Strain identifier
BacDive ID: 6167
Type strain:
Species: Devosia insulae
Strain Designation: DS-56
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 408174 (species)
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
@ref | history |
---|---|
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
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
32140 | negative | 0.5-2.0 µm | 0.3-0.5 µm | rod-shaped | yes |
67771 | negative |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
7288 | positive | growth | 25 | mesophilic |
32140 | positive | growth | 10-31 | |
32140 | positive | optimum | 25 | mesophilic |
67771 | positive | growth | 25 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32140 | positive | growth | 6.5-7.5 |
32140 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
32140 | NaCl | positive | growth | 0-2 % |
32140 | NaCl | positive | optimum | 0.5 % |
enzymes
- @ref: 32140
- value: urease
- activity: +
- ec: 3.5.1.5
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7288 | soil | Dokdo | Republic of Korea | KOR | Asia |
67771 | From soil | Dokdo | Republic of Korea | KOR | Asia |
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
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
32140 | Devosia insulae strain DS-56 16S ribosomal RNA gene, partial sequence | EF012357. | 1437 | nuccore | 1116389 |
7288 | Devosia insulae strain DS-56 16S ribosomal RNA gene, partial sequence | EF012357 | 1437 | ena | 1116389 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Devosia insulae DS-56 | GCA_000970465 | contig | ncbi | 1116389 |
66792 | Devosia insulae DS-56 | 1116389.3 | wgs | patric | 1116389 |
66792 | Devosia insulae DS-56 | 2636415773 | draft | img | 1116389 |
GC content
@ref | GC-content | method |
---|---|---|
7288 | 66.2 | high performance liquid chromatography (HPLC) |
32140 | 66.2 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 76.733 | no |
flagellated | no | 74.92 | no |
gram-positive | no | 96.36 | yes |
anaerobic | no | 98.74 | yes |
aerobic | yes | 92.368 | yes |
halophile | no | 93.143 | yes |
spore-forming | no | 95.513 | no |
glucose-util | yes | 89.557 | no |
thermophile | no | 95.408 | no |
glucose-ferment | no | 89.614 | no |
External links
@ref: 7288
culture collection no.: DSM 17955, KCTC 12821
straininfo link
- @ref: 75652
- straininfo: 399685
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17551048 | Devosia insulae sp. nov., isolated from soil, and emended description of the genus Devosia. | Yoon JH, Kang SJ, Park S, Oh TK | Int J Syst Evol Microbiol | 10.1099/ijs.0.65028-0 | 2007 | Aerobiosis, 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/analysis | Genetics |
Phylogeny | 26475689 | Methyloterrigena soli gen. nov., sp. nov., a methanol-utilizing bacterium isolated from chloroethylene-contaminated soil. | Kim HS, Srinivasan S, Lee SS | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000680 | 2015 | Bacterial 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 Chloride | Genetics |
Phylogeny | 26514816 | Devosia 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 TH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000724 | 2015 | Bacterial 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/chemistry | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
7288 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17955) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17955 | |||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | |||
32140 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28384 | 28776041 | |
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
69479 | João 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 | |||
75652 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID399685.1 | StrainInfo: A central database for resolving microbial strain identifiers |