Strain identifier

BacDive ID: 13165

Type strain: Yes

Species: Pseudomonas japonica

Strain Designation: WL

Strain history: IAM 15071 <-- W. Pungrasmi.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
256466species
1215104strain

strain history

@refhistory
16305<- NBRC <- W. Pungrasmi, Univ. Tokyo, Japan
67770IAM 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

@refgrowthtypetemperaturerange
16305positivegrowth28mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

observation

  • @ref: 67770
  • observation: quinones: Q-9

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate+assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine+hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate-reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase+3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
16305---+----+------+-++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
16305activated sludge from sewage treatment plantOdaii, Adachi-ku, TokyoJapanJPNAsia
67770Activated sludge from sewage treatment plantOdaii, Adachi-ku, TokyoJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#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

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudomonas japonica gene for 16S rRNA, partial sequence, strain: NBRC 103040AB6819201462ena1215104
16305Pseudomonas japonica gene for 16S rRNA, partial sequenceAB1266211498ena1215104

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas japonica NBRC 103040 = DSM 223481215104.3wgspatric1215104
66792Pseudomonas japonica strain DSM 22348256466.3wgspatric256466
66792Pseudomonas japonica NBRC 1030402585427681draftimg1215104
66792Pseudomonas japonica DSM 223482700988710draftimg256466
67770Pseudomonas japonica NBRC 103040 = DSM 22348GCA_000730585contigncbi1215104
67770Pseudomonas japonica DSM 22348GCA_900188455scaffoldncbi256466

GC content

  • @ref: 16305
  • GC-content: 66.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes89.387no
gram-positiveno98.063no
anaerobicno98.623no
aerobicyes96.277no
halophileno86.55no
spore-formingno96.015no
thermophileno99.862no
glucose-utilyes90.73no
flagellatedyes82.279no
glucose-fermentno87.131no

External links

@ref: 16305

culture collection no.: DSM 22348, IAM 15071, JCM 21532, NBRC 103040, TISTR 1526

straininfo link

  • @ref: 82373
  • straininfo: 132666

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18323682Pseudomonas japonica sp. nov., a novel species that assimilates straight chain alkylphenols.Pungrasmi W, Lee HS, Yokota A, Ohta AJ Gen Appl Microbiol10.2323/jgam.54.612008Bacterial 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, TokyoGenetics
Phylogeny30798341Pseudomonas qingdaonensis sp. nov., an aflatoxin-degrading bacterium, isolated from peanut rhizospheric soil.Wang MQ, Wang Z, Yu LN, Zhang CS, Bi J, Sun JArch Microbiol10.1007/s00203-019-01636-w2019Aflatoxin 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 MicrobiologyMetabolism
Phylogeny32877324Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan.Sawada H, Fujikawa T, Horita HInt J Syst Evol Microbiol10.1099/ijsem.0.0044122020Bacterial 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, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
16305Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22348)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22348
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68369Automatically annotated from API 20NE
82373Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID132666.1StrainInfo: A central database for resolving microbial strain identifiers