Strain identifier

BacDive ID: 6167

Type strain: Yes

Species: Devosia insulae

Strain Designation: DS-56

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 408174 (species)

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

@ref: 7288

BacDive-ID: 6167

DSM-Number: 17955

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Devosia insulae DS-56 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from soil.

NCBI tax id

  • NCBI tax id: 408174
  • Matching level: species

strain history

@refhistory
7288<- J.-H. Yoon, KRIBB; DS-56
67771<- JH Yoon, KRIBB

doi: 10.13145/bacdive6167.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Devosiaceae
  • genus: Devosia
  • species: Devosia insulae
  • full scientific name: Devosia insulae Yoon et al. 2007
  • synonyms

    • @ref: 20215
    • synonym: Devosia terrae

@ref: 7288

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Devosiaceae

genus: Devosia

species: Devosia insulae

full scientific name: Devosia insulae Yoon et al. 2007

strain designation: DS-56

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32140negative0.5-2.0 µm0.3-0.5 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 32140
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 7288
  • name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/545
  • composition: Name: TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545) Composition: Casein peptone 17.0 g/l NaCl 5.0 g/l Soy peptone 3.0 g/l D(+)-Glucose 2.5 g/l K2HPO4 2.5 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
7288positivegrowth25mesophilic
32140positivegrowth10-31
32140positiveoptimum25mesophilic
67771positivegrowth25mesophilic

culture pH

@refabilitytypepH
32140positivegrowth6.5-7.5
32140positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

halophily

@refsaltgrowthtested relationconcentration
32140NaClpositivegrowth0-2 %
32140NaClpositiveoptimum0.5 %

enzymes

  • @ref: 32140
  • value: urease
  • activity: +
  • ec: 3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7288soilDokdoRepublic of KoreaKORAsia
67771From soilDokdoRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Terrestrial
  • Cat3: #Soil

taxonmaps

  • @ref: 69479
  • File name: preview.99_584.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_371;97_419;98_478;99_584&stattab=map
  • Last taxonomy: Devosia insulae subclade
  • 16S sequence: EF012357
  • Sequence Identity:
  • Total samples: 1040
  • soil counts: 308
  • aquatic counts: 368
  • animal counts: 219
  • plant counts: 145

Safety information

risk assessment

  • @ref: 7288
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32140Devosia insulae strain DS-56 16S ribosomal RNA gene, partial sequenceEF012357.1437nuccore1116389
7288Devosia insulae strain DS-56 16S ribosomal RNA gene, partial sequenceEF0123571437ena1116389

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Devosia insulae DS-56GCA_000970465contigncbi1116389
66792Devosia insulae DS-561116389.3wgspatric1116389
66792Devosia insulae DS-562636415773draftimg1116389

GC content

@refGC-contentmethod
728866.2high performance liquid chromatography (HPLC)
3214066.2

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes76.733no
flagellatedno74.92no
gram-positiveno96.36yes
anaerobicno98.74yes
aerobicyes92.368yes
halophileno93.143yes
spore-formingno95.513no
glucose-utilyes89.557no
thermophileno95.408no
glucose-fermentno89.614no

External links

@ref: 7288

culture collection no.: DSM 17955, KCTC 12821

straininfo link

  • @ref: 75652
  • straininfo: 399685

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17551048Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia.Yoon JH, Kang SJ, Park S, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.65028-02007Aerobiosis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Hydrogen-Ion Concentration, Hyphomicrobiaceae/*classification/genetics/*isolation & purification/physiology, Korea, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Sodium Chloride/metabolism, *Soil Microbiology, Temperature, Ubiquinone/analysisGenetics
Phylogeny26475689Methyloterrigena soli gen. nov., sp. nov., a methanol-utilizing bacterium isolated from chloroethylene-contaminated soil.Kim HS, Srinivasan S, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0006802015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Methanol/*metabolism, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants, Ubiquinone/analogs & derivatives/chemistry, Vinyl ChlorideGenetics
Phylogeny26514816Devosia humi sp. nov., isolated from soil of a Korean pine (Pinus koraiensis) garden.Du J, Kook M, Akter S, Singh H, Won K, Ngo HTT, Yi THInt J Syst Evol Microbiol10.1099/ijsem.0.0007242015Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Hyphomicrobiaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phospholipids/chemistry, *Phylogeny, Pinus/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/chemistryGenetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
7288Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17955)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17955
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
32140Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2838428776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75652Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID399685.1StrainInfo: A central database for resolving microbial strain identifiers