Strain identifier

BacDive ID: 134162

Type strain: Yes

Species: Shewanella hafniensis

Strain Designation: P010

Strain history: CIP <- 2006, NBRC <- M. Satomi, Japan: strain P010

NCBI tax ID(s): 365590 (species)

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General

@ref: 31629

BacDive-ID: 134162

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

description: Shewanella hafniensis P010 is an aerobe, Gram-negative, motile bacterium that was isolated from Cod, Gadus morhua.

NCBI tax id

  • NCBI tax id: 365590
  • Matching level: species

strain history

  • @ref: 119784
  • history: CIP <- 2006, NBRC <- M. Satomi, Japan: strain P010

doi: 10.13145/bacdive134162.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Alteromonadales
  • family: Shewanellaceae
  • genus: Shewanella
  • species: Shewanella hafniensis
  • full scientific name: Shewanella hafniensis Satomi et al. 2006

@ref: 31629

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella hafniensis

strain designation: P010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31629negative1-1.2 µm0.5-0.7 µmrod-shapedyes
119784negativerod-shapedyes

colony morphology

  • @ref: 119784

pigmentation

  • @ref: 31629
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37469Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119784CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31629positivegrowth04-25
31629positiveoptimum25mesophilic
37469positivegrowth25mesophilic

culture pH

@refabilitytypepH
31629positivegrowth7
31629positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31629aerobe
119784facultative anaerobe

spore formation

  • @ref: 31629
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31629NaClpositivegrowth0-6 %
31629NaClpositiveoptimum0-6 %

observation

  • @ref: 31629
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3162916947citrate+carbon source
3162924265gluconate+carbon source
3162917234glucose+carbon source
3162924996lactate+carbon source
3162925115malate+carbon source
3162917306maltose+carbon source
31629506227N-acetylglucosamine+carbon source
3162917632nitrate+reduction
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
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-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
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-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
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose-builds acid from
6837115824D-fructose-builds acid from
6837117634D-glucose-builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837116988D-ribose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
11978417632nitrate+reduction
11978416301nitrite+reduction

metabolite production

  • @ref: 119784
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
31629catalase+1.11.1.6
31629cytochrome oxidase+1.9.3.1
119784oxidase+
119784alcohol dehydrogenase-1.1.1.1
119784catalase+1.11.1.6
119784lysine decarboxylase-4.1.1.18
119784ornithine decarboxylase+4.1.1.17
119784urease-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
119784-+++-+++++++++++++++

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119784---------------------+/------+/-------------------+--

Isolation, sampling and environmental information

isolation

  • @ref: 119784
  • sample type: Cod, Gadus morhua
  • geographic location: Baltic Sea
  • country: Denmark
  • origin.country: DNK
  • continent: Europe
  • isolation date: 2001

taxonmaps

  • @ref: 69479
  • File name: preview.99_3799.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_126;97_134;98_151;99_3799&stattab=map
  • Last taxonomy: Shewanella
  • 16S sequence: AB205566
  • Sequence Identity:
  • Total samples: 6
  • aquatic counts: 2
  • animal counts: 4

Safety information

risk assessment

  • @ref: 119784
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31629
  • description: Shewanella hafniensis gene for 16S rRNA, partial sequence, strain: P010
  • accession: AB205566
  • length: 1418
  • database: nuccore
  • NCBI tax ID: 365590

GC content

  • @ref: 31629
  • GC-content: 47

External links

@ref: 31629

culture collection no.: ATCC BAA 1207, NBRC 100975, CIP 109108

straininfo link

  • @ref: 91760
  • straininfo: 289874

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16403893Shewanella hafniensis sp. nov. and Shewanella morhuae sp. nov., isolated from marine fish of the Baltic Sea.Satomi M, Vogel BF, Gram L, Venkateswaran KInt J Syst Evol Microbiol10.1099/ijs.0.63931-02006Animals, Base Composition, DNA Gyrase/genetics, DNA, Bacterial/chemistry, Denmark, Flounder/*microbiology, Gadiformes/*microbiology, Molecular Sequence Data, Oceans and Seas, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Homology, Nucleic Acid, Shewanella/chemistry/*classification/isolation & purification/physiology, Species SpecificityGenetics
Phylogeny18676478Shewanella basaltis sp. nov., a marine bacterium isolated from black sand.Chang HW, Roh SW, Kim KH, Nam YD, Jeon CO, Oh HM, Bae JWInt J Syst Evol Microbiol10.1099/ijs.0.65725-02008Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Korea, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification/physiology, *Silicon Dioxide, Species SpecificityGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
31629Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172791428776041
37469Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6813
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91760Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID289874.1
119784Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109108Collection of Institut Pasteur (CIP 109108)