Strain identifier

BacDive ID: 14076

Type strain: Yes

Species: Shewanella abyssi

Strain Designation: c941

Strain history: CIP <- 2016, DSMZ <- JCM <- 2005, M. Miyakaki, JAMSTEC, Yokosuka, Japan: strain c941

NCBI tax ID(s): 311789 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6806

BacDive-ID: 14076

DSM-Number: 17171

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

description: Shewanella abyssi c941 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from deep-sea sediment.

NCBI tax id

  • NCBI tax id: 311789
  • Matching level: species

strain history

@refhistory
6806<- M. Miyazaki; c941
67770M. Miyazaki c941.
115986CIP <- 2016, DSMZ <- JCM <- 2005, M. Miyakaki, JAMSTEC, Yokosuka, Japan: strain c941

doi: 10.13145/bacdive14076.20230509.8.1

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

@ref: 6806

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella abyssi

full scientific name: Shewanella abyssi Miyazaki et al. 2006

strain designation: c941

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31747negative2-2.5 µm0.8-1 µmrod-shapedyes
115986negativerod-shapedyes

pigmentation

  • @ref: 31747
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6806BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
115986CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6806positivegrowth10psychrophilic
31747positivegrowth02-18psychrophilic
31747positiveoptimum10psychrophilic
67770positivegrowth10psychrophilic

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
31747NaClpositivegrowth01-05 %
31747NaClpositiveoptimum03-05 %

observation

@refobservation
31747aggregates in chains
67770quinones: Q-7, Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3174717057cellobiose+carbon source
3174717632nitrate+reduction

metabolite production

@refChebi-IDmetaboliteproduction
3174716136hydrogen sulfideyes
3174735581indoleyes

metabolite tests

  • @ref: 31747
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31747catalase+1.11.1.6
31747cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling date
6806deep-sea sedimentSuruga BayJapanJPNAsia
67770Deep-sea sediment in Suruga BayJapanJPNAsia
115986Environment, Deep sea sediments at a depth of 2406-2409 mSuruga bayJapanJPNAsia1995

isolation source categories

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

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
68061Risk group (German classification)
1159861Risk group (French classification)

Sequence information

16S sequences

  • @ref: 20218
  • description: Shewanella abyssi gene for 16S rRNA, partial sequence, strain: c941
  • accession: AB201475
  • length: 1487
  • database: ena
  • NCBI tax ID: 311789

Genome sequences

  • @ref: 66792
  • description: Shewanella abyssi DSM 17171
  • accession: GCA_023284025
  • assembly level: contig
  • database: ncbi
  • NCBI tax ID: 311789

GC content

@refGC-contentmethod
3174743.5-43.6
6777043.5-43.6high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes87.999no
gram-positiveno99.183yes
anaerobicno97.075no
aerobicno80.999no
halophileyes55.798no
spore-formingno94.977yes
motileyes90.671yes
glucose-fermentno63.141no
thermophileno99.348no
glucose-utilyes88.599no

External links

@ref: 6806

culture collection no.: DSM 17171, JCM 13041, CIP 109339

straininfo link

  • @ref: 83245
  • straininfo: 297320

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
6806Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17171)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17171
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/
83245Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID297320.1StrainInfo: A central database for resolving microbial strain identifiers
115986Curators of the CIPCollection of Institut Pasteur (CIP 109339)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109339