Strain identifier

BacDive ID: 17321

Type strain: Yes

Species: Vibrio fluvialis

Strain Designation: VL 5125, 5125

Strain history: CIP <- 1989, NCTC <- 1979, J.V. Lee, Preston Hall Hosp., Maidston, UK: strain VL5125, Group F Vibrio <- Cholera Res. Lab., Dacca Bangladesh

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

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General

@ref: 7995

BacDive-ID: 17321

DSM-Number: 19283

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, motile

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

NCBI tax id

NCBI tax idMatching level
676species
1219074strain

strain history

@refhistory
7995<- CCM; CCM 3689 <- J. V. Lee; 5125
67770NCTC 11327 <-- J. V. Lee VL 5125 <-- I. Hug 30.
119414CIP <- 1989, NCTC <- 1979, J.V. Lee, Preston Hall Hosp., Maidston, UK: strain VL5125, Group F Vibrio <- Cholera Res. Lab., Dacca Bangladesh

doi: 10.13145/bacdive17321.20230509.8.1

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 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, 5125

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram staincell shape
69480yes96.489
6948099.98negative
119414yesnegativerod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7995BACTO 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
7995COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium693.pdf
7995TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://www.dsmz.de/microorganisms/medium/pdf/DSMZ_Medium92.pdf
41864Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119414CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
7995positivegrowth30mesophilic
41864positivegrowth25mesophilic
67770positivegrowth30mesophilic
119414positivegrowth15-41
119414nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 119414
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.959

halophily

  • @ref: 119414
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 0-10 %

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
6836830849L-arabinose-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis
11941416947citrate+carbon source
1194144853esculin+hydrolysis
11941417234glucose+fermentation
11941417716lactose-fermentation
11941417632nitrate+reduction
11941416301nitrite-reduction
119414132112sodium thiosulfate-builds gas from
11941417632nitrate+respiration

antibiotic resistance

  • @ref: 119414
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11941435581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
6836815688acetoin-
6836835581indole+
11941415688acetoin-
11941417234glucose+

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
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase+3.2.1.23
119414oxidase+
119414beta-galactosidase+3.2.1.23
119414alcohol dehydrogenase-1.1.1.1
119414gelatinase+
119414amylase+
119414DNase+
119414caseinase+3.4.21.50
119414catalase+1.11.1.6
119414tween esterase+
119414gamma-glutamyltransferase+2.3.2.2
119414lecithinase+
119414lipase+
119414lysine decarboxylase-4.1.1.18
119414ornithine decarboxylase-4.1.1.17
119414phenylalanine ammonia-lyase-4.3.1.24
119414protease+
119414tryptophan deaminase-
119414urease-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
119414-++++++---++-+-+++--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
7995++------+--+/-+-----+/--+

API 20NE

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

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
119414+++++--+-++--+-++++++-----+----+-+---------------++--+++---++-+++--------+-++++++-+---+-+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentlatitudelongitude
7995human faeces, diarrhoeaDaccaBangladeshBGDAsia23.710490.4074
67770Human fecesDaccaBangladeshBGDAsia
119414Human, FecesDhakaBangladeshBGDAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_418.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_312;98_347;99_418&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: LC050178
  • Sequence Identity:
  • Total samples: 3818
  • soil counts: 168
  • aquatic counts: 1720
  • animal counts: 1806
  • plant counts: 124

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
79952Risk group (German classification)
1194142Risk group (French 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 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 103150GCA_001598835contigncbi1219074
67770Vibrio fluvialis NCTC 11327GCA_001890655scaffoldncbi676
67770Vibrio fluvialis NCTC11327GCA_900460245contigncbi676

GC content

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

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedyes90.574no
flagellatedyes90.574no
gram-positiveno98.87no
gram-positiveno98.87no
anaerobicno97.724no
anaerobicno97.724no
aerobicyes84.613no
aerobicyes84.613no
halophileno54.622no
halophileno54.622no
spore-formingno94.788no
spore-formingno94.788no
thermophileno99.403yes
thermophileno99.403yes
glucose-utilyes91.639no
glucose-utilyes91.639no
motileyes91.933no
motileyes91.933no
glucose-fermentyes88.213no
glucose-fermentyes88.213no

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

  • @ref: 86321
  • straininfo: 389395

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
Phylogeny36269578Vibrio ostreae sp. nov., a novel gut bacterium isolated from a Yellow Sea oyster.Muhammad N, Nguyen TTH, Lee YJ, Ko J, Avila F, Kim SGInt J Syst Evol Microbiol10.1099/ijsem.0.0055862022Animals, Bacterial Typing Techniques, Base Composition, Cardiolipins, Catalase/genetics, DNA, Bacterial/genetics, Fatty Acids/chemistry, Nucleotides, *Ostreidae/microbiology, Phosphatidylethanolamines, Phospholipids/chemistry, Phylogeny, Quinones, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride, *Vibrio/genetics/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/
68368Automatically annotated from API 20E
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
86321Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID389395.1StrainInfo: A central database for resolving microbial strain identifiers
119414Curators of the CIPCollection of Institut Pasteur (CIP 103355)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20103355