Strain identifier

BacDive ID: 5715

Type strain: Yes

Species: Bizionia echini

Strain history: <- OI Nedashkovskaya, Pacific Institute of Bioorganic Chemistry, Russia

NCBI tax ID(s): 649333 (species)

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

@ref: 17308

BacDive-ID: 5715

DSM-Number: 23925

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

description: Bizionia echini DSM 23925 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea urchin Strongylocentrotus intermedius.

NCBI tax id

  • NCBI tax id: 649333
  • Matching level: species

strain history

@refhistory
17308<- KCTC <- O. I. Nedashkovskaya, Pacific Inst. Bioorg. Chem., RAS, Vladivostok, Russia
67771<- OI Nedashkovskaya, Pacific Institute of Bioorganic Chemistry, Russia

doi: 10.13145/bacdive5715.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Bizionia
  • species: Bizionia echini
  • full scientific name: Bizionia echini Nedashkovskaya et al. 2010
  • synonyms

    • @ref: 20215
    • synonym: Algorimicrobium echini

@ref: 17308

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Bizionia

species: Bizionia echini

full scientific name: Bizionia echini Nedashkovskaya et al. 2010

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
29440negative1.4-3.5 µm0.4-0.5 µmrod-shapedyesgliding
67771rod-shapedno
67771negative
69480negative99.985

pigmentation

  • @ref: 29440
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 17308
  • 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
17308positivegrowth28mesophilic
29440positivegrowth04-39
29440positiveoptimum30-37mesophilic
67771positivegrowth28mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29440aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.999

halophily

@refsaltgrowthtested relationconcentration
29440NaClpositivegrowth01-08 %
29440NaClpositiveoptimum02-03 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2944016947citrate+carbon source
2944017234glucose+carbon source
2944037684mannose+carbon source

metabolite production

  • @ref: 29440
  • Chebi-ID: 16136
  • metabolite: hydrogen sulfide
  • production: yes

enzymes

@refvalueactivityec
29440alkaline phosphatase+3.1.3.1
29440catalase+1.11.1.6
29440cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
17308sea urchin Strongylocentrotus intermediusStrongylocentrotus intermediusSea of Japan, Gulf of Peter the Great, Troitsa BayRussiaRUSAsia
67771From sea urchin `Strongylocentrotus intermedius`Troitsa Bay, Gulf of Peter the Great, East SeaRussiaRUSAsia

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Echinodermata
#Environmental#Aquatic#Marine

taxonmaps

  • @ref: 69479
  • File name: preview.99_7030.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_107;96_2813;97_3454;98_5165;99_7030&stattab=map
  • Last taxonomy: Bizionia
  • 16S sequence: FJ716799
  • Sequence Identity:
  • Total samples: 760
  • soil counts: 12
  • aquatic counts: 616
  • animal counts: 125
  • plant counts: 7

Safety information

risk assessment

  • @ref: 17308
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 17308
  • description: Bizionia echini 16S ribosomal RNA gene, partial sequence
  • accession: FJ716799
  • length: 1478
  • database: ena
  • NCBI tax ID: 649333

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Bizionia echini DSM 23925GCA_900115185scaffoldncbi649333
66792Bizionia echini strain DSM 23925649333.4wgspatric649333
66792Bizionia echini DSM 239252622736504draftimg649333

GC content

@refGC-contentmethod
1730834.4thermal denaturation, midpoint method (Tm)
2944034.4

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno88.535yes
flagellatedno95.096yes
gram-positiveno98.195yes
anaerobicno99.364yes
aerobicyes91.569no
halophileno69.093no
spore-formingno95.475no
glucose-fermentno91.694no
thermophileno98.284no
glucose-utilyes83.818no

External links

@ref: 17308

culture collection no.: DSM 23925, KCTC 22015, KMM 6177, LMG 25220

straininfo link

  • @ref: 75197
  • straininfo: 264738

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19661492Bizionia echini sp. nov., isolated from a sea urchin.Nedashkovskaya OI, Vancanneyt M, Kim SBInt J Syst Evol Microbiol10.1099/ijs.0.013193-02009Animals, Bacterial Typing Techniques, Base Composition, DNA, Ribosomal/analysis/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Genes, rRNA, Genotype, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Sequence Analysis, DNA, Species SpecificityGenetics
Phylogeny25103949Bizionia psychrotolerans sp. nov., a psychrophilic bacterium isolated from the intestine of a sea cucumber (Apostichopus japonicus).Song EJ, Lee MH, Seo MJ, Yim KJ, Hyun DW, Bae JW, Park SL, Roh SW, Nam YDAntonie Van Leeuwenhoek10.1007/s10482-014-0253-x2014Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification/physiology, Hydrogen-Ion Concentration, Intestines/microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sea Cucumbers/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature, Vitamin K 2/analysisGenetics
Phylogeny30303476Hanstruepera crassostreae sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from an oyster.He RH, Liang QY, Zhao JX, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0030532018Animals, Bacterial Typing Techniques, Base Composition, China, Crassostrea/*microbiology, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmed
17308Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 23925)https://www.dsmz.de/collection/catalogue/details/culture/DSM-23925
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
29440Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2584628776041
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
75197Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID264738.1StrainInfo: A central database for resolving microbial strain identifiers