Strain identifier

BacDive ID: 14075

Type strain: Yes

Species: Shewanella kaireitica

Strain Designation: c931

Strain history: Y. Nogi c931.

NCBI tax ID(s): 212021 (species)

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General

@ref: 6805

BacDive-ID: 14075

DSM-Number: 17170

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

description: Shewanella kaireitica c931 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 212021
  • Matching level: species

strain history

@refhistory
6805<- M. Miyazaki; c931
67770Y. Nogi c931.

doi: 10.13145/bacdive14075.20230509.8.1

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 kaireitica
  • full scientific name: Shewanella kaireitica Miyazaki et al. 2006

@ref: 6805

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella kaireitica

full scientific name: Shewanella kaireitica Miyazaki et al. 2006

strain designation: c931

type strain: yes

Morphology

cell morphology

  • @ref: 31747
  • gram stain: negative
  • cell length: 2.5-3 µm
  • cell width: 0.8-1 µm
  • cell shape: rod-shaped
  • motility: yes

pigmentation

  • @ref: 31747
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6805
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: 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

culture temp

@refgrowthtypetemperaturerange
6805positivegrowth25mesophilic
31747positivegrowth02-28
31747positiveoptimum24-25
67770positivegrowth25mesophilic

culture pH

@refabilitytypepH
31747positivegrowth7
31747positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 31747
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 31747
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31747NaClpositivegrowth03-07 %
31747NaClpositiveoptimum03-05 %

observation

@refobservation
31747aggregates in chains
67770quinones: Q-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3174717057cellobiose+carbon source
3174728757fructose+carbon source
3174728260galactose+carbon source
3174717234glucose+carbon source
3174717306maltose+carbon source
3174730911sorbitol+carbon source
3174717632nitrate+reduction

metabolite production

  • @ref: 31747
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
31747catalase+1.11.1.6
31747cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6805deep-sea sedimentSuruga BayJapanJPNAsia
67770Deep-sea sediment in Suruga BayJapanJPNAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_1492.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_759;97_997;98_1177;99_1492&stattab=map
  • Last taxonomy: Shewanella piezotolerans
  • 16S sequence: AB094598
  • Sequence Identity:
  • Total samples: 1250
  • soil counts: 65
  • aquatic counts: 924
  • animal counts: 253
  • plant counts: 8

Safety information

risk assessment

  • @ref: 6805
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Shewanella kaireitica gene for 16S rRNA, partial sequence, strain: c931
  • accession: AB094598
  • length: 1492
  • database: ena
  • NCBI tax ID: 212021

Genome sequences

  • @ref: 66792
  • description: Shewanella kaireitica DSM 17170
  • accession: GCA_023284045
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 212021

GC content

@refGC-contentmethod
3174743
6777043high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes89.718no
gram-positiveno99.163no
anaerobicno94.143no
aerobicno82.367yes
halophileyes58.186no
spore-formingno95.607yes
motileyes90.866no
glucose-fermentno64.87no
thermophileno99.539yes
glucose-utilyes89.311yes

External links

@ref: 6805

culture collection no.: DSM 17170, JCM 11836, CIP 109340, KCTC 22439

straininfo link

  • @ref: 83244
  • straininfo: 297323

literature

  • topic: Phylogeny
  • Pubmed-ID: 16825637
  • title: Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan.
  • authors: Miyazaki M, Nogi Y, Usami R, Horikoshi K
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64173-0
  • year: 2006
  • mesh: Bacterial Typing Techniques, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis/chemistry, Genes, rRNA, Geologic Sediments/*microbiology, Japan, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Shewanella/*classification/cytology/genetics/*isolation & purification, Water Microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6805Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17170)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17170
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
31747Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128021
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
83244Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297323.1StrainInfo: A central database for resolving microbial strain identifiers