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Strain identifier

BacDive ID: 8201

Type strain: Yes

Species: Psychrobacter namhaensis

Strain Designation: SW-242

Strain history: <- JH Yoon, KRIBB

NCBI tax ID(s): 292734 (species)

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For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 6372

BacDive-ID: 8201

DSM-Number: 16330

keywords: genome sequence, 16S sequence, Bacteria, anaerobe, mesophilic, Gram-negative, coccus-shaped

description: Psychrobacter namhaensis SW-242 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 292734
  • Matching level: species

strain history

doi: 10.13145/bacdive8201.20221219.7.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: Moraxellaceae
  • genus: Psychrobacter
  • species: Psychrobacter namhaensis
  • full scientific name: Psychrobacter namhaensis Yoon et al. 2005

@ref: 6372

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter namhaensis

full scientific name: Psychrobacter namhaensis Yoon et al. 2005

strain designation: SW-242

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31395negative2 µm1.1 µmcoccus-shapedno
67771negative
69480negative99.57

pigmentation

  • @ref: 31395
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6372BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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
34973Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)

culture temp

@refgrowthtypetemperaturerange
6372positivegrowth30mesophilic
31395positivegrowth04-37
31395positiveoptimum27.5mesophilic
34973positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepH
31395positivegrowth5-7.5
31395positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31395anaerobe
67771aerobe

spore formation

@refspore formationconfidence
31395no
69480no99.226

halophily

@refsaltgrowthtested relationconcentrationhalophily levelconfidence
31395NaClpositivegrowth0-13 %
31395NaClpositiveoptimum2.5 %
69480non-halophilic93.013

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3139530089acetate+carbon source
3139522599arabinose+carbon source
3139517057cellobiose+carbon source
3139528260galactose+carbon source
3139517234glucose+carbon source
3139517716lactose+carbon source
3139525115malate+carbon source
3139537684mannose+carbon source
3139528053melibiose+carbon source
3139515361pyruvate+carbon source
3139526546rhamnose+carbon source
3139533942ribose+carbon source
3139530031succinate+carbon source
3139553423tween 40+carbon source
3139553426tween 80+carbon source
3139518222xylose+carbon source

enzymes

@refvalueactivityec
31395alkaline phosphatase+3.1.3.1
31395catalase+1.11.1.6
31395cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6372sea waterSouth SeaRepublic of KoreaKORAsia
67771From seawaterWest seaRepublic of KoreaKORAsia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

Safety information

risk assessment

  • @ref: 6372
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 6372
  • description: Psychrobacter namhaensis strain SW-242 16S ribosomal RNA gene, partial sequence
  • accession: AY722805
  • length: 1494
  • database: ena
  • NCBI tax ID: 292734

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacter namhaensis DSM 16330GCA_016107545contigncbi292734
66792Psychrobacter namhaensis strain DSM 16330292734.5wgspatric292734
66792Streptococcus pneumoniae SMRU2606GCA_001135885contigpatric1313

GC content

@refGC-contentmethod
637245.3high performance liquid chromatography (HPLC)
3139545.3

External links

@ref: 6372

culture collection no.: DSM 16330, KCTC 12255, CIP 108796

straininfo link

@refpassport
20218http://www.straininfo.net/strains/387827
20218http://www.straininfo.net/strains/387828

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15879226Psychrobacter aquimaris sp. nov. and Psychrobacter namhaensis sp. nov., isolated from sea water of the South Sea in Korea.Yoon JH, Lee CH, Yeo SH, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63464-02005Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phenazines, Phylogeny, Psychrobacter/*classification/cytology/*isolation & purification/physiology, Quinones/analysis, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Temperature, Water MicrobiologyGenetics
Phylogeny19502339Psychrobacter fulvigenes sp. nov., isolated from a marine crustacean from the Sea of Japan.Romanenko LA, Tanaka N, Frolova GM, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.007195-02009Animals, Bacterial Typing Techniques, Base Composition, Crustacea/*microbiology, DNA Gyrase/genetics, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Oceans and Seas, Phenotype, Phylogeny, Polymerase Chain Reaction/methods, Psychrobacter/*classification/genetics/*isolation & purification/physiology, RNA, Ribosomal, 16S/genetics, Seawater, Sequence Analysis, DNA, Species SpecificityGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6372Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16330)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16330
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
2770510.1099/ijs.0.63464-015879226
31395Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127705
34973Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6465
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)