Strain identifier
BacDive ID: 13169
Type strain: 
Species: Halopseudomonas sabulinigri
Strain Designation: J64
Strain history: S. W. Roh J64.
NCBI tax ID(s): 472181 (species)
version 8.1 (current version)
General
@ref: 17462
BacDive-ID: 13169
DSM-Number: 23971
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Halopseudomonas sabulinigri J64 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from black sand originating from black volcanic basalt rock.
NCBI tax id
- NCBI tax id: 472181
- Matching level: species
strain history
| @ref | history |
|---|---|
| 17462 | <- KCTC <- J.-W. Bae, KRIBB |
| 67770 | S. W. Roh J64. |
doi: 10.13145/bacdive13169.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Pseudomonadales
- family: Pseudomonadaceae
- genus: Halopseudomonas
- species: Halopseudomonas sabulinigri
- full scientific name: Halopseudomonas sabulinigri (Kim et al. 2009) Rudra and Gupta 2021
synonyms
@ref synonym 20215 Neopseudomonas sabulinigri 20215 Pseudomonas sabulinigri
@ref: 17462
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas sabulinigri
full scientific name: Pseudomonas sabulinigri Kim et al. 2009
strain designation: J64
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32662 | negative | 1.75 µm | 0.85 µm | rod-shaped | yes | |
| 69480 | yes | 97.683 | ||||
| 69480 | negative | 99.99 |
Culture and growth conditions
culture medium
- @ref: 17462
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
| @ref | growth | type | temperature | range |
|---|---|---|---|---|
| 17462 | positive | growth | 30 | mesophilic |
| 32662 | positive | growth | 04-37 | |
| 67770 | positive | growth | 30 | mesophilic |
culture pH
- @ref: 32662
- ability: positive
- type: growth
- pH: 5.5-10.0
- PH range: alkaliphile
Physiology and metabolism
oxygen tolerance
- @ref: 32662
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.999 |
halophily
- @ref: 32662
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: 0-10 %
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32662 | 37054 | 3-hydroxybutyrate | + | carbon source |
| 32662 | 17128 | adipate | + | carbon source |
| 32662 | 22653 | asparagine | + | carbon source |
| 32662 | 16947 | citrate | + | carbon source |
| 32662 | 24996 | lactate | + | carbon source |
| 32662 | 51850 | methyl pyruvate | + | carbon source |
| 32662 | 26271 | proline | + | carbon source |
| 32662 | 17272 | propionate | + | carbon source |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32662 | acid phosphatase | + | 3.1.3.2 |
| 32662 | catalase | + | 1.11.1.6 |
| 32662 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 17462 | black sand originating from black volcanic basalt rock | Jeju Island, Soesgoggak | Republic of Korea | KOR | Asia |
| 67770 | Black sand collected from Soesoggak | Jeju Island | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Geologic |
| #Environmental | #Terrestrial | #Sandy |
| #Environmental | #Terrestrial | #Volcanic |
Safety information
risk assessment
- @ref: 17462
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 17462
- description: Pseudomonas sabulinigri strain J64 16S ribosomal RNA gene, partial sequence
- accession: EU143352
- length: 1403
- database: ena
- NCBI tax ID: 472181
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Halopseudomonas sabulinigri JCM 14963 | GCA_900105255 | chromosome | ncbi | 472181 |
| 66792 | Pseudomonas sabulinigri strain JCM 14963 | 472181.4 | complete | patric | 472181 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 17462 | 58.1 | |
| 67770 | 58.1 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 98.51 | no |
| anaerobic | no | 99.128 | yes |
| halophile | yes | 62.789 | no |
| spore-forming | no | 96.854 | no |
| glucose-util | no | 56.566 | no |
| aerobic | yes | 96.043 | yes |
| flagellated | yes | 91.69 | no |
| thermophile | no | 99.82 | yes |
| motile | yes | 90.854 | yes |
| glucose-ferment | no | 91.287 | no |
External links
@ref: 17462
culture collection no.: DSM 23971, JCM 14963, KCTC 22137
straininfo link
- @ref: 82377
- straininfo: 360526
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 17462 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23971) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-23971 | |||
| 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 | |||
| 32662 | 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 | 28873 | 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) | |||
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
| 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 | |||
| 82377 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID360526.1 | StrainInfo: A central database for resolving microbial strain identifiers |