Strain identifier

BacDive ID: 139663

Type strain: Yes

Species: Aequorivita vladivostokensis

Strain history: CIP <- 2005, KMM

NCBI tax ID(s): 171194 (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 8.1 (current version)

General

@ref: 42261

BacDive-ID: 139663

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

description: Aequorivita vladivostokensis CIP 108845 is a mesophilic, Gram-negative bacterium of the family Flavobacteriaceae.

NCBI tax id

  • NCBI tax id: 171194
  • Matching level: species

strain history

@refhistory
422612005, KMM
67770M. Suzuki R3516 <-- O. I. Nedashkovskaya.
42261CIP <- 2005, KMM

doi: 10.13145/bacdive139663.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aequorivita
  • species: Aequorivita vladivostokensis
  • full scientific name: Aequorivita vladivostokensis (Nedashkovskaya et al. 2003) Hahnke et al. 2017

  • synonyms

    • @ref: 20215
    • synonym: Vitellibacter vladivostokensis

@ref: 42261

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aequorivita

species: Aequorivita vladivostokensis

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.996
42261negativerod-shapedno

colony morphology

  • @ref: 42261

pigmentation

  • @ref: 42261
  • production: yes
  • name: Flexirubin

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
42261Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
42261CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
42261CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72

culture temp

@refgrowthtypetemperaturerange
42261positivegrowth25mesophilic
67770positivegrowth25mesophilic
42261positivegrowth15-37
42261nogrowth5psychrophilic
42261nogrowth41thermophilic
42261nogrowth45thermophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.991

halophily

  • @ref: 42261
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

observation

  • @ref: 67770
  • observation: quinones: MK-6

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
422614853esculin-hydrolysis
42261606565hippurate+hydrolysis
4226117632nitrate-reduction
4226116301nitrite-reduction
4226115792malonate-assimilation
4226117632nitrate-respiration

metabolite production

  • @ref: 42261
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testmethylred-test
4226115688acetoin-
4226117234glucose-

enzymes

@refvalueactivityec
42261oxidase-
42261beta-galactosidase+3.2.1.23
42261alcohol dehydrogenase-1.1.1.1
42261gelatinase+
42261amylase-
42261caseinase+3.4.21.50
42261catalase+1.11.1.6
42261tween esterase+
42261gamma-glutamyltransferase+2.3.2.2
42261lecithinase-
42261lipase-
42261lysine decarboxylase-4.1.1.18
42261ornithine decarboxylase-4.1.1.17
42261phenylalanine ammonia-lyase+4.3.1.24
42261protease+
42261tryptophan deaminase-
42261urease-3.5.1.5
68382alkaline phosphatase+3.1.3.1
68382esterase (C 4)+
68382esterase lipase (C 8)+
68382lipase (C 14)-
68382leucine arylamidase+3.4.11.1
68382valine arylamidase+
68382cystine arylamidase-3.4.11.3
68382trypsin+3.4.21.4
68382alpha-chymotrypsin+3.4.21.1
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-galactosidase-3.2.1.22
68382beta-galactosidase-3.2.1.23
68382beta-glucuronidase-3.2.1.31
68382alpha-glucosidase-3.2.1.20
68382beta-glucosidase-3.2.1.21
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382alpha-mannosidase-3.2.1.24
68382alpha-fucosidase-3.2.1.51

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
42261-+++-++-++++--------

Isolation, sampling and environmental information

isolation

@refgeographic locationcountryorigin.countrysample typehost speciescontinentisolation date
42261Troitsa baySea of JapanRUS
67770Sea of JapanHolothurian (Apostichopus japonicus) collected from Troitsa Bay in the Gulf of Peter the GreatApostichopus japonicus
42261Troitsa bay, Sea of JapanRussian FederationRUSHolothurian, Apostichopus japonicusEurope1997

taxonmaps

  • @ref: 69479
  • File name: preview.99_4389.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_74;96_535;97_2658;98_3295;99_4389&stattab=map
  • Last taxonomy: Aequorivita
  • 16S sequence: AB071382
  • Sequence Identity:
  • Total samples: 997
  • soil counts: 138
  • aquatic counts: 702
  • animal counts: 135
  • plant counts: 22

Safety information

risk assessment

  • @ref: 42261
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 67770
  • description: Vitellibacter vladivostokensis gene for 16S rRNA, partial sequence
  • accession: AB071382
  • length: 1400
  • database: ena
  • NCBI tax ID: 171194

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aequorivita vladivostokensis strain KMM 3516171194.13wgspatric171194
66792Aequorivita vladivostokensis KMM 35162627853707draftimg171194
67770Aequorivita vladivostokensis KMM 3516GCA_000952855contigncbi171194

GC content

  • @ref: 67770
  • GC-content: 41.3
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno85.567no
gram-positiveno98.503no
anaerobicno99.182no
aerobicyes92.33no
halophileyes66.421no
spore-formingno94.926no
thermophileno99.342yes
glucose-utilyes75.138no
flagellatedno95.188no
glucose-fermentno91.914no

External links

@ref: 42261

culture collection no.: CIP 108845, KMM 3516, IFO 16718, NBRC 16718, JCM 11732

straininfo link

  • @ref: 96123
  • straininfo: 99606

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny13130007Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga-Flavobacterium-Bacteroides.Nedashkovskaya OI, Suzuki M, Vysotskii MV, Mikhailov VVInt J Syst Evol Microbiol10.1099/ijs.0.02302-02003Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification/metabolism, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/microbiologyGenetics
Phylogeny25870254Vitellibacter echinoideorum sp. nov., isolated from a sea urchin (Tripneustes gratilla).Lin SY, Hameed A, Wen CZ, Liu YC, Hsu YH, Shen FT, Lai WA, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.0002582015Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phosphatidylethanolamines/chemistry, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sea Urchins/*microbiology, Seafood/*microbiology, Sequence Analysis, DNA, Taiwan, Vitamin K 2/analogs & derivatives/chemistryGenetics
Genetics25957696Draft genome sequence of Vitellibacter vladivostokensis KMM 3516(T): a protease-producing bacterium.Thevarajoo S, Selvaratnam C, Chan KG, Goh KM, Chong CSMar Genomics10.1016/j.margen.2015.04.0092015Bacterial Proteins/genetics/*metabolism, Bacteroidetes/*genetics, Gene Expression Regulation, Bacterial/physiology, Gene Expression Regulation, Enzymologic/physiology, Genome, Bacterial/*genetics, Peptide Hydrolases/genetics/*metabolismMetabolism
Phylogeny35133258Aequorivita iocasae sp. nov., a halophilic bacterium isolated from sediment collected at a cold seep field in the South China Sea.Zhang H, Wang H, Cao L, Chen H, Zhong Z, Wang M, Lian C, Liu R, Zhou L, Li CInt J Syst Evol Microbiol10.1099/ijsem.0.0051992022Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Flavobacteriaceae/*classification/isolation & purification, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
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
42261Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108845Collection of Institut Pasteur (CIP 108845)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68382Automatically annotated from API zym
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
96123Reimer, 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-ID99606.1