Strain identifier

BacDive ID: 17321

Type strain: Yes

Species: Vibrio fluvialis

Strain Designation: VL 5125

Strain history: NCTC 11327 <-- J. V. Lee VL 5125 <-- I. Hug 30.

NCBI tax ID(s): 1219074 (strain), 676 (species)

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

@ref: 7995

BacDive-ID: 17321

DSM-Number: 19283

keywords: Bacteria, 16S sequence, genome sequence, mesophilic

description: Vibrio fluvialis VL 5125 is a mesophilic bacterium that was isolated from human faeces, diarrhoea.

NCBI tax id

NCBI tax idMatching level
1219074strain
676species

strain history

doi: 10.13145/bacdive17321.20220920.7

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 fluvialis
  • full scientific name: Vibrio fluvialis Lee et al. 1981
  • synonyms

    • @ref: 20215
    • synonym: Allomonas enterica

@ref: 7995

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio fluvialis

full scientific name: Vibrio fluvialis Lee et al. 1981

strain designation: VL 5125

type strain: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7995BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://bacmedia.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
41864Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)

culture temp

@refgrowthtypetemperaturerange
7995positivegrowth30mesophilic
41864positivegrowth25mesophilic
67770positivegrowth30mesophilic

Physiology and metabolism

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

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

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

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7995++++--++++++++++-++-+

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7995human faeces, diarrhoeaDaccaBangladeshBGDAsia
67770Human fecesDaccaBangladeshBGDAsia

isolation source categories

Cat1Cat2Cat3
#Host#Human
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

  • @ref: 7995
  • biosafety level: 2
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio fluvialis DNA, 16S-23S rRNA intergenic spacer and 23S rRNA, partial sequence, strain: IAM 14403AB255719256ena676
20218Vibrio fluvialis strain ATCC 33809 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu gene, complete sequenceAF413005482ena676
20218Vibrio fluvialis 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu and tRNA-Val genes, complete sequenceAF413006679ena676
20218Vibrio fluvialis strain ATCC 33809 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Glu, tRNA-Ala, and tRNA-Val genes, complete sequenceAF413007710ena676
20218Vibrio fluvialis strain ATCC 33809 16S-23S ribosomal RNA intergenic spacer, partial sequence; tRNA-Ile and tRNA-Ala genes, complete sequenceAF413008557ena676
20218Vibrio fluvialis strain ATCC 33809 16S ribosomal RNA gene, partial sequenceGU048832460ena676
20218Vibrio fluvialis strain NCTC 11327 clone XMYP7 16S ribosomal RNA gene, partial sequenceJX0091431291ena676
20218V.fluvialis (NCTC 11327 T) 16S rRNA geneX763351537ena676
7995V.fluvialis (ATCC 33809T) gene for 16S ribosomal RNAX747031457ena676
67770Vibrio fluvialis gene for 16S ribosomal RNA, partial cds, strain: JCM 1281LC0501781475ena676

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio fluvialis ATCC 33809GCA_001558415completencbi676
66792Vibrio fluvialis NCTC11327GCA_900460245contigncbi676
66792Vibrio fluvialis NBRC 103150 NBRC 103150GCA_001598835contigncbi1219074
66792Vibrio fluvialis NCTC 11327GCA_001890655scaffoldncbi676
66792Vibrio fluvialis NBRC 1031501219074.3wgspatric1219074
66792Vibrio fluvialis strain ATCC 33809676.24completepatric676
66792Vibrio fluvialis strain NCTC 11327676.29wgspatric676
66792Vibrio fluvialis strain NCTC11327676.75wgspatric676
66792Vibrio fluvialis ATCC 338092718218390completeimg676
66792Vibrio fluvialis NBRC 1031502681812983draftimg1219074
67770Vibrio fluvialis NBRC 103150, whole genome shotgun sequencing projectBCZR00000000ncbi1219074
67770Vibrio fluvialis strain ATCC 33809 chromosome 1, complete sequenceCP014034ena676
67770Vibrio fluvialis strain ATCC 33809 chromosome 2, complete sequenceCP014035ena676
67770Vibrio fluvialis strain NCTC 11327, whole genome shotgun sequencing projectLMTE00000000ncbi676
67770Vibrio fluvialis strain NCTC11327, whole genome shotgun sequencing projectUHIP00000000ncbi676

GC content

  • @ref: 67770
  • GC-content: 50
  • method: thermal denaturation, midpoint method (Tm)

External links

@ref: 7995

culture collection no.: DSM 19283, ATCC 33809, CCM 3689, CCTM La 3552, CCUG 13622, CDC 9555-78, IAM 14403, JCM 3752, LMG 7894, NCIMB 2249, NCTC 11327, WDCM 00137, JCM 1281, BCRC 12830, CAIM 593, CCUG 15268, CCUG 20252, CDC 9555-18, CECT 4217, CGMCC 1.1608, CIP 103355, KCTC 2473, NBRC 103150, NRIC 0818

straininfo link

@refpassport
20218http://www.straininfo.net/strains/857699
20218http://www.straininfo.net/strains/22423
20218http://www.straininfo.net/strains/221202
20218http://www.straininfo.net/strains/221203
20218http://www.straininfo.net/strains/22425
20218http://www.straininfo.net/strains/147339
20218http://www.straininfo.net/strains/221204
20218http://www.straininfo.net/strains/156151
20218http://www.straininfo.net/strains/22422
20218http://www.straininfo.net/strains/206200
20218http://www.straininfo.net/strains/22429
20218http://www.straininfo.net/strains/841431
20218http://www.straininfo.net/strains/866289

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18599703Vibrio porteresiae sp. nov., a diazotrophic bacterium isolated from a mangrove-associated wild rice (Porteresia coarctata Tateoka).Rameshkumar N, Fukui Y, Sawabe T, Nair SInt J Syst Evol Microbiol10.1099/ijs.0.65604-02008Molecular Sequence Data, *Nitrogen Fixation, Oryza/*microbiology, Oxidoreductases/genetics, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity, Verbenaceae, Vibrio/*classification/genetics/isolation & purificationGenetics
Enzymology29375513High Hydrostatic Pressure Inducible Trimethylamine N-Oxide Reductase Improves the Pressure Tolerance of Piezosensitive Bacteria Vibrio fluvialis.Yin QJ, Zhang WJ, Qi XQ, Zhang SD, Jiang T, Li XG, Chen Y, Santini CL, Zhou H, Chou IM, Wu LFFront Microbiol10.3389/fmicb.2017.026462018
Phylogeny31702534Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea.Li Y, Liang J, Liu R, Xue CX, Zhou S, He X, Li B, Wang X, Zhang XHInt J Syst Evol Microbiol10.1099/ijsem.0.0038422020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vibrio/*classification/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
7995Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19283)https://www.dsmz.de/collection/catalogue/details/culture/DSM-19283
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
41864Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/15143
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/
68369Automatically annotated from API 20NE