Strain identifier

BacDive ID: 134204

Type strain: Yes

Species: Shewanella donghaensis

Strain Designation: LT17

Strain history: S.-J. Kim LT17.

NCBI tax ID(s): 238836 (species)

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General

@ref: 31833

BacDive-ID: 134204

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

description: Shewanella donghaensis LT17 is an anaerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment.

NCBI tax id

  • NCBI tax id: 238836
  • Matching level: species

strain history

  • @ref: 67770
  • history: S.-J. Kim LT17.

doi: 10.13145/bacdive134204.20230509.8.1

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 donghaensis
  • full scientific name: Shewanella donghaensis Yang et al. 2007

@ref: 31833

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella donghaensis

strain designation: LT17

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31833negative1.25 µm0.65 µmrod-shapedyes
69480yes97.217
69480negative99.985

pigmentation

  • @ref: 31833
  • production: yes

Culture and growth conditions

culture temp

@refgrowthtypetemperaturerange
31833positivegrowth05-22psychrophilic
31833positiveoptimum17psychrophilic
67770positivegrowth17psychrophilic

culture pH

@refabilitytypepHPH range
31833positivegrowth6.5-8.5alkaliphile
31833positiveoptimum7.25

Physiology and metabolism

oxygen tolerance

  • @ref: 31833
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.898

halophily

@refsaltgrowthtested relationconcentration
31833NaClpositivegrowth0.5-4.0 %
31833NaClpositiveoptimum2.5 %

observation

  • @ref: 31833
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
318335291gelatin+carbon source
318334853esculin+hydrolysis
3183317632nitrate+reduction

enzymes

@refvalueactivityec
31833catalase+1.11.1.6
31833gelatinase+
31833cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample type
31833marine sediment
67770Deep-sea sediment

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_50754.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_215;97_234;98_36458;99_50754&stattab=map
  • Last taxonomy: Shewanella donghaensis subclade
  • 16S sequence: AY326275
  • Sequence Identity:
  • Total samples: 20
  • soil counts: 3
  • aquatic counts: 15
  • animal counts: 2

Sequence information

16S sequences

  • @ref: 31833
  • description: Shewanella donghaensis strain LT17 16S ribosomal RNA gene, partial sequence
  • accession: AY326275
  • length: 1539
  • database: nuccore
  • NCBI tax ID: 238836

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella donghaensis LT17GCA_007567505completencbi238836
66792Shewanella donghaensis strain LT17238836.3completepatric238836

GC content

@refGC-contentmethod
3183338.8
6777038.8high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileyes88.711no
flagellatedyes82.954no
gram-positiveno99no
anaerobicno96.657no
aerobicno50.896yes
halophileyes59.087no
spore-formingno96.104no
glucose-utilyes87.427no
thermophileno99.582yes
glucose-fermentno68.235no

External links

@ref: 31833

culture collection no.: KCTC 10635BP, JCM 12524, CIP 109543

straininfo link

  • @ref: 91800
  • straininfo: 297321

literature

  • topic: Phylogeny
  • Pubmed-ID: 17267951
  • title: Shewanella donghaensis sp. nov., a psychrophilic, piezosensitive bacterium producing high levels of polyunsaturated fatty acid, isolated from deep-sea sediments.
  • authors: Yang SH, Lee JH, Ryu JS, Kato C, Kim SJ
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64469-0
  • year: 2007
  • mesh: Bacterial Proteins/analysis, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/analysis, Fatty Acids/analysis, Fatty Acids, Unsaturated/*biosynthesis, Genes, rRNA/genetics, Geologic Sediments/*microbiology, Hydrogen-Ion Concentration, Hydrostatic Pressure, Japan, Molecular Sequence Data, Movement, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Saline Solution, Hypertonic, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/*classification/cytology/isolation & purification/*metabolism, Temperature, Water Microbiology
  • topic2: Enzymology

Reference

@idauthorstitledoi/urlID_cross_referencepubmed
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
31833Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172809928776041
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/
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
91800Reimer, 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-ID297321.1