Strain identifier

BacDive ID: 130501

Type strain: Yes

Species: Sinobacterium caligoides

Strain Designation: SCSWE24

Strain history: <- LMG <- J. Su, Xiamen Univ., China

NCBI tax ID(s): 933926 (species)

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 22097

BacDive-ID: 130501

DSM-Number: 100316

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

description: Sinobacterium caligoides SCSWE24 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from seawater at 450m depth.

NCBI tax id

  • NCBI tax id: 933926
  • Matching level: species

strain history

  • @ref: 22097
  • history: <- LMG <- J. Su, Xiamen Univ., China

doi: 10.13145/bacdive130501.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Cellvibrionales
  • family: Spongiibacteraceae
  • genus: Sinobacterium
  • species: Sinobacterium caligoides
  • full scientific name: Sinobacterium caligoides Su et al. 2013

@ref: 22097

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Pseudomonadales

family: Spongiibacteraceae

genus: Sinobacterium

species: Sinobacterium caligoides

full scientific name: Sinobacterium caligoides Su et al. 2013 emend. Diéguez et al. 2015

strain designation: SCSWE24

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30216negative2 µm0.6 µmrod-shapedno
69480negative99.981

colony morphology

  • @ref: 22097
  • incubation period: 2-3 days

pigmentation

  • @ref: 30216
  • production: no

Culture and growth conditions

culture medium

  • @ref: 22097
  • 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
22097positivegrowth28mesophilic
30216positivegrowth04-37
30216positiveoptimum25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.949

halophily

@refsaltgrowthtested relationconcentration
30216NaClpositivegrowth1.5-4.5 %
30216NaClpositiveoptimum3.25 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3021617632nitrate+reduction
6836925115malate-assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol-assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose-assimilation
683695291gelatin-hydrolysis
683694853esculin-hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
30216acid phosphatase+3.1.3.2
30216alkaline phosphatase+3.1.3.1
30216alpha-galactosidase+3.2.1.22
30216catalase+1.11.1.6
30216cytochrome oxidase+1.9.3.1
30216urease+3.5.1.5
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
22097+---+---------------+

Isolation, sampling and environmental information

isolation

  • @ref: 22097
  • sample type: seawater at 450m depth
  • geographic location: South China Sea
  • country: China
  • origin.country: CHN
  • continent: Asia

isolation source categories

  • Cat1: #Environmental
  • Cat2: #Aquatic
  • Cat3: #Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_61730.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16634;96_8001;97_9624;98_43789;99_61730&stattab=map
  • Last taxonomy: Sinobacterium caligoides subclade
  • 16S sequence: HQ686140
  • Sequence Identity:
  • Total samples: 398
  • soil counts: 2
  • aquatic counts: 378
  • animal counts: 18

Safety information

risk assessment

  • @ref: 22097
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 22097
  • description: Sinobacterium caligoides strain SCSWE24 16S ribosomal RNA gene, partial sequence
  • accession: HQ686140
  • length: 1501
  • database: ena
  • NCBI tax ID: 933926

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Sinobacterium caligoides DSM 100316GCA_003752585scaffoldncbi933926
66792Sinobacterium caligoides strain DSM 100316933926.3wgspatric933926
66792Sinobacterium caligoides DSM 1003162788499881draftimg933926

GC content

@refGC-contentmethod
3021658.8
2209754fluorimetric

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno83.335yes
flagellatedno57.575no
gram-positiveno97.694yes
anaerobicno99.412no
aerobicyes77.251no
halophileyes65.645no
spore-formingno94.11no
glucose-utilyes74.021no
thermophileno99.653yes
glucose-fermentno77.15no

External links

@ref: 22097

culture collection no.: DSM 100316, CCTCC AB 209289, LMG 25705, MCCC 1F01088

straininfo link

  • @ref: 89024
  • straininfo: 369643

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny23087165Sinobacterium caligoides gen. nov., sp. nov., a new member of the family Oceanospirillaceae isolated from the South China Sea, and emended description of Amphritea japonica.Su J, Zhou Y, Lai Q, Li X, Dong P, Yang X, Zhang B, Zhang J, Zheng X, Tian Y, Zheng TInt J Syst Evol Microbiol10.1099/ijs.0.030965-02012Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oceanospirillaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water MicrobiologyGenetics
Phylogeny26267335Sinobacterium norvegicum sp. nov., isolated from great scallop (Pecten maximus) broodstock and emended description of Sinobacterium caligoides.Dieguez AL, Jacobsen A, Magnesen T, Romalde JLAntonie Van Leeuwenhoek10.1007/s10482-015-0551-y2015Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Norway, Nucleic Acid Hybridization, Pecten/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics

Reference

@idauthorstitledoi/urlcatalogueID_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
22097Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-100316Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100316)
30216Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172656028776041
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
68369Automatically annotated from API 20NE
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
89024Reimer, 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-ID369643.1