Strain identifier

BacDive ID: 134099

Type strain: Yes

Species: Shewanella aquimarina

Strain Designation: SW-120

Strain history: CIP <- 2005, JCM <- J.H. Yoon: strain SW-120

NCBI tax ID(s): 260365 (species)

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General

@ref: 31280

BacDive-ID: 134099

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

description: Shewanella aquimarina SW-120 is an anaerobe, Gram-negative, motile bacterium that was isolated from Seawater of the Yellow Sea.

NCBI tax id

  • NCBI tax id: 260365
  • Matching level: species

strain history

@refhistory
67770J.-H. Yoon SW-120.
116453CIP <- 2005, JCM <- J.H. Yoon: strain SW-120

doi: 10.13145/bacdive134099.20230509.8.1

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 aquimarina
  • full scientific name: Shewanella aquimarina Yoon et al. 2004

@ref: 31280

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella aquimarina

strain designation: SW-120

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31280negative3 µm0.75 µmrod-shapedyes
116453negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42247Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
116453CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
116453CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31280positivegrowth10-42
31280positiveoptimum33.5mesophilic
42247positivegrowth30mesophilic
67770positivegrowth30mesophilic
116453positivegrowth25-37mesophilic
116453nogrowth5psychrophilic
116453nogrowth10psychrophilic
116453nogrowth41thermophilic

culture pH

@refabilitytypepH
31280positivegrowth05-08
31280positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31280anaerobe
116453facultative anaerobe

spore formation

  • @ref: 31280
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31280NaClpositivegrowth02-08 %
31280NaClpositiveoptimum2.5 %
116453NaClpositivegrowth2-8 %
116453NaClnogrowth0 %
116453NaClnogrowth10 %

observation

  • @ref: 67770
  • observation: quinones: Q-7, Q-8, MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3128028260galactose+carbon source
3128024996lactate+carbon source
3128025115malate+carbon source
3128017306maltose+carbon source
3128030031succinate+carbon source
3128017632nitrate+reduction
11645316947citrate-carbon source
1164534853esculin-hydrolysis
11645317632nitrate+reduction
11645316301nitrite+reduction
116453132112sodium thiosulfate+builds gas from
11645317632nitrate+respiration

antibiotic resistance

  • @ref: 116453
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
3128016136hydrogen sulfideyes
11645335581indoleno

enzymes

@refvalueactivityec
31280catalase+1.11.1.6
31280gelatinase+
31280cytochrome oxidase+1.9.3.1
116453oxidase+
116453beta-galactosidase-3.2.1.23
116453alcohol dehydrogenase-1.1.1.1
116453gelatinase+/-
116453amylase-
116453DNase+
116453caseinase-3.4.21.50
116453catalase+1.11.1.6
116453tween esterase-
116453lecithinase-
116453lipase-
116453lysine decarboxylase-4.1.1.18
116453ornithine decarboxylase-4.1.1.17
116453protease+
116453tryptophan deaminase-
116453urease-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
116453-+++-+-+++++--------

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
116453+++-+----++----+---+--+++----------------++------+----++---+------------+--+--+++-+-------++-++-++-

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67770Seawater of the Yellow SeaRepublic of KoreaKORAsia
116453Environment, Sea water of the Yellow SeaRepublic of KoreaKORAsiaYellow Sea

taxonmaps

  • @ref: 69479
  • File name: preview.99_1310.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_759;97_884;98_1035;99_1310&stattab=map
  • Last taxonomy: Shewanella loihica
  • 16S sequence: AY485225
  • Sequence Identity:
  • Total samples: 1108
  • soil counts: 89
  • aquatic counts: 720
  • animal counts: 279
  • plant counts: 20

Safety information

risk assessment

  • @ref: 116453
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31280
  • description: Shewanella aquimarina 16S ribosomal RNA gene, partial sequence
  • accession: AY485225
  • length: 1499
  • database: nuccore
  • NCBI tax ID: 260365

Genome sequences

  • @ref: 66792
  • description: Shewanella aquimarina JCM 12193
  • accession: GCA_023349185
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 260365

GC content

@refGC-contentmethod
3128054
6777054high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes93.328no
gram-positiveno99.206yes
anaerobicno94.728no
aerobicno78.951yes
halophileyes65.945no
spore-formingno96.732no
motileyes92.891yes
glucose-fermentno66.548no
thermophileno99.189yes
glucose-utilyes92.742no

External links

@ref: 31280

culture collection no.: KCCM 41821, JCM 12193, CIP 108633, KCTC 22430

straininfo link

  • @ref: 91706
  • straininfo: 134441

literature

  • topic: Phylogeny
  • Pubmed-ID: 15545482
  • title: Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.
  • authors: Yoon JH, Yeo SH, Kim IG, Oh TK
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63198-0
  • year: 2004
  • mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/isolation & purification, DNA, Ribosomal/chemistry/isolation & purification, Fatty Acids/analysis/isolation & purification, Genes, rRNA, Gentian Violet, Korea, Molecular Sequence Data, Movement, Oceans and Seas, Phenazines, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/cytology/*isolation & purification/physiology, Spores, Bacterial, Ubiquinone/analysis/isolation & purification, Vitamin K 2/analysis/isolation & purification, Water Microbiology
  • topic2: Enzymology

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
31280Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172760028776041
42247Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6283
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
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/
91706Reimer, 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-ID134441.1
116453Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108633Collection of Institut Pasteur (CIP 108633)