Strain identifier

BacDive ID: 14070

Type strain: Yes

Species: Shewanella japonica

Strain Designation: RIOSW1, R10SW1

Strain history: CIP <- 2003, E. Ivanova, Swinburne Inst., Victoria, Australia: strain R10SW1

NCBI tax ID(s): 93973 (species)

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General

@ref: 5805

BacDive-ID: 14070

DSM-Number: 15445

keywords: 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, rod-shaped

description: Shewanella japonica RIOSW1 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.

NCBI tax id

  • NCBI tax id: 93973
  • Matching level: species

strain history

@refhistory
5805<- E. Ivanova; RIOSW1
418782003, E. Ivanova, Swinburne Inst., Victoria, Australia: strain R10SW1
121500CIP <- 2003, E. Ivanova, Swinburne Inst., Victoria, Australia: strain R10SW1

doi: 10.13145/bacdive14070.20230509.8.1

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 japonica
  • full scientific name: Shewanella japonica Ivanova et al. 2001

  • synonyms

    • @ref: 20215
    • synonym: Shewanella pacifica

@ref: 5805

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella pacifica

full scientific name: Shewanella pacifica Ivanova et al. 2004

strain designation: RIOSW1, R10SW1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
30143negative1.5 µm0.7 µmrod-shapedyes
121500negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
5805BACTO 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
41878Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
121500CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
5805positivegrowth25mesophilic
30143positivegrowth4.0-33
30143positiveoptimum22.5psychrophilic
41878positivegrowth25mesophilic
121500positivegrowth5-30
121500nogrowth37mesophilic
121500nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 30143
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 30143
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
30143NaClpositivegrowth0.5-6.0 %
30143NaClpositiveoptimum3.3 %
121500NaClpositivegrowth2-6 %
121500NaClnogrowth0 %
121500NaClnogrowth8 %
121500NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3014316000ethanolamine+carbon source
30143620642,3-butanediol+carbon source
3014316449alanine+carbon source
30143286442-oxopentanoate+carbon source
3014322599arabinose+carbon source
3014335391aspartate+carbon source
3014317126DL-carnitine+carbon source
3014317057cellobiose+carbon source
3014317234glucose+carbon source
3014329987glutamate+carbon source
3014317754glycerol+carbon source
3014317306maltose+carbon source
3014318257ornithine+carbon source
3014326271proline+carbon source
3014317148putrescine+carbon source
3014317822serine+carbon source
3014330031succinate+carbon source
3014326986threonine+carbon source
3014353424tween 20+carbon source
3014353423tween 40+carbon source
3014353426tween 80+carbon source
3014327248urocanic acid+carbon source
3014317632nitrate+reduction
12150016947citrate-carbon source
1215004853esculin+hydrolysis
12150017632nitrate+reduction
12150016301nitrite+reduction
121500132112sodium thiosulfate-builds gas from

metabolite production

@refChebi-IDmetaboliteproduction
3014316136hydrogen sulfideyes
12150035581indoleno

enzymes

@refvalueactivityec
30143catalase+1.11.1.6
30143gelatinase+
30143cytochrome oxidase+1.9.3.1
121500oxidase+
121500beta-galactosidase-3.2.1.23
121500alcohol dehydrogenase-1.1.1.1
121500gelatinase+
121500amylase+
121500caseinase+3.4.21.50
121500catalase+1.11.1.6
121500tween esterase+
121500lecithinase-
121500lipase-
121500lysine decarboxylase-4.1.1.18
121500ornithine decarboxylase-4.1.1.17
121500protease+
121500tryptophan deaminase-
121500urease-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
121500-+++-+---+++-----+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
121500+-+------++----+--+--+---------------------------+---------+-------------------++-----+--++--++-+--

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
5805sea waterCharhma Bay, Sea of Japan, Pacific oceanRussiaRUSAsia
121500Environment, Sea water sampleJapanJPNAsia2000

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_310.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_215;97_234;98_263;99_310&stattab=map
  • Last taxonomy: Shewanella japonica
  • 16S sequence: AF500075
  • Sequence Identity:
  • Total samples: 4858
  • soil counts: 182
  • aquatic counts: 2532
  • animal counts: 2105
  • plant counts: 39

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
58051Risk group (German classification)
1215001Risk group (French classification)

Sequence information

16S sequences

  • @ref: 5805
  • description: Shewanella pacifica KMM 3597 16S ribosomal RNA gene, partial sequence
  • accession: AF500075
  • length: 1485
  • database: ena
  • NCBI tax ID: 93973

GC content

@refGC-content
580539.7
3014340

External links

@ref: 5805

culture collection no.: DSM 15445, DSM 16475, KMM 3597, CIP 107849

straininfo link

  • @ref: 83239
  • straininfo: 99584

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15280273Shewanella pacifica sp. nov., a polyunsaturated fatty acid-producing bacterium isolated from sea water.Ivanova EP, Gorshkova NM, Bowman JP, Lysenko AM, Zhukova NV, Sergeev AF, Mikhailov VV, Nicolau DVInt J Syst Evol Microbiol10.1099/ijs.0.02993-02004Base Composition, DNA, Bacterial/chemistry, DNA, Ribosomal/chemistry, Fatty Acids/analysis/isolation & purification, Fatty Acids, Unsaturated/*biosynthesis, Genes, rRNA, Hemolysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Nucleic Acid Hybridization, Pacific Ocean, Phylogeny, Polysaccharides/metabolism, Polysorbates/metabolism, Quinones/analysis/isolation & purification, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Shewanella/*classification/genetics/*isolation & purification/physiology, Temperature, Water MicrobiologyEnzymology
Phylogeny28629494Shewanella intestini sp. nov., isolated from the intestine of abalone, Haliotis diversicolor.Gai Y, Huang Z, Lai Q, Shao ZInt J Syst Evol Microbiol10.1099/ijsem.0.0018782017Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gastropoda/*microbiology, Intestines/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shewanella/*classification/genetics/isolation & purification, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
5805Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15445)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15445
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
30143Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2649428776041
41878Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5405
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
83239Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID99584.1StrainInfo: A central database for resolving microbial strain identifiers
121500Curators of the CIPCollection of Institut Pasteur (CIP 107849)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107849