Strain identifier
BacDive ID: 1988
Type strain: 
Species: Paraburkholderia sabiae
Strain history: <- LMG <- P. Vandamme, University Ghent, Laboratory of Microbiology <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan <- S. M. de Faria, EMBRAPA-Agrobiologia Brazil; Br3407
NCBI tax ID(s): 273251 (species)
version 8.1 (current version)
General
@ref: 17184
BacDive-ID: 1988
DSM-Number: 23623
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Paraburkholderia sabiae DSM 23623 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from root nodule of Mimosa caesalpiniifolia.
NCBI tax id
- NCBI tax id: 273251
- Matching level: species
strain history
- @ref: 17184
- history: <- LMG <- P. Vandamme, University Ghent, Laboratory of Microbiology <- W.-M. Chen, Natl. Kaohsiung Marine Univ. Taiwan <- S. M. de Faria, EMBRAPA-Agrobiologia Brazil; Br3407
doi: 10.13145/bacdive1988.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Paraburkholderia
- species: Paraburkholderia sabiae
- full scientific name: Paraburkholderia sabiae (Chen et al. 2008) Sawana et al. 2015
synonyms
- @ref: 20215
- synonym: Burkholderia sabiae
@ref: 17184
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Paraburkholderia
species: Paraburkholderia sabiae
full scientific name: Paraburkholderia sabiae (Chen et al. 2008) Sawana et al. 2015
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | confidence |
|---|---|---|---|---|---|
| 32630 | negative | 0.6-1.5 µm | 0.4-0.6 µm | rod-shaped | |
| 69480 | negative | 99.961 |
colony morphology
- @ref: 17184
- type of hemolysis: gamma
pigmentation
- @ref: 32630
- production: yes
Culture and growth conditions
culture medium
- @ref: 17184
- 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
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17184 | positive | growth | 30 | mesophilic |
| 32630 | positive | growth | 28-37 | mesophilic |
| 32630 | positive | optimum | 28 | mesophilic |
| 61593 | positive | growth | 28 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 32630 | positive | growth | 7 |
| 32630 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 32630 | aerobe |
| 61593 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32630 | no | |
| 69481 | no | 98 |
| 69480 | no | 99.98 |
observation
- @ref: 32630
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32630 | 22599 | arabinose | + | carbon source |
| 32630 | 27689 | decanoate | + | carbon source |
| 32630 | 16947 | citrate | + | carbon source |
| 32630 | 24265 | gluconate | + | carbon source |
| 32630 | 17234 | glucose | + | carbon source |
| 32630 | 25115 | malate | + | carbon source |
| 32630 | 29864 | mannitol | + | carbon source |
| 32630 | 37684 | mannose | + | carbon source |
| 32630 | 18401 | phenylacetate | + | carbon source |
| 68369 | 25115 | malate | + | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | + | assimilation |
| 68369 | 24265 | gluconate | + | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | + | assimilation |
| 68369 | 16899 | D-mannitol | + | assimilation |
| 68369 | 16024 | D-mannose | + | assimilation |
| 68369 | 30849 | L-arabinose | + | assimilation |
| 68369 | 17634 | D-glucose | + | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | + | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 17184 | catalase | + | 1.11.1.6 |
| 17184 | cytochrome-c oxidase | + | 1.9.3.1 |
| 32630 | catalase | + | 1.11.1.6 |
| 32630 | cytochrome oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 17184 | + | - | - | - | - | - | - | + | + | + | + | + | + | - | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 17184 | root nodule of Mimosa caesalpiniifolia | Mimosa caesalpiniifolia | Brazil | BRA | Middle and South America | |
| 61593 | Root nodules of Mimosa caesalpiniifolia | Brazil | BRA | Middle and South America | 2000 |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Plants | #Herbaceous plants (Grass,Crops) |
| #Host Body-Site | #Plant | #Root nodule |
Safety information
risk assessment
- @ref: 17184
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17184
- description: Burkholderia sabiae strain Br3407 16S ribosomal RNA gene, partial sequence
- accession: AY773186
- length: 1483
- database: ena
- NCBI tax ID: 273251
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Paraburkholderia sabiae LMG 24235 | GCA_904848645 | contig | ncbi | 273251 |
| 66792 | Paraburkholderia sabiae strain LMG 24235 | 273251.3 | wgs | patric | 273251 |
GC content
- @ref: 32630
- GC-content: 64.5
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 98 | no |
| motile | yes | 87.286 | no |
| gram-positive | no | 97.913 | yes |
| anaerobic | no | 98.494 | yes |
| halophile | no | 93.899 | no |
| spore-forming | no | 91.601 | no |
| glucose-util | yes | 92.707 | no |
| aerobic | yes | 88.717 | no |
| thermophile | no | 99.554 | yes |
| flagellated | no | 87.463 | no |
| glucose-ferment | no | 89.864 | yes |
External links
@ref: 17184
culture collection no.: DSM 23623, BCRC 17587, LMG 24235, CCUG 58093, BR Br3407, BR 3407
straininfo link
- @ref: 71635
- straininfo: 307396
literature
- topic: Phylogeny
- Pubmed-ID: 18768625
- title: Burkholderia sabiae sp. nov., isolated from root nodules of Mimosa caesalpiniifolia.
- authors: Chen WM, de Faria SM, Chou JH, James EK, Elliott GN, Sprent JI, Bontemps C, Young JP, Vandamme P
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65816-0
- year: 2008
- mesh: Bacterial Proteins/analysis, Bacterial Typing Techniques, Brazil, Burkholderia/*classification/genetics/*isolation & purification/physiology, Cluster Analysis, DNA Fingerprinting, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Electrophoresis, Gel, Pulsed-Field, Fatty Acids/analysis, Genes, rRNA, Mimosa/*microbiology, Molecular Sequence Data, Nitrogen Fixation, Nucleic Acid Hybridization, Phylogeny, Plant Roots/microbiology, Proteome/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid
- topic2: Enzymology
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17184 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23623) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23623 | |||
| 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 | |||
| 32630 | 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 | 28841 | 28776041 | |
| 61593 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58093) | https://www.ccug.se/strain?id=58093 | |||
| 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) | |||
| 68369 | Automatically annotated from API 20NE | |||||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | |||
| 71635 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID307396.1 | StrainInfo: A central database for resolving microbial strain identifiers |