Strain identifier

BacDive ID: 8180

Type strain: Yes

Species: Psychrobacter frigidicola

Strain history: CIP <- 1997, ACAM <- Jeremy Austin

NCBI tax ID(s): 45611 (species)

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

@ref: 4548

BacDive-ID: 8180

DSM-Number: 12411

keywords: genome sequence, 16S sequence, Bacteria, aerobe, psychrophilic, Gram-negative

description: Psychrobacter frigidicola DSM 12411 is an aerobe, psychrophilic, Gram-negative bacterium that was isolated from ornithogenic soil.

NCBI tax id

  • NCBI tax id: 45611
  • Matching level: species

strain history

@refhistory
4548<- ACAM <- J. P. Bowman <- J. Austin
119462CIP <- 1997, ACAM <- Jeremy Austin

doi: 10.13145/bacdive8180.20230509.8.1

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 frigidicola
  • full scientific name: Psychrobacter frigidicola Bowman et al. 1996

@ref: 4548

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Moraxellaceae

genus: Psychrobacter

species: Psychrobacter frigidicola

full scientific name: Psychrobacter frigidicola Bowman et al. 1996

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.999
119462negativecoccus-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
4548BACTO 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
41492MEDIUM 118 - for Pasteurella, Actinobacillus and Psychrobacter frigidicolayesDistilled water make up to (1000.000 ml);Yeast extract (1.000 g);Tryptocasein soy agar (40.000 g)
119462CIP Medium 118-byeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=118-b

culture temp

@refgrowthtypetemperaturerange
4548positivegrowth10psychrophilic
41492positivegrowth10psychrophilic
52069positivegrowth10-15psychrophilic
119462positivegrowth5-30
119462nogrowth37mesophilic
119462nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
52069aerobe
119462obligate aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

  • @ref: 119462
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose-builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen-builds acid from28087
68371starch-builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose-builds acid from27082
68371sucrose-builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose-builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine-builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol-builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose-builds acid from16024
68371D-fructose-builds acid from15824
68371D-glucose-builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose-builds acid from16988
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
119462citrate-carbon source16947
119462esculin-hydrolysis4853
119462glucose-fermentation17234
119462lactose-fermentation17716
119462nitrate-reduction17632
119462nitrite-reduction16301
119462sodium thiosulfate-builds gas from132112
119462glucose-degradation17234
119462nitrate-respiration17632

antibiotic resistance

  • @ref: 119462
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

  • @ref: 119462
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
11946215688acetoin-
11946217234glucose-

enzymes

@refvalueactivityec
119462oxidase+
119462beta-galactosidase-3.2.1.23
119462alcohol dehydrogenase-1.1.1.1
119462gelatinase-
119462amylase-
119462DNase-
119462caseinase-3.4.21.50
119462catalase+1.11.1.6
119462tween esterase-
119462gamma-glutamyltransferase+2.3.2.2
119462lecithinase-
119462lipase-
119462lysine decarboxylase-4.1.1.18
119462ornithine decarboxylase-4.1.1.17
119462phenylalanine ammonia-lyase-4.3.1.24
119462tryptophan deaminase-
119462urease+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

fatty acid profile

  • fatty acids

    @reffatty acidpercentageECL
    52069C9:00.59
    52069C10:03.510
    52069C16:01.316
    52069C18:00.618
    52069C12:0 3OH2.613.455
    52069C14:0 3OH/C16:1 ISO I1.215.485
    52069C15:0 ISO 3OH4.816.135
    52069C16:1 ω11c0.415.757
    52069C16:1 ω7c21.115.819
    52069C17:0 iso0.516.629
    52069C17:1 ω9c2.516.773
    52069C18:1 ω9c27.217.769
    52069C18:2 ω6,9c/C18:0 ANTE1.517.724
    52069Unidentified18.19.143
    52069Unidentified2.59.432
    52069Unidentified1.510.239
    52069Unidentified1.912.672
    52069Unidentified0.616.289
    52069Unidentified0.617.109
    52069Unidentified7.318.093
  • type of FA analysis: whole cell analysis
  • method/protocol: CCUG

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
119462--++-------+--------

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119462-------------------------------------------------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119462---------------------------------------------------------------------------++--++---------+-------+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcontinentlatitudelongitudesampling datecountryorigin.countryisolation date
4548ornithogenic soilS68°32'30" E77°54'30", Magnetic Island, Vest fold HillsAustralia and Oceania-68.541777.9083
52069Soil,ornithogenicAntarctic coast,Magnetic IslandAustralia and Oceania1991-12-01AntarcticaATA
119462Environment, Ornithogenic soilAntarcticaAntarcticaATA1990

isolation source categories

Cat1Cat2Cat3
#Environmental#Terrestrial#Soil
#Host#Birds
#Host Body Product#Gastrointestinal tract#Feces (Stool)

taxonmaps

  • @ref: 69479
  • File name: preview.99_275.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_80;96_193;97_209;98_234;99_275&stattab=map
  • Last taxonomy: Psychrobacter
  • 16S sequence: AJ609556
  • Sequence Identity:
  • Total samples: 2913
  • soil counts: 306
  • aquatic counts: 1127
  • animal counts: 1430
  • plant counts: 50

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
45481Risk group (German classification)
1194621Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Psychrobacter frigidicola ACAM 304 16S ribosomal RNA geneU461431484ena45611
4548Psychrobacter frigidicola 16S rRNA gene, type strain DSM 12411TAJ6095561528ena45611

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Psychrobacter frigidicola Psychrobacter frigidicola ACAM304GCA_904845925contigncbi45611
66792Psychrobacter frigidicola ACAM 304GCA_007997305contigncbi45611
66792Psychrobacter frigidicola strain ACAM 30445611.3wgspatric45611
66792Psychrobacter frigidicola strain Psychrobacter frigidicola ACAM30445611.4wgspatric45611

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
gram-positiveno98.614no
anaerobicno98.678yes
halophileyes71.801no
spore-formingno96.982no
glucose-utilno63.418no
aerobicyes78.08no
flagellatedno92.924no
thermophileno99.525yes
motileno90.186no
glucose-fermentno93.713no

External links

@ref: 4548

culture collection no.: DSM 12411, ACAM 304, ATCC 700361, CCUG 34377, CIP 10501, CIP 105101

straininfo link

  • @ref: 77583
  • straininfo: 46959

literature

  • topic: Pathogenicity
  • Pubmed-ID: 8863407
  • title: Novel Psychrobacter species from Antarctic ornithogenic soils.
  • authors: Bowman JP, Cavanagh J, Austin JJ, Sanderson K
  • journal: Int J Syst Bacteriol
  • DOI: 10.1099/00207713-46-4-841
  • year: 1996
  • mesh: Antarctic Regions, Base Composition, Base Sequence, DNA, Ribosomal/chemistry, Humans, Lipids/analysis, Molecular Sequence Data, Moraxella/chemistry/*classification/genetics, Phenotype, RNA, Ribosomal, 16S/genetics, *Soil Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
4548Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 12411)https://www.dsmz.de/collection/catalogue/details/culture/DSM-12411
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
41492Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/17082
52069Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 34377)https://www.ccug.se/strain?id=34377
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)
68371Automatically annotated from API 50CH acid
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
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)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
77583Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID46959.1StrainInfo: A central database for resolving microbial strain identifiers
119462Curators of the CIPCollection of Institut Pasteur (CIP 105101)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20105101