Strain identifier
BacDive ID: 13100
Type strain:
Species: Pseudomonas jinjuensis
Strain history: CIP <- 2005, KACC <- Nat. Inst. Agricult. Biotechn., Korea: strain Pss 26
NCBI tax ID(s): 1215105 (strain), 198616 (species)
General
@ref: 6522
BacDive-ID: 13100
DSM-Number: 16612
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Pseudomonas jinjuensis CCUG 69580 is an aerobe, mesophilic, motile bacterium that was isolated from agricultural soil.
NCBI tax id
NCBI tax id | Matching level |
---|---|
198616 | species |
1215105 | strain |
strain history
@ref | history |
---|---|
6522 | <- S. W. Kwon; Pss 26 |
67770 | IAM 15166 <-- LMG 21316 <-- S.-W. Kwon Pss 26. |
120352 | CIP <- 2005, KACC <- Nat. Inst. Agricult. Biotechn., Korea: strain Pss 26 |
doi: 10.13145/bacdive13100.20230509.8.1
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 jinjuensis
- full scientific name: Pseudomonas jinjuensis Kwon et al. 2003
@ref: 6522
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas jinjuensis
full scientific name: Pseudomonas jinjuensis Kwon et al. 2003
type strain: yes
Morphology
cell morphology
@ref | motility | confidence | gram stain | cell shape |
---|---|---|---|---|
69480 | yes | 94.68 | ||
69480 | 99.991 | negative | ||
120352 | yes | negative | rod-shaped |
pigmentation
- @ref: 120352
- production: no
- name: Pyocyanin
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
6522 | CASO AGAR (MERCK 105458) (DSMZ Medium 220) | yes | https://mediadive.dsmz.de/medium/220 | Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water |
38284 | MEDIUM 72- for trypto casein soja agar | yes | Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g) | |
120352 | CIP Medium 72 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
6522 | positive | growth | 30 | mesophilic |
38284 | positive | growth | 30 | mesophilic |
63626 | positive | growth | 30 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
120352 | positive | growth | 10-41 | |
120352 | no | growth | 5 | psychrophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
63626 | aerobe |
120352 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.978 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
120352 | NaCl | positive | growth | 0-4 % |
120352 | NaCl | no | growth | 6 % |
120352 | NaCl | no | growth | 8 % |
120352 | NaCl | no | growth | 10 % |
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 |
120352 | 16947 | citrate | + | carbon source |
120352 | 4853 | esculin | - | hydrolysis |
120352 | 17632 | nitrate | + | reduction |
120352 | 16301 | nitrite | + | reduction |
120352 | 17632 | nitrate | + | respiration |
antibiotic resistance
- @ref: 120352
- metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
- is antibiotic: yes
- is sensitive: no
- is resistant: yes
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | no |
120352 | 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 |
120352 | oxidase | + | |
120352 | beta-galactosidase | - | 3.2.1.23 |
120352 | alcohol dehydrogenase | + | 1.1.1.1 |
120352 | gelatinase | - | |
120352 | amylase | - | |
120352 | DNase | - | |
120352 | caseinase | - | 3.4.21.50 |
120352 | catalase | + | 1.11.1.6 |
120352 | tween esterase | - | |
120352 | lecithinase | - | |
120352 | lipase | - | |
120352 | lysine decarboxylase | - | 4.1.1.18 |
120352 | ornithine decarboxylase | - | 4.1.1.17 |
120352 | protease | - | |
120352 | tryptophan deaminase | - | |
120352 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120352 | - | + | + | + | - | + | - | - | - | - | + | + | - | - | - | - | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
6522 | + | - | - | + | - | - | - | - | + | - | - | - | - | - | + | + | + | + | + | + | + |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
120352 | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | + | + | + | + | - | - | + | - | - | + | - | - | - | + | + | + | + | + | - | - | + | - | - | + | + | + | + | + | + | + | + | + | + | + | + | - | + | - | - | - | + | + | + | + | + | + | + | + | - | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|
6522 | agricultural soil | Jinju region | Republic of Korea | KOR | Asia | |
63626 | Agricultural soil | Jinju Region | Republic of Korea | KOR | Asia | |
67770 | Soil | |||||
120352 | Environment, Soil | Jinju region | Republic of Korea | KOR | Asia | 2000 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Agriculture | |
#Environmental | #Terrestrial | #Soil |
taxonmaps
- @ref: 69479
- File name: preview.99_5527.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_203;97_221;98_4126;99_5527&stattab=map
- Last taxonomy: Pseudomonas jinjuensis subclade
- 16S sequence: AF468448
- Sequence Identity:
- Total samples: 135
- soil counts: 62
- aquatic counts: 28
- animal counts: 39
- plant counts: 6
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
6522 | 1 | Risk group (German classification) |
120352 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 6522
- description: Pseudomonas sp. Pss 26 16S ribosomal RNA gene, partial sequence
- accession: AF468448
- length: 1454
- database: ena
- NCBI tax ID: 198616
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas jinjuensis NBRC 103047 strain NBRC 103047 | 1215105.3 | wgs | patric | 1215105 |
66792 | Pseudomonas jinjuensis strain JCM 21621 | 198616.7 | wgs | patric | 198616 |
66792 | Pseudomonas jinjuensis JCM 21621 | 2663762768 | draft | img | 198616 |
67770 | Pseudomonas jinjuensis NBRC 103047 | GCA_002091655 | contig | ncbi | 1215105 |
67770 | Pseudomonas jinjuensis JCM 21621 | GCA_900103845 | scaffold | ncbi | 198616 |
GC content
- @ref: 67770
- GC-content: 66.9
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 90.149 | no |
gram-positive | no | 97.935 | no |
anaerobic | no | 97.798 | yes |
aerobic | yes | 90.465 | yes |
halophile | no | 82.743 | no |
spore-forming | no | 95.268 | no |
thermophile | no | 99.389 | yes |
glucose-util | yes | 85.127 | no |
flagellated | yes | 67.098 | no |
glucose-ferment | no | 90.378 | yes |
External links
@ref: 6522
culture collection no.: CCUG 69580, DSM 16612, KACC 10760, LMG 21316, Pss 26, JCM 21621, IAM 15166, NBRC 103047, CIP 108617
straininfo link
- @ref: 82310
- straininfo: 86036
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 12656147 | Pseudomonas koreensis sp. nov., Pseudomonas umsongensis sp. nov. and Pseudomonas jinjuensis sp. nov., novel species from farm soils in Korea. | Kwon SW, Kim JS, Park IC, Yoon SH, Park DH, Lim CK, Go SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.02326-0 | 2003 | Agriculture, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Korea, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/metabolism, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, *Soil Microbiology, Species Specificity | Genetics |
Phylogeny | 17329778 | Pseudomonas delhiensis sp. nov., from a fly ash dumping site of a thermal power plant. | Prakash O, Kumari K, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.64456-0 | 2007 | Acyclic Monoterpenes, *Carbon, Coal Ash, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, India, Molecular Sequence Data, Monoterpenes/metabolism, *Particulate Matter, Phenanthrenes/metabolism, Phylogeny, *Power Plants, Pseudomonas/*classification/genetics/isolation & purification/metabolism, RNA, Ribosomal, 16S/genetics | Metabolism |
Phylogeny | 17329787 | Pseudomonas knackmussii sp. nov. | Stolz A, Busse HJ, Kampfer P | Int J Syst Evol Microbiol | 10.1099/ijs.0.64761-0 | 2007 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Pseudomonas/chemistry/*classification/genetics/physiology, RNA, Ribosomal, 16S/genetics | Genetics |
Phylogeny | 18523175 | Pseudomonas panipatensis sp. nov., isolated from an oil-contaminated site. | Gupta SK, Kumari R, Prakash O, Lal R | Int J Syst Evol Microbiol | 10.1099/ijs.0.65401-0 | 2008 | Bacterial Typing Techniques, Base Sequence, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, India, Molecular Sequence Data, Nucleic Acid Hybridization, *Petroleum, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Analysis, DNA, *Soil Microbiology, *Soil Pollutants, Species Specificity | Genetics |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
6522 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16612) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-16612 | |||
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 | |||
38284 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6266 | ||||
63626 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 69580) | https://www.ccug.se/strain?id=69580 | |||
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 | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | |||
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 | |||
82310 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID86036.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
120352 | Curators of the CIP | Collection of Institut Pasteur (CIP 108617) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108617 |