Strain identifier

BacDive ID: 139656

Type strain: Yes

Species: Shewanella violacea

Strain history: CIP <- 1999, JCM <- Y. Nogi: strain DSS12

NCBI tax ID(s): 637905 (strain), 60217 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 8.1 (current version)

General

@ref: 42242

BacDive-ID: 139656

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

description: Shewanella violacea CIP 106290 is a psychrophilic, Gram-negative, motile bacterium of the family Shewanellaceae.

NCBI tax id

NCBI tax idMatching level
60217species
637905strain

strain history

@refhistory
67770Y. Nogi DSS12.
42242CIP <- 1999, JCM <- Y. Nogi: strain DSS12

doi: 10.13145/bacdive139656.20230509.8.1

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 violacea
  • full scientific name: Shewanella violacea Nogi et al. 1999

@ref: 42242

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella violacea

type strain: yes

Morphology

cell morphology

  • @ref: 42242
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42242Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
42242CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
42242positivegrowth4psychrophilic
67770positivegrowth4psychrophilic
42242positivegrowth5-10psychrophilic
42242nogrowth22psychrophilic
42242nogrowth25mesophilic
42242nogrowth30mesophilic
42242nogrowth37mesophilic
42242nogrowth41thermophilic

Physiology and metabolism

halophily

@refsaltgrowthtested relationconcentration
42242NaClpositivegrowth2-4 %
42242NaClnogrowth0 %
42242NaClnogrowth6 %
42242NaClnogrowth8 %
42242NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-8 (Q-7)

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4224216947citrate-carbon source
422424853esculin-hydrolysis
4224217632nitrate+reduction
4224216301nitrite-reduction

metabolite production

  • @ref: 42242
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
42242oxidase+
42242beta-galactosidase+3.2.1.23
42242alcohol dehydrogenase-1.1.1.1
42242gelatinase+
42242amylase-
42242caseinase+3.4.21.50
42242catalase+1.11.1.6
42242tween esterase-
42242lecithinase-
42242lipase-
42242lysine decarboxylase-4.1.1.18
42242ornithine decarboxylase-4.1.1.17
42242protease-
42242tryptophan deaminase-
42242urease-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
42242-+---+----++-----+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
42242---------------------------------------------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refcountryorigin.countrycontinentsample typegeographic location
42242JapanJPNAsia
67770Pacific OceanMarine sediment at a depth of 5,110 mRyukyu Trench
42242JapanJPNAsiaEnvironment, Deep sea sediments, Isolated from the Ryukyu Trench at a depth of 5,110 m by means of a sterilized sediment sampler using the Shinkai 6500 system operated by the Japan Marine Science and Technology Center.

taxonmaps

  • @ref: 69479
  • File name: preview.99_2830.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_759;97_1185;98_1416;99_2830&stattab=map
  • Last taxonomy: Shewanella violacea
  • 16S sequence: D21225
  • Sequence Identity:
  • Total samples: 313
  • soil counts: 31
  • aquatic counts: 253
  • animal counts: 29

Safety information

risk assessment

  • @ref: 42242
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Shewanella violacea gene for 16S rRNA, partial sequence
  • accession: D21225
  • length: 1506
  • database: ena
  • NCBI tax ID: 637905

GC content

  • @ref: 67770
  • GC-content: 47
  • method: high performance liquid chromatography (HPLC)

External links

@ref: 42242

culture collection no.: CIP 106290, JCM 10179, LMG 19151, DSS 12

straininfo link

  • @ref: 96117
  • straininfo: 13318

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny9818352Taxonomic studies of deep-sea barophilic Shewanella strains and description of Shewanella violacea sp. nov.Nogi Y, Kato C, Horikoshi KArch Microbiol10.1007/s0020300506501998Bacteria, Anaerobic/*classification/growth & development/isolation & purification/ultrastructure, Base Sequence, DNA, Bacterial/analysis, Geologic Sediments/microbiology, Microscopy, Electron, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/analysis, Seawater/*microbiology, Temperature, *Water MicrobiologyGenetics
Phylogeny17220442Shewanella psychrophila sp. nov. and Shewanella piezotolerans sp. nov., isolated from west Pacific deep-sea sediment.Xiao X, Wang P, Zeng X, Bartlett DH, Wang FInt J Syst Evol Microbiol10.1099/ijs.0.64500-02007Bacterial Typing Techniques, China, Cold Temperature, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification/physiologyGenetics

Reference

@idauthorstitledoi/urlcatalogue
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
42242Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106290Collection of Institut Pasteur (CIP 106290)
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
96117Reimer, 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-ID13318.1