Strain identifier

BacDive ID: 17342

Type strain: Yes

Species: Vibrio rarus

Strain Designation: RW22

Strain history: CIP <- 2007, NBRC <- 2006, T. Sawabe, Hokkaido Univ., Hokkaido, Japan: strain RW22

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

@ref: 8239

BacDive-ID: 17342

DSM-Number: 19662

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

description: Vibrio rarus RW22 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of abalone Haliotis rufescens.

NCBI tax id

NCBI tax idMatching level
413403species
1219063strain

strain history

@refhistory
8239<- T. Sawabe, Faculty of Fisheries Sciences, Hokkaido; RW22
122140CIP <- 2007, NBRC <- 2006, T. Sawabe, Hokkaido Univ., Hokkaido, Japan: strain RW22

doi: 10.13145/bacdive17342.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio rarus
  • full scientific name: Vibrio rarus Sawabe et al. 2007

@ref: 8239

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio rarus

full scientific name: Vibrio rarus Sawabe et al. 2007

strain designation: RW22

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
32001negative1.5 µm0.75 µmrod-shapedno
122140negativerod-shapedno

pigmentation

  • @ref: 32001
  • production: no

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
8239BACTO 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
37653Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122140CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
8239positivegrowth28mesophilic
32001positivegrowth15-30
37653positivegrowth20psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 32001
  • oxygen tolerance: facultative anaerobe

spore formation

  • @ref: 32001
  • spore formation: no

halophily

  • @ref: 32001
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: <6 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3200130089acetate+carbon source
3200117057cellobiose+carbon source
3200124265gluconate+carbon source
3200117234glucose+carbon source
3200129987glutamate+carbon source
3200117306maltose+carbon source
3200129864mannitol+carbon source
3200137684mannose+carbon source
32001506227N-acetylglucosamine+carbon source
3200126271proline+carbon source
3200115361pyruvate+carbon source
3200130911sorbitol+carbon source
3200130031succinate+carbon source
3200117992sucrose+carbon source
3200118222xylose+carbon source
3200117632nitrate+reduction
12214017632nitrate+reduction
12214016301nitrite-reduction

metabolite production

@refChebi-IDmetaboliteproduction
3200135581indoleyes
12214035581indoleno

metabolite tests

  • @ref: 32001
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
32001catalase+1.11.1.6
32001cytochrome oxidase+1.9.3.1
122140oxidase+
122140catalase+1.11.1.6
122140urease-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
122140-++--+-----+--------

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
8239gut of abalone Haliotis rufescensHaliotis rufescensLa JollaUSAUSANorth America
122140Gut, Californian abalone Haliotis rufescenceLa Jolla, CaliforniaUnited States of AmericaUSANorth America2005

isolation source categories

Cat1Cat2Cat3
#Host#Invertebrates (Other)#Mollusca
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_75043.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_40270;98_52471;99_75043&stattab=map
  • Last taxonomy: Vibrio rarus subclade
  • 16S sequence: AB681696
  • Sequence Identity:
  • Total samples: 386
  • soil counts: 6
  • aquatic counts: 141
  • animal counts: 233
  • plant counts: 6

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
82391Risk group (German classification)
1221402Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio rarus gene for 16S rRNA, partial sequence, strain: NBRC 102084AB6816961495ena413403
8239Vibrio rarus strain RW22 16S ribosomal RNA gene, partial sequenceDQ9142391403ena413403

Genome sequences

  • @ref: 66792
  • description: Vibrio rarus LMG 23674
  • accession: GCA_024347075
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 413403

GC content

  • @ref: 32001
  • GC-content: 43.8

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno90.518yes
gram-positiveno98.338yes
anaerobicno95.984yes
aerobicyes51.512yes
halophileyes86.104yes
spore-formingno96.252yes
motileno86.451yes
glucose-fermentyes83.39no
thermophileno99.335no
glucose-utilyes88.161yes

External links

@ref: 8239

culture collection no.: DSM 19662, LMG 23674, NBRC 102084, CIP 109638

straininfo link

  • @ref: 86342
  • straininfo: 307807

literature

  • topic: Phylogeny
  • Pubmed-ID: 17473233
  • title: Vibrio comitans sp. nov., Vibrio rarus sp. nov. and Vibrio inusitatus sp. nov., from the gut of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens.
  • authors: Sawabe T, Fujimura Y, Niwa K, Aono H
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.64789-0
  • year: 2007
  • mesh: Adhesins, Bacterial/genetics, Aerobiosis, Alginates/metabolism, Anaerobiosis, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gastrointestinal Tract/microbiology, Gastropoda/*microbiology, Genes, rRNA/genetics, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vibrio/*classification/*isolation & purification/metabolism
  • topic2: Metabolism

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
8239Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19662)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19662
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
32001Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604128255
37653Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7404
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)
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.https://microbeatlas.org/MicrobeAtlas 1.0 beta
86342Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID307807.1StrainInfo: A central database for resolving microbial strain identifiers
122140Curators of the CIPCollection of Institut Pasteur (CIP 109638)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109638