Strain identifier

BacDive ID: 14074

Type strain: Yes

Species: Shewanella sediminis

Strain Designation: A010-1, HAW-EB3

Strain history: CIP <- 2005, NCIMB

NCBI tax ID(s): 271097 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 9.3 (current version):
version 9.2:
version 9.1:
version 9:
version 8.1:
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 9.3 (current version)

General

@ref: 6724

BacDive-ID: 14074

DSM-Number: 17055

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

description: Shewanella sediminis A010-1 is a facultative anaerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sediment of Emerald Basin in 215 meter deep.

NCBI tax id

  • NCBI tax id: 271097
  • Matching level: species

strain history

@refhistory
6724<- J.-S. Zhao; HAW-EB3
383682005, NCIMB
122537CIP <- 2005, NCIMB

doi: 10.13145/bacdive14074.20250331.9.3

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 sediminis
  • full scientific name: Shewanella sediminis Zhao et al. 2005

@ref: 6724

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Alteromonadales

family: Shewanellaceae

genus: Shewanella

species: Shewanella sediminis

full scientific name: Shewanella sediminis Zhao et al. 2005

strain designation: A010-1, HAW-EB3

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31456negative1.7 µm0.7 µmrod-shapedyes
125438negative98.5
125439negative96.7

pigmentation

  • @ref: 31456
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6724BACTO 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
38368Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122537CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperature
6724positivegrowth10-20
31456positivegrowth04-25
31456positiveoptimum10
38368positivegrowth15

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
31456facultative anaerobe
125439obligate aerobe91.8

spore formation

@refspore formationconfidence
31456no
125439no90.1

halophily

@refsaltgrowthtested relationconcentration
31456NaClpositivegrowth01-04 %
31456NaClpositiveoptimum2 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3145630089acetate+carbon source
3145616449alanine+carbon source
3145635391aspartate+carbon source
3145629987glutamate+carbon source
3145617596inosine+carbon source
3145624996lactate+carbon source
3145651850methyl pyruvate+carbon source
31456506227N-acetylglucosamine+carbon source
3145618257ornithine+carbon source
3145626271proline+carbon source
3145617272propionate+carbon source
3145615361pyruvate+carbon source
3145617822serine+carbon source
3145630031succinate+carbon source
3145617748thymidine+carbon source
3145653424tween 20+carbon source
3145653423tween 40+carbon source
3145653426tween 80+carbon source
3145616199urea+carbon source
3145631011valerate+carbon source
3145617632nitrate+reduction

enzymes

@refvalueactivityec
31456alkaline phosphatase+3.1.3.1
31456catalase+1.11.1.6
31456cytochrome oxidase+1.9.3.1
31456urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
6724marine sediment of Emerald Basin in 215 meter deepHalifaxCanadaCANNorth America
122537Environment, SedimentHalifax harbour, Nova ScotiaCanadaCANNorth America

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_789.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_59;96_479;97_547;98_630;99_789&stattab=map
  • Last taxonomy: Shewanella sediminis
  • 16S sequence: FR733715
  • Sequence Identity:
  • Total samples: 3109
  • soil counts: 163
  • aquatic counts: 2554
  • animal counts: 381
  • plant counts: 11

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67241Risk group (German classification)
1225371Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Shewanella sediminis partial 16S rRNA gene, type strain DSM17055TFR7337151530nuccore271097
31456Shewanella sediminis strain HAW-EB3 16S ribosomal RNA gene, partial sequenceAY5797501288nuccore425104

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Shewanella sediminis HAW-EB3GCA_000018025completencbi425104
66792Shewanella sediminis HAW-EB3425104.7completepatric425104
66792Shewanella sediminis HAW-EB3640753050completeimg425104

GC content

  • @ref: 6724
  • GC-content: 45

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingno98.5yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.739yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no65.829yes
125438spore-formingspore-formingAbility to form endo- or exosporesno87.203yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno97.5yes
125438motile2+flagellatedAbility to perform flagellated movementyes88.345no
125439BacteriaNetspore_formationAbility to form endo- or exosporesno90.1
125439BacteriaNetmotilityAbility to perform movementyes74.9
125439BacteriaNetgram_stainReaction to gram-stainingnegative96.7
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthobligate aerobe91.8

External links

@ref: 6724

culture collection no.: DSM 17055, CIP 109531, NCIMB 14036, CIP 108924

straininfo link

  • @ref: 83243
  • straininfo: 237174

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny16014474Shewanella sediminis sp. nov., a novel Na+-requiring and hexahydro-1,3,5-trinitro-1,3,5-triazine-degrading bacterium from marine sediment.Zhao JS, Manno D, Beaulieu C, Paquet L, Hawari JInt J Syst Evol Microbiol10.1099/ijs.0.63604-02005Bacterial Typing Techniques, Biodegradation, Environmental, DNA, Bacterial, DNA, Ribosomal, Genes, rRNA, Genotype, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, RNA, Ribosomal, 16S, Seawater/*microbiology, Sequence Analysis, DNA, Shewanella/chemistry/*classification/genetics/physiology, Sodium/*metabolism, Triazines/*metabolismGenetics
Phylogeny34904941Shewanella nanhaiensis sp. nov., a marine bacterium isolated from sediment of South China Sea, and emended descriptions of Shewanella woodyi, Shewanella hanedai and Shewanella canadensis.Cao WR, Li X, Sun YY, Jiang MY, Xu XD, Li YJInt J Syst Evol Microbiol10.1099/ijsem.0.0051522021Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Shewanella/classification/isolation & purification, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6724Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17055)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17055
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
31456Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127758
38368Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/6608
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)
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
83243Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID237174.1StrainInfo: A central database for resolving microbial strain identifiers
122537Curators of the CIPCollection of Institut Pasteur (CIP 108924)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108924
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann10.1101/2024.08.12.607695Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardyhttps://github.com/GenomeNet/deepGdeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1