Strain identifier

BacDive ID: 17304

Type strain: Yes

Species: Vibrio xuii

Strain Designation: STD3-1071, R-15052, R129

Strain history: CIP <- 2004, B. Gomez-Gil, CAID, Mazatlan, Sinaloa, Mexico

NCBI tax ID(s): 170661 (species)

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General

@ref: 6718

BacDive-ID: 17304

DSM-Number: 17185

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

description: Vibrio xuii STD3-1071 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from shrimp culture water.

NCBI tax id

  • NCBI tax id: 170661
  • Matching level: species

strain history

@refhistory
6718<- CAIM <- F. L. Thompson; R-15052
67771<- DSM <- CAIM <- F L Thompson, R-15052
123991CIP <- 2004, B. Gomez-Gil, CAID, Mazatlan, Sinaloa, Mexico

doi: 10.13145/bacdive17304.20230509.8.1

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 xuii
  • full scientific name: Vibrio xuii Thompson et al. 2003

@ref: 6718

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio xuii

full scientific name: Vibrio xuii Thompson et al. 2003

strain designation: STD3-1071, R-15052, R129

type strain: yes

Morphology

cell morphology

@refgram stainmotilityconfidencecell shape
67771negative
69480yes95.854
69480negative99.988
123991negativenorod-shaped

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6718BACTO 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
37421MEDIUM 326 - for Cellulophaga balticayesDistilled water make up to (1000.000 ml);Sodium chloride (20.000 g);Tryptic soy agar (40.000 g)
123991CIP Medium 326yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=326

culture temp

@refgrowthtypetemperaturerange
6718positivegrowth28mesophilic
37421positivegrowth25mesophilic
67771positivegrowth28mesophilic
123991positivegrowth15-37
123991nogrowth5psychrophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
123991facultative anaerobe

spore formation

@refspore formationconfidence
69481no99
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
123991NaClpositivegrowth2-10 %
123991NaClnogrowth0 %

metabolite utilization

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
68371gluconate-builds acid from24265
68371L-arabitol-builds acid from18403
68371D-arabitol-builds acid from18333
68371L-fucose+builds acid from18287
68371D-fucose-builds acid from28847
68371D-tagatose-builds acid from16443
68371D-lyxose-builds acid from62318
68371turanose-builds acid from32528
68371gentiobiose-builds acid from28066
68371xylitol-builds acid from17151
68371glycogen+builds acid from28087
68371starch+builds acid from28017
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371trehalose+builds acid from27082
68371sucrose+builds acid from17992
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
68371maltose+builds acid from17306
68371cellobiose-builds acid from17057
68371salicin-builds acid from17814
68371esculin-builds acid from4853
68371arbutin-builds acid from18305
68371amygdalin-builds acid from27613
68371N-acetylglucosamine+builds acid from59640
68371methyl alpha-D-glucopyranoside-builds acid from320061
68371methyl alpha-D-mannoside-builds acid from43943
68371D-sorbitol-builds acid from17924
68371D-mannitol+builds acid from16899
68371myo-inositol-builds acid from17268
68371galactitol-builds acid from16813
68371L-rhamnose-builds acid from62345
68371L-sorbose-builds acid from17266
68371D-mannose+builds acid from16024
68371D-fructose+builds acid from15824
68371D-glucose+builds acid from17634
68371D-galactose-builds acid from12936
68371methyl beta-D-xylopyranoside-builds acid from74863
68371ribitol-builds acid from15963
68371L-xylose-builds acid from65328
68371D-xylose-builds acid from65327
68371D-ribose+builds acid from16988
68371L-arabinose+builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
68369malate+assimilation25115
68369adipate-assimilation17128
68369decanoate+assimilation27689
68369gluconate+assimilation24265
68369maltose+assimilation17306
68369N-acetylglucosamine+assimilation59640
68369D-mannitol+assimilation16899
68369D-mannose+assimilation16024
68369L-arabinose+assimilation30849
68369D-glucose+assimilation17634
68369gelatin-hydrolysis5291
68369esculin-hydrolysis4853
68369urea-hydrolysis16199
68369arginine+hydrolysis29016
68369D-glucose+fermentation17634
68369tryptophan+energy source27897
68369nitrate+reduction17632
123991citrate-carbon source16947
123991esculin-hydrolysis4853
123991glucose+fermentation17234
123991lactose-fermentation17716
123991nitrate+reduction17632
123991nitrite-reduction16301
123991sodium thiosulfate-builds gas from132112

antibiotic resistance

  • @ref: 123991
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: no
  • is resistant: yes

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleyes
12399135581indoleyes

metabolite tests

@refChebi-IDmetaboliteindole testvoges-proskauer-testmethylred-test
6836935581indole+
12399115688acetoin-
12399117234glucose-

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
123991oxidase+
123991beta-galactosidase-3.2.1.23
123991alcohol dehydrogenase+1.1.1.1
123991gelatinase-
123991amylase+
123991caseinase-3.4.21.50
123991catalase+1.11.1.6
123991tween esterase+
123991gamma-glutamyltransferase+2.3.2.2
123991lecithinase+
123991lipase-
123991lysine decarboxylase-4.1.1.18
123991ornithine decarboxylase-4.1.1.17
123991phenylalanine ammonia-lyase+4.3.1.24
123991protease+
123991tryptophan deaminase-
123991urease-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
123991-+++-++---++--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6718++++----++++++++-++-+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
123991---++-----+++----+---+-----+--++---++------+-----

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
123991++-++--+-++----+---++---+------+-+-+-------------++--+-----++-----------++-++-+++-+---+-+++++++-+++

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentisolation date
6718shrimp culture waterDahuaChinaCHNAsia
67771From shrimp culture water in ChinaChinaCHNAsia
123991Environment, Shrimp culture waterDahuaChinaCHNAsia1995

isolation source categories

Cat1Cat2Cat3
#Engineered#Food production#Aquaculture
#Environmental#Aquatic
#Host#Arthropoda#Crustacea

taxonmaps

  • @ref: 69479
  • File name: preview.99_4420.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_312;98_347;99_4420&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: AJ316181
  • Sequence Identity:
  • Total samples: 247
  • soil counts: 6
  • aquatic counts: 188
  • animal counts: 52
  • plant counts: 1

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
67181Risk group (German classification)
1239912Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6718
  • description: Vibrio sp. R-15052 16S rRNA gene, strain R-15052
  • accession: AJ316181
  • length: 1435
  • database: ena
  • NCBI tax ID: 170661

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio xuii DSM 17185GCA_001274855contigncbi170661
66792Vibrio xuii strain DSM 17185170661.3wgspatric170661
66792Vibrio xuii DSM 171852740892532draftimg170661

GC content

  • @ref: 67771
  • GC-content: 46.6

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileyes91.097no
gram-positiveno98.392no
anaerobicno96.496yes
aerobicyes87.258yes
halophileyes57.673no
spore-formingno95.236no
thermophileno99.356yes
glucose-utilyes89.738yes
flagellatedyes90.855no
glucose-fermentyes86.37yes

External links

@ref: 6718

culture collection no.: DSM 17185, CAIM 467, CIP 108271, KCTC 12703, LMG 21346, KCTC 12122

straininfo link

  • @ref: 86304
  • straininfo: 86394

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12656180Vibrio neptunius sp. nov., Vibrio brasiliensis sp. nov. and Vibrio xuii sp. nov., isolated from the marine aquaculture environment (bivalves, fish, rotifers and shrimps).Thompson FL, Li Y, Gomez-Gil B, Thompson CC, Hoste B, Vandemeulebroecke K, Rupp GS, Pereira A, De Bem MM, Sorgeloos P, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02447-02003Animals, Aquaculture, Base Composition, Crustacea/microbiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Fatty Acids/analysis, Fishes/microbiology, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Phenotype, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Rotifera/microbiology, Species Specificity, Vibrio/*classification/genetics/*isolation & purification/metabolismGenetics
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/urltitle
6718Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17185)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17185
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
37421Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5875
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68371Automatically annotated from API 50CH acid
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
86304Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID86394.1StrainInfo: A central database for resolving microbial strain identifiers
123991Curators of the CIPCollection of Institut Pasteur (CIP 108271)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108271