Strain identifier

BacDive ID: 13120

Type strain: Yes

Species: Pseudomonas psychrophila

Strain Designation: E-3

Strain history: CIP <- 2003, JCM <- 2000, I. Yumoto: strain E-3

NCBI tax ID(s): 122355 (species)

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General

@ref: 7048

BacDive-ID: 13120

DSM-Number: 17535

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Pseudomonas psychrophila E-3 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coldroom for food storage.

NCBI tax id

  • NCBI tax id: 122355
  • Matching level: species

strain history

@refhistory
7048<- I. Yumoto, AIST, Sapporo; E-3
67770I. Yumoto E-3.
122021CIP <- 2003, JCM <- 2000, I. Yumoto: strain E-3

doi: 10.13145/bacdive13120.20230509.8.1

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 psychrophila
  • full scientific name: Pseudomonas psychrophila Yumoto et al. 2002

@ref: 7048

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Pseudomonadaceae

genus: Pseudomonas

species: Pseudomonas psychrophila

full scientific name: Pseudomonas psychrophila Yumoto et al. 2002

strain designation: E-3

type strain: yes

Morphology

cell morphology

  • @ref: 122021
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

colony morphology

  • @ref: 60047
  • incubation period: 1 day

pigmentation

  • @ref: 122021
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7048LB (Luria-Bertani) MEDIUM (DSMZ Medium 381)yeshttps://mediadive.dsmz.de/medium/381Name: LB (Luria-Bertani) MEDIUM (DSMZ Medium 381) Composition: Agar 20.0 g/l NaCl 10.0 g/l Tryptone 10.0 g/l Yeast extract 5.0 g/l Distilled water
33178MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
122021CIP Medium 469yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=469
122021CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
7048positivegrowth25mesophilic
33178positivegrowth30mesophilic
60047positivegrowth30mesophilic
67770positivegrowth30mesophilic
122021positivegrowth5-30
122021nogrowth37mesophilic
122021nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
60047aerobe
122021obligate aerobe

halophily

  • @ref: 122021
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
12202116947citrate+carbon source
1220214853esculin-hydrolysis
12202117632nitrate-reduction
12202116301nitrite-reduction
12202117632nitrate-respiration

antibiotic resistance

  • @ref: 122021
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 122021
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
122021oxidase+
122021beta-galactosidase-3.2.1.23
122021alcohol dehydrogenase+1.1.1.1
122021gelatinase-
122021amylase+
122021DNase-
122021caseinase-3.4.21.50
122021catalase+1.11.1.6
122021tween esterase-
122021lecithinase-
122021lipase-
122021lysine decarboxylase-4.1.1.18
122021ornithine decarboxylase-4.1.1.17
122021protease-
122021tryptophan deaminase-
122021urease-3.5.1.5
68382alkaline phosphatase-3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin-3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122021--++-++-+-++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122021+++++--+-----------+++--+-+----+-+---------++-+--+++++++++--+-+++--+-+--++-+++-+++++---+++++++--+++

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
7048coldroom for food storageJapanJPNAsia
60047Cold room for food storage
67770Cold room for food storage
122021Cold room for food storage

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment
#Engineered#Food production#Food

taxonmaps

  • @ref: 69479
  • File name: preview.99_442.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_23;96_61;97_89;98_368;99_442&stattab=map
  • Last taxonomy: Pseudomonas
  • 16S sequence: AB041885
  • Sequence Identity:
  • Total samples: 2942
  • soil counts: 460
  • aquatic counts: 830
  • animal counts: 1081
  • plant counts: 571

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
70481Risk group (German classification)
1220211Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7048
  • description: Pseudomonas sp. E-3 gene for 16S rRNA, partial sequence
  • accession: AB041885
  • length: 1528
  • database: ena
  • NCBI tax ID: 122355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudomonas psychrophila DSM 17535GCA_001043005contigncbi122355
66792Pseudomonas psychrophila CCUG 53877GCA_008801485contigncbi122355
66792Pseudomonas psychrophila strain CCUG 53877122355.16wgspatric122355
66792Pseudomonas psychrophila strain DSM 17535122355.7wgspatric122355
66792Pseudomonas psychrophila DSM 175352667527575draftimg122355

GC content

@refGC-contentmethod
704857.2
6777057.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes90.412no
gram-positiveno98.279no
anaerobicno98.748no
aerobicyes94.594yes
halophileno85.577no
spore-formingno96.808no
glucose-utilyes89.585no
thermophileno99.701yes
glucose-fermentno88.721no
flagellatedyes86.177no

External links

@ref: 7048

culture collection no.: DSM 17535, JCM 10889, CCUG 53877, CIP 107901

straininfo link

  • @ref: 82328
  • straininfo: 100889

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11699648Assignment of Pseudomonas sp. strain E-3 to Pseudomonas psychrophila sp. nov., a new facultatively psychrophilic bacterium.Yumoto I, Kusano T, Shingyo T, Nodasaka Y, Matsuyama H, Okuyama HExtremophiles10.1007/s0079201001992001Base Composition, Cold Temperature, DNA, Bacterial/chemistry/genetics, Microscopy, Electron, Phenotype, Phylogeny, Pseudomonas/chemistry/*classification/*genetics/ultrastructure, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic AcidPhenotype
Phylogeny34097596Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef.Lick S, Wibberg D, Winkler A, Blom J, Grimmler C, Goesmann A, Kalinowski J, Krockel LInt J Syst Evol Microbiol10.1099/ijsem.0.0048222021Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Food Microbiology, Genes, Bacterial, Germany, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, Pseudomonas/*classification/isolation & purification, RNA, Ribosomal, 16S/genetics, Red Meat/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistryBiotechnology

Reference

@idauthorscataloguedoi/urltitle
7048Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17535)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17535
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
33178Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5464
60047Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 53877)https://www.ccug.se/strain?id=53877
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/
68382Automatically annotated from API zym
69479João 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
82328Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID100889.1StrainInfo: A central database for resolving microbial strain identifiers
122021Curators of the CIPCollection of Institut Pasteur (CIP 107901)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107901