Strain identifier

BacDive ID: 17307

Type strain: Yes

Species: Vibrio rotiferianus

Strain Designation: R-14939, RFT 16

Strain history: CIP <- 2003, B. Gomez Gil, CIAD, Mazatlan, Mexico

NCBI tax ID(s): 1224743 (strain), 190895 (species)

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General

@ref: 6719

BacDive-ID: 17307

DSM-Number: 17186

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

description: Vibrio rotiferianus R-14939 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from rotifer Brachionus plicatilis culture.

NCBI tax id

NCBI tax idMatching level
1224743strain
190895species

strain history

@refhistory
6719<- CAIM <- LMG <- F. L. Thompson <- J. Vandenberghe
122269CIP <- 2003, B. Gomez Gil, CIAD, Mazatlan, Mexico

doi: 10.13145/bacdive17307.20230509.8.1

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 rotiferianus
  • full scientific name: Vibrio rotiferianus Gomez-Gil et al. 2003

@ref: 6719

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio rotiferianus

full scientific name: Vibrio rotiferianus Gomez-Gil et al. 2003

strain designation: R-14939, RFT 16

type strain: yes

Morphology

cell morphology

  • @ref: 122269
  • gram stain: negative
  • cell shape: rod-shaped
  • motility: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6719BACTO 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
33181Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
122269CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6719positivegrowth28mesophilic
33181positivegrowth25mesophilic
122269positivegrowth15-37
122269nogrowth5psychrophilic
122269nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 122269
  • oxygen tolerance: facultative anaerobe

halophily

@refsaltgrowthtested relationconcentration
122269NaClpositivegrowth2-8 %
122269NaClnogrowth0 %
122269NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
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
12226916947citrate-carbon source
1222694853esculin+hydrolysis
12226917234glucose+fermentation
12226917716lactose-fermentation
12226917632nitrate+reduction
12226916301nitrite-reduction
122269132112sodium thiosulfate-builds gas from
12226917632nitrate+respiration

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12226935581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
12226915688acetoin-
12226917234glucose+

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase+3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
122269oxidase+
122269beta-galactosidase+3.2.1.23
122269alcohol dehydrogenase-1.1.1.1
122269gelatinase+/-
122269amylase+
122269caseinase+3.4.21.50
122269catalase+1.11.1.6
122269tween esterase+
122269gamma-glutamyltransferase+2.3.2.2
122269lecithinase+
122269lipase+
122269lysine decarboxylase+4.1.1.18
122269ornithine decarboxylase+4.1.1.17
122269phenylalanine ammonia-lyase-4.3.1.24
122269tryptophan deaminase-
122269urease-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
122269-++--++-++++-----+--

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6719+++--+++++++++++-+--+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
122269--+---+-+----++---+++-----------+-+--------------+----+----++--------------+---++-----+--++++++----

Isolation, sampling and environmental information

isolation

@refsample typehost speciescountryorigin.countrycontinentgeographic locationisolation date
6719rotifer Brachionus plicatilis cultureBrachionus plicatilisBelgiumBELEurope
122269Brachionus plicatilis culturesBelgiumBELEuropeGhent1999

isolation source categories

  • Cat1: #Host
  • Cat2: #Other

taxonmaps

  • @ref: 69479
  • File name: preview.99_89.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_74;98_81;99_89&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: AJ316187
  • Sequence Identity:
  • Total samples: 5164
  • soil counts: 169
  • aquatic counts: 3075
  • animal counts: 1856
  • plant counts: 64

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67191Risk group (German classification)
1222692Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6719
  • description: Vibrio rotiferatus 16S rRNA gene, type strain LMG 21460T
  • accession: AJ316187
  • length: 1468
  • database: ena
  • NCBI tax ID: 1224743

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio rotiferianus CAIM 577 = LMG 21460GCA_002741985contigncbi1224743
66792Vibrio rotiferianus CAIM 577 = LMG 214601224743.3wgspatric1224743
66792Vibrio rotiferianus CAIM 577 = LMG 214601224743.12wgspatric1224743
66792Vibrio rotiferianus CAIM 5772579778863draftimg1224743
66792Vibrio rotiferianus CAIM 577 = LMG 21460GCA_000400405scaffoldncbi1224743

GC content

@refGC-contentmethod
671944.2sequence analysis
671944.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileyes91.715no
flagellatedyes89.393no
gram-positiveno98.751no
anaerobicno97.548no
aerobicyes82.717no
halophileyes53.058no
spore-formingno92.831no
thermophileno99.583yes
glucose-utilyes91.308yes
glucose-fermentyes89.321yes

External links

@ref: 6719

culture collection no.: DSM 17186, CAIM 577, LMG 21460, CIP 107930, KCTC 12125

straininfo link

  • @ref: 86307
  • straininfo: 29151

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656179Vibrio rotiferianus sp. nov., isolated from cultures of the rotifer Brachionus plicatilis.Gomez-Gil B, Thompson FL, Thompson CC, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02430-02003Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rotifera/*microbiology, Species Specificity, Vibrio/*classification/genetics/*isolation & purification/metabolismGenetics
Phylogeny20002183Vibrio owensii sp. nov., isolated from cultured crustaceans in Australia.Cano-Gomez A, Goulden EF, Owens L, Hoj LFEMS Microbiol Lett10.1111/j.1574-6968.2009.01850.x2009Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Palinuridae/*microbiology, Penaeidae/*microbiology, Phylogeny, Queensland, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/chemistry/*classification/genetics/*isolation & purificationGenetics
Genetics23710045Taxonomic revision of Harveyi clade bacteria (family Vibrionaceae) based on analysis of whole genome sequences.Urbanczyk H, Ogura Y, Hayashi TInt J Syst Evol Microbiol10.1099/ijs.0.051110-02013Bacterial Typing Techniques, DNA, Bacterial/genetics, *Genome, Bacterial, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Vibrio/*classification/geneticsPhylogeny
Genetics26476690Complete genome sequence of a giant Vibrio bacteriophage VH7D.Luo ZH, Yu YP, Jost G, Xu W, Huang XLMar Genomics10.1016/j.margen.2015.10.0052015Bacteriophages/classification/*genetics, Gene Expression Regulation, Viral, *Genome, Viral, Molecular Sequence Data, RNA, Viral/*genetics, Species Specificity, Vibrio/*virology, Viral Proteins/genetics/metabolismPhylogeny
Phylogeny30851004First report of isolation and complete genome of Vibrio rotiferianus strain SSVR1601 from cage-cultured black rockfish (Sebastes schlegelii) associated with skin ulcer.Zhang Z, Yu YX, Jiang Y, Wang YG, Liao MJ, Rong XJ, Wang K, Zhang H, Chen JJ Fish Dis10.1111/jfd.129632019Animals, Fish Diseases/microbiology/*pathology, *Fishes, *Genome, Bacterial, Phylogeny, Sequence Analysis, DNA/veterinary, Skin Ulcer/microbiology/pathology/*veterinary, Vibrio/classification/*genetics/*pathogenicity, Vibrio Infections/microbiology/pathology/*veterinaryGenetics

Reference

@idauthorscataloguedoi/urltitle
6719Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17186)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17186
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
33181Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5496
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)
68369Automatically annotated from API 20NE
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
86307Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID29151.1StrainInfo: A central database for resolving microbial strain identifiers
122269Curators of the CIPCollection of Institut Pasteur (CIP 107930)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107930