Strain identifier
BacDive ID: 13165
Type strain:
Species: Pseudomonas japonica
Strain Designation: WL
Strain history: IAM 15071 <-- W. Pungrasmi.
NCBI tax ID(s): 1215104 (strain), 256466 (species)
General
@ref: 16305
BacDive-ID: 13165
DSM-Number: 22348
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Pseudomonas japonica WL is a mesophilic bacterium that was isolated from activated sludge from sewage treatment plant.
NCBI tax id
NCBI tax id | Matching level |
---|---|
256466 | species |
1215104 | strain |
strain history
@ref | history |
---|---|
16305 | <- NBRC <- W. Pungrasmi, Univ. Tokyo, Japan |
67770 | IAM 15071 <-- W. Pungrasmi. |
doi: 10.13145/bacdive13165.20230509.8.1
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 japonica
- full scientific name: Pseudomonas japonica Pungrasmi et al. 2008
@ref: 16305
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Pseudomonadaceae
genus: Pseudomonas
species: Pseudomonas japonica
full scientific name: Pseudomonas japonica Pungrasmi et al. 2008
strain designation: WL
type strain: yes
Culture and growth conditions
culture medium
- @ref: 16305
- name: REACTIVATION WITH LIQUID MEDIUM 1 (DSMZ Medium 1a)
- growth: yes
- link: https://mediadive.dsmz.de/medium/1a
- composition: 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 | growth | type | temperature | range |
---|---|---|---|---|
16305 | positive | growth | 28 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
Physiology and metabolism
observation
- @ref: 67770
- observation: quinones: Q-9
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 |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: 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 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
16305 | - | - | - | + | - | - | - | - | + | - | - | - | - | - | - | + | - | + | + | + | + |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
16305 | activated sludge from sewage treatment plant | Odaii, Adachi-ku, Tokyo | Japan | JPN | Asia |
67770 | Activated sludge from sewage treatment plant | Odaii, Adachi-ku, Tokyo | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Waste | #Activated sludge |
#Engineered | #Waste | #Water treatment plant |
Safety information
risk assessment
- @ref: 16305
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Pseudomonas japonica gene for 16S rRNA, partial sequence, strain: NBRC 103040 | AB681920 | 1462 | ena | 1215104 |
16305 | Pseudomonas japonica gene for 16S rRNA, partial sequence | AB126621 | 1498 | ena | 1215104 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Pseudomonas japonica NBRC 103040 = DSM 22348 | 1215104.3 | wgs | patric | 1215104 |
66792 | Pseudomonas japonica strain DSM 22348 | 256466.3 | wgs | patric | 256466 |
66792 | Pseudomonas japonica NBRC 103040 | 2585427681 | draft | img | 1215104 |
66792 | Pseudomonas japonica DSM 22348 | 2700988710 | draft | img | 256466 |
67770 | Pseudomonas japonica NBRC 103040 = DSM 22348 | GCA_000730585 | contig | ncbi | 1215104 |
67770 | Pseudomonas japonica DSM 22348 | GCA_900188455 | scaffold | ncbi | 256466 |
GC content
- @ref: 16305
- GC-content: 66.0
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 89.387 | no |
gram-positive | no | 98.063 | no |
anaerobic | no | 98.623 | no |
aerobic | yes | 96.277 | no |
halophile | no | 86.55 | no |
spore-forming | no | 96.015 | no |
thermophile | no | 99.862 | no |
glucose-util | yes | 90.73 | no |
flagellated | yes | 82.279 | no |
glucose-ferment | no | 87.131 | no |
External links
@ref: 16305
culture collection no.: DSM 22348, IAM 15071, JCM 21532, NBRC 103040, TISTR 1526
straininfo link
- @ref: 82373
- straininfo: 132666
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18323682 | Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols. | Pungrasmi W, Lee HS, Yokota A, Ohta A | J Gen Appl Microbiol | 10.2323/jgam.54.61 | 2008 | Bacterial Typing Techniques, Base Composition, Fatty Acids/analysis, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenols/*chemistry/*metabolism, Phenotype, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity, Tokyo | Genetics |
Phylogeny | 30798341 | Pseudomonas qingdaonensis sp. nov., an aflatoxin-degrading bacterium, isolated from peanut rhizospheric soil. | Wang MQ, Wang Z, Yu LN, Zhang CS, Bi J, Sun J | Arch Microbiol | 10.1007/s00203-019-01636-w | 2019 | Aflatoxin B1/*metabolism, Arachis/*microbiology, Bacterial Typing Techniques, Base Composition/genetics, Catalase/analysis, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Genes, Bacterial, Multilocus Sequence Typing, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phospholipids/analysis, Phylogeny, Pseudomonas/*classification/genetics/isolation & purification/*metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Soil, Soil Microbiology | Metabolism |
Phylogeny | 32877324 | Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan. | Sawada H, Fujikawa T, Horita H | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004412 | 2020 | Bacterial Typing Techniques, Base Composition, Brassica/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Genes, Bacterial, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pigmentation, Plant Diseases/*microbiology, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
16305 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22348) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22348 | |||
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 | |||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
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/ | ||||
68369 | Automatically annotated from API 20NE | |||||
82373 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID132666.1 | StrainInfo: A central database for resolving microbial strain identifiers |