Strain identifier
BacDive ID: 24385
Type strain: 
Species: Pseudomonas putida
Strain Designation: B6-2
Strain history: <- P. Xu, Shanghai Jiao Tong Univ., China; B6-2
NCBI tax ID(s): 303 (species)
version 8.1 (current version)
General
@ref: 20320
BacDive-ID: 24385
DSM-Number: 28064
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, human pathogen
description: Pseudomonas putida B6-2 is a mesophilic human pathogen that was isolated from biphenyl contaminated soil.
NCBI tax id
- NCBI tax id: 303
- Matching level: species
strain history
- @ref: 20320
- history: <- P. Xu, Shanghai Jiao Tong Univ., China; B6-2
doi: 10.13145/bacdive24385.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Pseudomonas
- species: Pseudomonas putida
- full scientific name: Pseudomonas putida (Trevisan 1889) Migula 1895 (Approved Lists 1980)
synonyms
@ref synonym 20215 Bacillus putidus 20215 Arthrobacter siderocapsulatus
@ref: 20320
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas putida
full scientific name: Pseudomonas putida (Trevisan 1889) Migula 1895
strain designation: B6-2
type strain: no
Morphology
multimedia
- @ref: 20320
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_28064.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
| @ref | name | growth | link | composition |
|---|---|---|---|---|
| 20320 | MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) | yes | https://mediadive.dsmz.de/medium/457 | Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water |
| 20320 | REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a) | yes | https://mediadive.dsmz.de/medium/1a | 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: 20320
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 20320
- sample type: biphenyl contaminated soil
- geographic location: Shandong Province, Jinan
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Soil |
| #Engineered | #Contamination |
taxonmaps
- @ref: 69479
- File name: preview.99_239.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_203;99_239&stattab=map
- Last taxonomy: Pseudomonas
- 16S sequence: EF672104
- Sequence Identity:
- Total samples: 2133
- soil counts: 368
- aquatic counts: 543
- animal counts: 799
- plant counts: 423
Safety information
risk assessment
- @ref: 20320
- pathogenicity human: yes
- pathogenicity animal: yes
- biosafety level: 2
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20320
- description: Pseudomonas sp. B6-2 16S ribosomal RNA gene, partial sequence
- accession: EF672104
- length: 1402
- database: ena
- NCBI tax ID: 453577
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Pseudomonas putida B6-2 | GCA_000226035 | complete | ncbi | 1081940 |
| 66792 | Pseudomonas putida B6-2 | 1081940.5 | wgs | patric | 1081940 |
| 66792 | Pseudomonas putida B6-2 | 2548876715 | complete | img | 1081940 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| motile | yes | 92.581 | no |
| motile | yes | 92.581 | no |
| flagellated | yes | 80.286 | no |
| flagellated | yes | 80.286 | no |
| gram-positive | no | 98.438 | no |
| gram-positive | no | 98.438 | no |
| anaerobic | no | 98.214 | no |
| anaerobic | no | 98.214 | no |
| aerobic | yes | 94.51 | no |
| aerobic | yes | 94.51 | no |
| halophile | no | 81.608 | no |
| halophile | no | 81.608 | no |
| spore-forming | no | 96.049 | no |
| spore-forming | no | 96.049 | no |
| thermophile | no | 99.925 | no |
| thermophile | no | 99.925 | no |
| glucose-util | yes | 91.747 | no |
| glucose-util | yes | 91.747 | no |
| glucose-ferment | no | 90.149 | no |
| glucose-ferment | no | 90.149 | no |
External links
@ref: 20320
culture collection no.: DSM 28064
straininfo link
- @ref: 88295
- straininfo: 407704
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Metabolism | 20028064 | New metabolites in dibenzofuran cometabolic degradation by a biphenyl-cultivated Pseudomonas putida strain B6-2. | Li Q, Wang X, Yin G, Gai Z, Tang H, Ma C, Deng Z, Xu P | Environ Sci Technol | 10.1021/es901991d | 2009 | Benzofurans/*metabolism, Biodegradation, Environmental, Cloning, Molecular, Environmental Pollutants/*metabolism, Gene Expression Regulation, Bacterial, Genes, Bacterial, Molecular Structure, Pseudomonas putida/genetics/*metabolism | Enzymology |
| Genetics | 22072645 | Genome sequence of Pseudomonas putida strain B6-2, a superdegrader of polycyclic aromatic hydrocarbons and dioxin-like compounds. | Tang H, Yu H, Li Q, Wang X, Gai Z, Yin G, Su F, Tao F, Ma C, Xu P | J Bacteriol | 10.1128/JB.06201-11 | 2011 | Base Sequence, Biodegradation, Environmental, Dioxins/*metabolism, *Genome, Bacterial, Molecular Sequence Data, Polycyclic Aromatic Hydrocarbons/*metabolism, Pseudomonas putida/*genetics/*metabolism | Metabolism |
| Metabolism | 29030440 | Multiple Roles for Two Efflux Pumps in the Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas putida Strain B6-2 (DSM 28064). | Yao X, Tao F, Zhang K, Tang H, Xu P | Appl Environ Microbiol | 10.1128/AEM.01882-17 | 2017 | Bacterial Proteins/*genetics/metabolism, *Gene Expression Regulation, Bacterial, Polycyclic Aromatic Hydrocarbons/metabolism/toxicity, Pseudomonas putida/*genetics/*metabolism, Solvents/metabolism/toxicity | |
| Metabolism | 32945019 | Unique regulator SrpR mediates crosstalk between efflux pumps TtgABC and SrpABC in Pseudomonas putida B6-2 (DSM 28064). | Yao X, Tao F, Tang H, Hu H, Wang W, Xu P | Mol Microbiol | 10.1111/mmi.14605 | 2020 | Bacterial Proteins/metabolism, Biological Transport/genetics, Gene Expression Regulation, Bacterial/genetics, Membrane Transport Proteins/genetics/*metabolism, Promoter Regions, Genetic/genetics, Protein Binding/genetics, Pseudomonas putida/genetics/*metabolism, Repressor Proteins/genetics/*metabolism, Transcription, Genetic/genetics | Genetics |
| 34056829 | Genetic mapping of highly versatile and solvent-tolerant Pseudomonas putida B6-2 (ATCC BAA-2545) as a 'superstar' for mineralization of PAHs and dioxin-like compounds. | Wang W, Li Q, Zhang L, Cui J, Yu H, Wang X, Ouyang X, Tao F, Xu P, Tang H | Environ Microbiol | 10.1111/1462-2920.15613 | 2021 | Biodegradation, Environmental, *Dioxins, *Polycyclic Aromatic Hydrocarbons, *Pseudomonas putida/genetics, Solvents |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 20320 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-28064 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 28064) | |
| 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 | |
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |
| 88295 | 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-ID407704.1 |