type: growth
  • temperature: 28
  • range: mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.998

Isolation, sampling and environmental information

isolation

  • @ref: 21575
  • sample type: root nodule of soybean
  • geographic location: Shaanxi province, suburb of Baoji City (107°9'38.3''E, 34°22'30.3''N)
  • country: China
  • origin.country: CHN
  • continent: Asia
  • latitude: 34.3751
  • longitude: 107.161

isolation source categories

Cat1Cat2Cat3
#Host#Plants#Herbaceous plants (Grass,Crops)
#Host Body-Site#Plant#Root nodule

taxonmaps

  • @ref: 69479
  • File name: preview.99_48649.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_3532;97_16370;98_35035;99_48649&stattab=map
  • Last taxonomy: Comamonadaceae
  • 16S sequence: KC825337
  • Sequence Identity:
  • Total samples: 235
  • soil counts: 57
  • aquatic counts: 110
  • animal counts: 35
  • plant counts: 33

Sequence information

16S sequences

  • @ref: 21575
  • description: Comamonadaceae bacterium BN30 16S ribosomal RNA gene, partial sequence
  • accession: KC825337
  • length: 1349
  • database: ena
  • NCBI tax ID: 1352536

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Diaphorobacter ruginosibacter DSM 27467GCA_014395975completencbi1715720
66792Diaphorobacter ruginosibacter strain DSM 274671715720.3completepatric1715720
66792Diaphorobacter ruginosibacter DSM 274672894023352completeimg1715720

GC content

  • @ref: 21575
  • GC-content: 65.2
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno79.618no
gram-positiveno98.69no
anaerobicno99.08no
aerobicyes96.176no
halophileno94.94no
spore-formingno93.994no
thermophileno98.884no
glucose-utilno69.893no
motileno62.512no
glucose-fermentno90.69no

External links

@ref: 21575

culture collection no.: DSM 27467, ACCC 06116

literature

  • topic: Phylogeny
  • Pubmed-ID: 25763990
  • title: Diaphorobacter ruginosibacter sp. nov., isolated from soybean root nodule, and emended description of the genus Diaphorobacter.
  • authors: Wei XL, Han MS, Xia CC, Ding SL, Xu L, Lin YB, Wang L, Wei GH
  • journal: Arch Microbiol
  • DOI: 10.1007/s00203-015-1102-7
  • year: 2015
  • mesh: Bacterial Typing Techniques, Base Composition, Comamonadaceae/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Root Nodules, Plant/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Soybeans/*microbiology
  • topic2: Transcriptome

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
21575Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-27467Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 27467)
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
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