Strain identifier

BacDive ID: 134289

Type strain: Yes

Species: Shewanella algae

Strain Designation: DW01

Strain history: <- CN Seong, Sunchon Natl. Univ.

NCBI tax ID(s): 1236541 (strain), 38313 (species)

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General

@ref: 32284

BacDive-ID: 134289

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

description: Shewanella algae DW01 is a facultative anaerobe, Gram-negative, motile bacterium that was isolated from marine sediment.

NCBI tax id

NCBI tax idMatching level
1236541strain
38313species

strain history

@refhistory
67770C. N. Seong DW01.
67771<- CN Seong, Sunchon Natl. Univ.

doi: 10.13145/bacdive134289.20230509.8.1

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 algae
  • full scientific name: Shewanella algae corrig. Simidu et al. 1990

  • synonyms

    @refsynonym
    20215Shewanella haliotis
    20215Shewanella alga
    20215Shewanella upenei

@ref: 32284

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella haliotis

strain designation: DW01

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
32284negative3.15 µm0.6 µmrod-shapedyes
67771negative
69480yes98.993
69480negative99.993

pigmentation

  • @ref: 32284
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
32284positivegrowth10-42
32284positiveoptimum37mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
32284positivegrowth05-11alkaliphile
32284positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32284facultative anaerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.799

halophily

@refsaltgrowthtested relationconcentration
32284NaClpositivegrowth0-10 %
32284NaClpositiveoptimum4 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3228427689decanoate+carbon source
3228425115malate+carbon source
32284506227N-acetylglucosamine+carbon source
3228417632nitrate+reduction

metabolite production

  • @ref: 32284
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
32284alkaline phosphatase+3.1.3.1
32284catalase+1.11.1.6
32284gelatinase+
32284cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
32284marine sediment
67770Gut microflora of abalone
67771From intestine of abaloneYoesuRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Sediment

taxonmaps

  • @ref: 69479
  • File name: preview.99_1099.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_641;97_744;98_863;99_1099&stattab=map
  • Last taxonomy: Shewanella algae
  • 16S sequence: HM016086
  • Sequence Identity:
  • Total samples: 4840
  • soil counts: 118
  • aquatic counts: 730
  • animal counts: 3902
  • plant counts: 90

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
32284Shewanella haliotis strain DW01 16S ribosomal RNA gene, partial sequenceEF1782821420nuccore418642
67770Shewanella haliotis strain DW01 16S ribosomal RNA gene, partial sequenceHM0160861495ena38313

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella haliotis JCM 147581236541.3wgspatric1236541
66792Shewanella haliotis JCM 147582565956593draftimg1236541
67770Shewanella algae JCM 14758GCA_000614935contigncbi1236541

GC content

@refGC-contentmethod
3228453.7
6777053.7thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes94.72yes
gram-positiveno99.023no
anaerobicno94.53no
aerobicyes59.529no
halophileno61.152no
spore-formingno95.858no
glucose-utilyes91.275no
flagellatedyes91.609no
thermophileno99.465yes
glucose-fermentno63.908no

External links

@ref: 32284

culture collection no.: KCTC 12896, JCM 14758, BCRC 80906

straininfo link

  • @ref: 91873
  • straininfo: 323267

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18048751Shewanella haliotis sp. nov., isolated from the gut microflora of abalone, Haliotis discus hannai.Kim D, Baik KS, Kim MS, Jung BM, Shin TS, Chung GH, Rhee MS, Seong CNInt J Syst Evol Microbiol10.1099/ijs.0.65257-02007Aerobiosis/physiology, Anaerobiosis/physiology, Animals, Bacterial Typing Techniques, Base Composition, Catalase/analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gastrointestinal Tract/microbiology, Gastropoda/*microbiology, Genes, rRNA, Korea, Locomotion/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidoreductases/analysis, Phylogeny, Pigments, Biological/metabolism, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Shewanella/chemistry/*classification/genetics/*isolation & purificationGenetics
Phylogeny21717322Shewanella upenei sp. nov., a lipolytic bacterium isolated from bensasi goatfish Upeneus bensasi.Kim KK, Kim YO, Park S, Kang SJ, Nam BH, Kim DN, Oh TK, Yoon JHJ Microbiol10.1007/s12275-011-0175-52011Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, rRNA, Lipolysis, Molecular Sequence Data, Perciformes/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shewanella/*classification/genetics/*isolation & purification/physiology, Species SpecificityGenetics
Phylogeny29504926Whole-genome sequencing reveals that Shewanella haliotis Kim et al. 2007 can be considered a later heterotypic synonym of Shewanella algae Simidu et al. 1990.Szeinbaum N, Kellum CE, Glass JB, Janda JM, DiChristina TJInt J Syst Evol Microbiol10.1099/ijsem.0.0026782018Bacterial Typing Techniques, DNA, Bacterial/genetics, *Genome, Bacterial, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Shewanella/*classification, Whole Genome SequencingGenetics

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournal
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
32284Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172852428776041
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
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
91873Reimer, 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-ID323267.1