Strain identifier

BacDive ID: 134098

Type strain: Yes

Species: Shewanella marisflavi

Strain Designation: SW-117

Strain history: CIP <- 2005, JCM <- J. H. Yoon: strain SW-117

NCBI tax ID(s): 260364 (species)

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General

@ref: 31280

BacDive-ID: 134098

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

description: Shewanella marisflavi SW-117 is an anaerobe, Gram-negative, motile bacterium that was isolated from Seawater of the Yellow Sea.

NCBI tax id

  • NCBI tax id: 260364
  • Matching level: species

strain history

@refhistory
67770J.-H. Yoon SW-117.
120832CIP <- 2005, JCM <- J. H. Yoon: strain SW-117

doi: 10.13145/bacdive134098.20230509.8.1

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

@ref: 31280

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella marisflavi

strain designation: SW-117

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31280negative2.75 µm0.95 µmrod-shapedyes
120832negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
34004Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
120832CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
31280positivegrowth04-42
31280positiveoptimum33.5mesophilic
34004positivegrowth30mesophilic
67770positivegrowth30mesophilic
120832positivegrowth10-37
120832nogrowth5psychrophilic
120832nogrowth41thermophilic

culture pH

@refabilitytypepH
31280positivegrowth05-08
31280positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31280anaerobe
120832facultative anaerobe

spore formation

  • @ref: 31280
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31280NaClpositivegrowth0-8 %
31280NaClpositiveoptimum2.5 %
120832NaClpositivegrowth0-10 %

observation

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

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3128024996lactate+carbon source
3128025115malate+carbon source
3128017306maltose+carbon source
3128030031succinate+carbon source
3128017632nitrate+reduction
12083216947citrate-carbon source
1208324853esculin-hydrolysis
12083217632nitrate+reduction
12083216301nitrite+reduction
120832132112sodium thiosulfate+builds gas from

antibiotic resistance

  • @ref: 120832
  • 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
12083235581indoleno

enzymes

@refvalueactivityec
31280catalase+1.11.1.6
31280gelatinase+
31280cytochrome oxidase+1.9.3.1
120832oxidase+
120832beta-galactosidase-3.2.1.23
120832alcohol dehydrogenase-1.1.1.1
120832gelatinase+
120832amylase-
120832DNase+
120832caseinase+3.4.21.50
120832catalase+1.11.1.6
120832tween esterase+
120832lecithinase-
120832lipase+
120832lysine decarboxylase+4.1.1.18
120832ornithine decarboxylase-4.1.1.17
120832protease-
120832tryptophan deaminase-
120832urease-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
120832-+++-+-+++++---+-+--

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120832+--------++----+---+-----------------------------+---------+------------++-+--+++-+---+--+++-++-+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentgeographic location
67770Seawater of the Yellow SeaRepublic of KoreaKORAsia
120832Environment, Sea water of the Yellow SeaRepublic of KoreaKORAsiaYellow Sea

taxonmaps

  • @ref: 69479
  • File name: preview.99_37974.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_759;97_1181;98_1412;99_37974&stattab=map
  • Last taxonomy: Shewanella marisflavi
  • 16S sequence: AY485224
  • Sequence Identity:
  • Total samples: 1212
  • soil counts: 55
  • aquatic counts: 864
  • animal counts: 281
  • plant counts: 12

Safety information

risk assessment

  • @ref: 120832
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 31280
  • description: Shewanella marisflavi 16S ribosomal RNA gene, partial sequence
  • accession: AY485224
  • length: 1500
  • database: nuccore
  • NCBI tax ID: 260364

Genome sequences

  • @ref: 66792
  • description: Shewanella marisflavi JCM 12192
  • accession: GCA_023283925
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 260364

GC content

@refGC-contentmethod
3128051
6777051high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes91.857no
gram-positiveno99.169yes
anaerobicno93.043yes
aerobicno74.476no
halophileyes59.649no
spore-formingno96.245no
motileyes91.967yes
glucose-fermentno67.157no
thermophileno98.571yes
glucose-utilyes90.227no

External links

@ref: 31280

culture collection no.: KCCM 41822, JCM 12192, CIP 108637, KCTC 22432

straininfo link

  • @ref: 91705
  • straininfo: 134443

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15545482Shewanella marisflavi sp. nov. and Shewanella aquimarina sp. nov., slightly halophilic organisms isolated from sea water of the Yellow Sea in Korea.Yoon JH, Yeo SH, Kim IG, Oh TKInt J Syst Evol Microbiol10.1099/ijs.0.63198-02004Bacterial 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 MicrobiologyEnzymology
Phylogeny19915103Shewanella corallii sp. nov., a marine bacterium isolated from a Red Sea coral.Shnit-Orland M, Sivan A, Kushmaro AInt J Syst Evol Microbiol10.1099/ijs.0.015768-02009Animals, Anthozoa/*microbiology, Antibiosis, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella, Indian Ocean, Israel, Locomotion, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shewanella/*classification/genetics/*isolation & purification/physiology, Sodium Chloride/metabolismGenetics
Phylogeny21039606Biological characteristics and pathogenicity of a highly pathogenic Shewanella marisflavi infecting sea cucumber, Apostichopus japonicus.Li H, Qiao G, Li Q, Zhou W, Won KM, Xu DH, Park SIJ Fish Dis10.1111/j.1365-2761.2010.01189.x2010Animals, Bacterial Proteins/genetics/isolation & purification, Base Sequence, DNA, Bacterial/chemistry/genetics, Mice, Microscopy, Electron, Transmission, Molecular Sequence Data, Phylogeny, Polymerase Chain Reaction, RNA, Ribosomal, 16S/chemistry/genetics, Sequence Alignment, Shewanella/genetics/pathogenicity/*physiology/ultrastructure, Stichopus/*microbiology, VirulenceGenetics

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
34004Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6288
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/
91705Reimer, 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-ID134443.1
120832Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108637Collection of Institut Pasteur (CIP 108637)