Strain identifier

BacDive ID: 13736

Type strain: Yes

Species: Pseudovibrio ascidiaceicola

Strain Designation: F423

Strain history: <- M Kurahashi, IAM, Japan

NCBI tax ID(s): 285279 (species)

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General

@ref: 6425

BacDive-ID: 13736

DSM-Number: 16392

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

description: Pseudovibrio ascidiaceicola F423 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sea squirt Polycitor proliferus.

NCBI tax id

  • NCBI tax id: 285279
  • Matching level: species

strain history

@refhistory
6425<- M. Kurahashi <- Y. Fukunaga; F423
67770IAM 15084 <-- Y. Fukunaga F423.
67771<- M Kurahashi, IAM, Japan

doi: 10.13145/bacdive13736.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Stappiaceae
  • genus: Pseudovibrio
  • species: Pseudovibrio ascidiaceicola
  • full scientific name: Pseudovibrio ascidiaceicola Fukunaga et al. 2006

@ref: 6425

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Stappiaceae

genus: Pseudovibrio

species: Pseudovibrio ascidiaceicola

full scientific name: Pseudovibrio ascidiaceicola Fukunaga et al. 2006

strain designation: F423

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
31604negative1.2-8 µm0.8-1.3 µmrod-shapedyes
67771negative

pigmentation

  • @ref: 31604
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 6425
  • 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
6425positivegrowth25mesophilic
31604positivegrowth10-30
31604positiveoptimum10-30
67770positivegrowth25mesophilic
67771positivegrowth23psychrophilic

culture pH

@refabilitytypepHPH range
31604positivegrowth05-09alkaliphile
31604positiveoptimum05-09

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31604aerobe
67771aerobe

spore formation

  • @ref: 31604
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
31604NaClpositivegrowth03-05 %
31604NaClpositiveoptimum03-05 %

observation

  • @ref: 31604
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3160416449alanine+carbon source
3160435391aspartate+carbon source
3160423652dextrin+carbon source
3160433984fucose+carbon source
3160428260galactose+carbon source
3160424265gluconate+carbon source
3160417234glucose+carbon source
3160429987glutamate+carbon source
3160417754glycerol+carbon source
3160424996lactate+carbon source
3160417306maltose+carbon source
3160437684mannose+carbon source
3160428053melibiose+carbon source
31604506227N-acetylglucosamine+carbon source
3160426271proline+carbon source
3160416634raffinose+carbon source
3160417822serine+carbon source
3160417992sucrose+carbon source
3160427082trehalose+carbon source
316044853esculin+hydrolysis

metabolite production

  • @ref: 31604
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 31604
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
31604catalase+1.11.1.6
31604cytochrome oxidase+1.9.3.1
31604urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
6425sea squirt Polycitor proliferusPolycitor proliferusBoso peninsulaJapanJPNAsia
67770Sea squirt, Polycitor proliferusPolycitor proliferusBoso peninsulaJapanJPNAsia
67771From `Polycitor proliferus`, ProtochordataKatsuura, ChibaJapanJPNAsia

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Tunicata

taxonmaps

  • @ref: 69479
  • File name: preview.99_919.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_441;97_504;98_579;99_919&stattab=map
  • Last taxonomy: Pseudovibrio
  • 16S sequence: AB681198
  • Sequence Identity:
  • Total samples: 1084
  • soil counts: 30
  • aquatic counts: 989
  • animal counts: 47
  • plant counts: 18

Safety information

risk assessment

  • @ref: 6425
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Pseudovibrio ascidiaceicola gene for 16S rRNA, partial sequence, strain: NBRC 100514AB6811981409ena285279
6425Pseudovibrio ascidiaceicola gene for 16S rRNA, partial sequenceAB1756631419ena285279

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudovibrio ascidiaceicola strain DSM 16392285279.6wgspatric285279
66792Pseudovibrio ascidiaceicola DSM 163922615840717draftimg285279
67770Pseudovibrio ascidiaceicola DSM 16392GCA_900114245scaffoldncbi285279

GC content

@refGC-contentmethod
642552.0
3160451.2
6777051.2high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes92.284no
gram-positiveno98.438no
anaerobicno97.896no
halophileyes53.523no
spore-formingno95.01no
glucose-utilyes92.582no
flagellatedyes63.82no
aerobicyes85.33yes
thermophileno96.902no
glucose-fermentno83.221no

External links

@ref: 6425

culture collection no.: DSM 16392, IAM 15084, KCTC 12308, NBRC 100514, JCM 21545

straininfo link

  • @ref: 82918
  • straininfo: 289982

literature

  • topic: Phylogeny
  • Pubmed-ID: 16449437
  • title: Pseudovibrio ascidiaceicola sp. nov., isolated from ascidians (sea squirts).
  • authors: Fukunaga Y, Kurahashi M, Tanaka K, Yanagi K, Yokota A, Harayama S
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.63879-0
  • year: 2006
  • mesh: Animals, Bacterial Typing Techniques, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification/physiology, Sequence Analysis, DNA, Urochordata/*microbiology
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6425Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16392)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16392
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
31604Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604127892
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/
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
82918Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID289982.1StrainInfo: A central database for resolving microbial strain identifiers