Strain identifier

BacDive ID: 8201

Type strain: Yes

Species: Psychrobacter namhaensis

Strain Designation: SW-242

Strain history: CIP <- 2005, KCTC <- J. H. Yoon: strain SW-242

NCBI tax ID(s): 292734 (species)

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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

@refhistory
6372<- J.-H. Yoon; SW-242
67771<- JH Yoon, KRIBB
121226CIP <- 2005, KCTC <- J. H. Yoon: strain SW-242

doi: 10.13145/bacdive8201.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Pseudomonadales
  • family: 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 shapemotility
31395negative2 µm1.1 µmcoccus-shapedno
67771negative
121226negativeoval-shapedno

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)
121226CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6372positivegrowth30mesophilic
31395positivegrowth04-37
31395positiveoptimum27.5mesophilic
34973positivegrowth30mesophilic
67771positivegrowth30mesophilic
121226positivegrowth5-37
121226nogrowth41thermophilic

culture pH

@refabilitytypepH
31395positivegrowth5-7.5
31395positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31395anaerobe
67771aerobe
121226obligate aerobe

spore formation

  • @ref: 31395
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31395NaClpositivegrowth0-13 %
31395NaClpositiveoptimum2.5 %
121226NaClpositivegrowth0-10 %

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
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837124265gluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen-builds acid from
6837128017starch-builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837117306maltose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine-builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol-builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837117266L-sorbose-builds acid from
6837115824D-fructose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
12122616947citrate-carbon source
1212264853esculin-hydrolysis
12122617632nitrate+reduction
12122616301nitrite-reduction
12122617632nitrate-respiration

metabolite production

  • @ref: 121226
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
12122615688acetoin-
12122617234glucose-

enzymes

@refvalueactivityec
31395alkaline phosphatase+3.1.3.1
31395catalase+1.11.1.6
31395cytochrome oxidase+1.9.3.1
121226oxidase+
121226beta-galactosidase+3.2.1.23
121226alcohol dehydrogenase-1.1.1.1
121226gelatinase-
121226amylase-
121226DNase-
121226caseinase-3.4.21.50
121226catalase+1.11.1.6
121226tween esterase+
121226gamma-glutamyltransferase+2.3.2.2
121226lecithinase-
121226lipase-
121226lysine decarboxylase-4.1.1.18
121226ornithine decarboxylase-4.1.1.17
121226phenylalanine ammonia-lyase-4.3.1.24
121226tryptophan deaminase-
121226urease-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
121226-+++-+----++--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
121226--+/-+/-+/-+/----+/-+/--+/--+/------------+/--+/-+/---------+/----+/-------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121226+-+-+-------+------++++--++--+++-++-+----+-+----+---------------+--+-----+-+--+--+-+----+++++--++++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6372sea waterSouth SeaRepublic of KoreaKORAsia
67771From seawaterWest seaRepublic of KoreaKORAsia
121226Environment, Sea waterSouth SeaRepublic of KoreaKORAsia

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
63721Risk group (German classification)
1212261Risk group (French 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

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
gram-positiveno98.087yes
anaerobicno98.571no
halophileyes86.511no
spore-formingno96.626yes
glucose-utilno50no
motileno86.956yes
flagellatedno90.489yes
aerobicyes87.787no
thermophileno99.318yes
glucose-fermentno92.545no

External links

@ref: 6372

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

straininfo link

  • @ref: 77604
  • straininfo: 139003

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/urltitleID_cross_referencepubmed
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
31395Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2770528776041
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
68371Automatically annotated from API 50CH acid
68382Automatically annotated from API zym
77604Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID139003.1StrainInfo: A central database for resolving microbial strain identifiers
121226Curators of the CIPCollection of Institut Pasteur (CIP 108796)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108796