Strain identifier
version 8.1 (current version)
General
@ref: 62941
BacDive-ID: 156584
keywords: genome sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Caballeronia choica CCUG 63063 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from Rhizosphere soil.
NCBI tax id
- NCBI tax id: 326476
- Matching level: species
doi: 10.13145/bacdive156584.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Burkholderiaceae
- genus: Caballeronia
- species: Caballeronia choica
- full scientific name: Caballeronia choica (Vandamme et al. 2013) Dobritsa and Samadpour 2016
synonyms
@ref synonym 20215 Paraburkholderia choica 20215 Burkholderia choica
@ref: 62941
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Burkholderiaceae
genus: Caballeronia
species: Caballeronia choica
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
colony morphology
- @ref: 62941
- incubation period: >3 days
Culture and growth conditions
culture temp
- @ref: 62941
- growth: positive
- type: growth
- temperature: 30
- range: mesophilic
Physiology and metabolism
oxygen tolerance
- @ref: 62941
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69480 | no | 99.997 |
| 69481 | no | 100 |
Isolation, sampling and environmental information
isolation
- @ref: 62941
- sample type: Rhizosphere soil
- sampling date: 2003
- country: Netherlands
- origin.country: NLD
- continent: Europe
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Host Body-Site | #Plant | #Rhizosphere |
| #Host | #Plants |
Sequence information
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Caballeronia choica LMG 22940 | GCA_001544535 | contig | ncbi | 326476 |
| 66792 | Burkholderia choica strain LMG 22940 | 326476.3 | wgs | patric | 326476 |
| 66792 | Caballeronia choica LMG 22940 | 2724679467 | draft | img | 326476 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.135 | no |
| anaerobic | no | 98.726 | yes |
| halophile | no | 93.6 | no |
| spore-forming | no | 92.999 | no |
| glucose-util | yes | 87.937 | no |
| motile | yes | 83.928 | no |
| flagellated | no | 86.509 | no |
| aerobic | yes | 91.606 | no |
| thermophile | no | 99.49 | yes |
| glucose-ferment | no | 88.594 | no |
External links
@ref: 62941
culture collection no.: CCUG 63063, LMG 22940
straininfo link
- @ref: 109797
- straininfo: 136998
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 23959831 | Burkholderia humi sp. nov., Burkholderia choica sp. nov., Burkholderia telluris sp. nov., Burkholderia terrestris sp. nov. and Burkholderia udeis sp. nov.: Burkholderia glathei-like bacteria from soil and rhizosphere soil. | Vandamme P, De Brandt E, Houf K, Salles JF, Dirk van Elsas J, Spilker T, LiPuma JJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.048900-0 | 2013 | Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, China, DNA Gyrase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Humans, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Rhizosphere, Sequence Analysis, DNA, *Soil Microbiology, Waste Water/microbiology | Pathogenicity |
| Phylogeny | 24981326 | Burkholderia jiangsuensis sp. nov., a methyl parathion degrading bacterium, isolated from methyl parathion contaminated soil. | Liu XY, Li CX, Luo XJ, Lai QL, Xu JH | Int J Syst Evol Microbiol | 10.1099/ijs.0.064444-0 | 2014 | Bacterial Typing Techniques, Base Composition, Burkholderia/*classification/genetics/isolation & purification, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Insecticides/metabolism, Methyl Parathion/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Soil Pollutants/metabolism, Ubiquinone/chemistry | Metabolism |
| Phylogeny | 30288561 | Caballeronia ginsengisoli sp. nov., isolated from ginseng cultivating soil. | Quan XT, Liu QZ, Siddiqi MZ, Im WT | Arch Microbiol | 10.1007/s00203-018-1577-0 | 2018 | Base Composition, Burkholderiaceae/chemistry/*classification/genetics/isolation & purification, DNA, Bacterial/chemistry, Fatty Acids/analysis, Panax, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Soil, *Soil Microbiology | Enzymology |
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, 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 DSMZ | 10.1099/ijsem.0.004332 | |||
| 62941 | Curators of the CCUG | https://www.ccug.se/strain?id=63063 | Culture Collection University of Gothenburg (CCUG) (CCUG 63063) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions 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 | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 109797 | Reimer, 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 identifiers | 10.60712/SI-ID136998.1 |