Strain identifier
BacDive ID: 13132
Type strain:
Species: Pseudomonas pohangensis
Strain Designation: H3-R18
Strain history: CIP <- 2006, DSMZ <- S.-W. Kwon: strain H3-R18 <- H.-Y. Weon et al.
NCBI tax ID(s): 364197 (species)
General
@ref: 7212
BacDive-ID: 13132
DSM-Number: 17875
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Pseudomonas pohangensis H3-R18 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea shore sand.
NCBI tax id
- NCBI tax id: 364197
- Matching level: species
strain history
@ref | history |
---|---|
7212 | <- S.-W. Kwon; H3-R18 <- H.-Y. Weon et al. |
37531 | 2006, DSMZ |
67770 | KACC 11517 <-- S.-W. Kwon H3-R18. |
121920 | CIP <- 2006, DSMZ <- S.-W. Kwon: strain H3-R18 <- H.-Y. Weon et al. |
doi: 10.13145/bacdive13132.20230509.8.1
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 pohangensis
- full scientific name: Pseudomonas pohangensis Weon et al. 2006
@ref: 7212
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas pohangensis
full scientific name: Pseudomonas pohangensis Weon et al. 2006 emend. Hameed et al. 2014
strain designation: H3-R18
type strain: yes
Morphology
cell morphology
@ref | gram stain | confidence | cell shape | motility |
---|---|---|---|---|
69480 | negative | 99.995 | ||
121920 | negative | rod-shaped | no |
colony morphology
- @ref: 63627
- incubation period: 3 days
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7212 | REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) | yes | https://mediadive.dsmz.de/medium/514c | Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water |
37531 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
121920 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7212 | positive | growth | 28 | mesophilic |
37531 | positive | growth | 30 | mesophilic |
63627 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 63627
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 100 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
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 |
121920 | 17632 | nitrate | + | reduction |
121920 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
121920 | 35581 | indole | no |
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
@ref | value | activity | ec |
---|---|---|---|
68369 | 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 |
121920 | oxidase | + | |
121920 | catalase | + | 1.11.1.6 |
121920 | urease | + | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | - | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
121920 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7212 | + | - | - | + | - | - | - | + | - | - | - | - | - | - | - | + | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
7212 | sea shore sand | Republic of Korea | KOR | Asia | |
63627 | Seashore sand | Republic of Korea | KOR | Asia | Pohang City,Homi Cape |
67770 | Seashore sand from Homi cape | Republic of Korea | KOR | Asia | Pohang City |
121920 | Environment, Seashore sand | Republic of Korea | KOR | Asia | Homi cape, Pohang city |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Terrestrial | #Coast |
#Environmental | #Terrestrial | #Sandy |
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
7212 | 1 | Risk group (German classification) |
121920 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 7212
- description: Pseudomonas pohangensis strain H3-R18 16S ribosomal RNA gene, partial sequence
- accession: DQ339144
- length: 1456
- database: ena
- NCBI tax ID: 364197
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas pohangensis DSM 17875 | GCA_900105995 | chromosome | ncbi | 364197 |
66792 | Pseudomonas pohangensis strain DSM 17875 | 364197.3 | complete | patric | 364197 |
66792 | Pseudomonas pohangensis DSM 17875 | 2667527387 | draft | img | 364197 |
67770 | Pseudomonas pohangensis strain DSM 17875 genome assembly, chromosome: I | LT629785 | ncbi | 364197 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
gram-positive | no | 97.954 | no |
anaerobic | no | 98.424 | yes |
halophile | no | 62.636 | no |
spore-forming | no | 97.401 | no |
glucose-util | no | 70.512 | yes |
aerobic | yes | 84.225 | yes |
motile | no | 75.683 | no |
flagellated | no | 72.779 | no |
thermophile | no | 99.464 | yes |
glucose-ferment | no | 89.101 | yes |
External links
@ref: 7212
culture collection no.: DSM 17875, KACC 11517, CCUG 69581, JCM 16393, CIP 109373
straininfo link
- @ref: 82340
- straininfo: 292704
literature
- topic: Phylogeny
- Pubmed-ID: 16957113
- title: Pseudomonas pohangensis sp. nov., isolated from seashore sand in Korea.
- authors: Weon HY, Kim BY, Yoo SH, Baek YK, Lee SY, Kwon SW, Go SJ, Stackebrandt E
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64274-0
- year: 2006
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Korea, Molecular Sequence Data, Pseudomonas/classification/genetics/*isolation & purification, RNA, Ribosomal, 16S/*analysis, Silicon Dioxide, Soil Microbiology
- topic2: Genetics
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
7212 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17875) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17875 | |||
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 | |||
37531 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7107 | ||||
63627 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 69581) | https://www.ccug.se/strain?id=69581 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
68369 | Automatically annotated from API 20NE | |||||
68382 | Automatically annotated from API zym | |||||
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 | |||
82340 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID292704.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
121920 | Curators of the CIP | Collection of Institut Pasteur (CIP 109373) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109373 |