Strain identifier

BacDive ID: 17299

Type strain: Yes

Species: Vibrio gallicus

Strain Designation: HT2-1, HT 2-1

Strain history: CIP <- 2003, T. Sawabe, Hakodate, Japan: strain HT 2-1

NCBI tax ID(s): 190897 (species)

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General

@ref: 6542

BacDive-ID: 17299

DSM-Number: 16639

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

description: Vibrio gallicus HT2-1 is an anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of abalone Haliotis tuberculata.

NCBI tax id

  • NCBI tax id: 190897
  • Matching level: species

strain history

@refhistory
6542<- T. Sawabe; HT2-1
119510CIP <- 2003, T. Sawabe, Hakodate, Japan: strain HT 2-1

doi: 10.13145/bacdive17299.20230509.8.1

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 gallicus
  • full scientific name: Vibrio gallicus Sawabe et al. 2004

@ref: 6542

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio gallicus

full scientific name: Vibrio gallicus Sawabe et al. 2004

strain designation: HT2-1, HT 2-1

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotility
29995negative2.1 µm0.55 µmrod-shapedno
119510negativerod-shapedno

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6542BACTO 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
33172Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
119510CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13

culture temp

@refgrowthtypetemperaturerange
6542positivegrowth25mesophilic
29995positivegrowth15-30
29995positiveoptimum22.5psychrophilic
33172positivegrowth25mesophilic
61146positivegrowth30mesophilic
119510positivegrowth15-30
119510nogrowth5psychrophilic
119510nogrowth37mesophilic
119510nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29995anaerobe
61146aerobe

spore formation

  • @ref: 29995
  • spore formation: no

halophily

@refsaltgrowthtested relationconcentration
119510NaClpositivegrowth2-6 %
119510NaClnogrowth0 %
119510NaClnogrowth8 %
119510NaClnogrowth10 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2999528757fructose+carbon source
2999517234glucose+carbon source
2999517306maltose+carbon source
2999529864mannitol+carbon source
2999517632nitrate+reduction
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
6837118403L-arabitol-builds acid from
6837118333D-arabitol-builds acid from
6837118287L-fucose-builds acid from
6837128847D-fucose-builds acid from
6837116443D-tagatose-builds acid from
6837162318D-lyxose-builds acid from
6837132528turanose-builds acid from
6837128066gentiobiose-builds acid from
6837117151xylitol-builds acid from
6837128087glycogen+builds acid from
6837116634raffinose-builds acid from
683716731melezitose-builds acid from
6837115443inulin-builds acid from
6837127082trehalose-builds acid from
6837117992sucrose-builds acid from
6837128053melibiose-builds acid from
6837117716lactose-builds acid from
6837117306maltose+builds acid from
6837117057cellobiose-builds acid from
6837117814salicin-builds acid from
683714853esculin-builds acid from
6837118305arbutin-builds acid from
6837127613amygdalin-builds acid from
6837159640N-acetylglucosamine+builds acid from
68371320061methyl alpha-D-glucopyranoside-builds acid from
6837143943methyl alpha-D-mannoside-builds acid from
6837117924D-sorbitol-builds acid from
6837116899D-mannitol+builds acid from
6837117268myo-inositol-builds acid from
6837116813galactitol-builds acid from
6837162345L-rhamnose-builds acid from
6837117266L-sorbose-builds acid from
6837116024D-mannose+builds acid from
6837115824D-fructose+builds acid from
6837117634D-glucose+builds acid from
6837112936D-galactose-builds acid from
6837174863methyl beta-D-xylopyranoside-builds acid from
6837115963ribitol-builds acid from
6837165328L-xylose-builds acid from
6837165327D-xylose-builds acid from
6837130849L-arabinose-builds acid from
6837117108D-arabinose-builds acid from
6837117113erythritol-builds acid from
6837117754glycerol-builds acid from
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol+fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine-hydrolysis
11951016947citrate-carbon source
1195104853esculin-hydrolysis
11951017234glucose-fermentation
11951017716lactose-fermentation
11951017632nitrate+reduction
11951016301nitrite-reduction
119510132112sodium thiosulfate-builds gas from

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno
11951035581indoleno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole testmethylred-test
6836815688acetoin-
6836835581indole+
11951015688acetoin-
11951017234glucose+

enzymes

@refvalueactivityec
29995catalase+1.11.1.6
29995cytochrome oxidase+1.9.3.1
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
119510oxidase+
119510beta-galactosidase-3.2.1.23
119510alcohol dehydrogenase-1.1.1.1
119510gelatinase-
119510amylase+
119510caseinase-3.4.21.50
119510catalase+1.11.1.6
119510tween esterase-
119510gamma-glutamyltransferase-2.3.2.2
119510lecithinase-
119510lipase-
119510lysine decarboxylase-4.1.1.18
119510ornithine decarboxylase-4.1.1.17
119510tryptophan deaminase-
119510urease-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
119510-+++-+-----------+--

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
6542--------+--++-------+

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
119510----+/------+++----+---+-----+-------+/-+---------+/---

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
6542gut of abalone Haliotis tuberculataHaliotis tuberculataBrestFranceFRAEurope
61146Gut of abalone Haliotis tuberculataFranceFRAEurope
119510Animal, Abalone, gutRoscoffFranceFRAEurope2001

isolation source categories

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

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: AJ440009
  • 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
65421Risk group (German classification)
1195102Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio gallicus partial 16S rRNA gene, type strain LMG 21330AJ4400091435ena190897
29995Vibrio gallicus strain CIP 107863 16S ribosomal RNA gene, partial sequenceAY2579721516nuccore190897

Genome sequences

  • @ref: 66792
  • description: Vibrio gallicus CIP 107863
  • accession: GCA_024346875
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 190897

GC content

  • @ref: 29995
  • GC-content: 43.95

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno90.631yes
gram-positiveno98.856yes
anaerobicno98.115no
aerobicyes52.993no
halophileyes85.803no
spore-formingno97.014yes
motileno86.659yes
glucose-fermentyes87.757yes
thermophileno99.256yes
glucose-utilyes86.742yes

External links

@ref: 6542

culture collection no.: DSM 16639, CIP 107863, LMG 21878, CCUG 56967, LMG 21330

straininfo link

  • @ref: 86299
  • straininfo: 97546

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny15143033Vibrio gallicus sp. nov., isolated from the gut of the French abalone Haliotis tuberculata.Sawabe T, Hayashi K, Moriwaki J, Thompson FL, Swings J, Potin P, Christen R, Ezura YInt J Syst Evol Microbiol10.1099/ijs.0.02804-02004Animals, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Digestive System/microbiology, France, Molecular Sequence Data, Mollusca/*microbiology, Phenotype, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Species Specificity, Vibrio/*classification/genetics/*isolation & purification/metabolismGenetics
Phylogeny27262360Vibrio ishigakensis sp. nov., in Halioticoli clade isolated from seawater in Okinawa coral reef area, Japan.Gao F, Al-Saari N, Rohul Amin AK, Sato K, Mino S, Suda W, Oshima K, Hattori M, Ohkuma M, Hargreaves PI, Meirelles PM, Thompson FL, Thompson C, Gomez-Gil B, Sawabe T, Sawabe TSyst Appl Microbiol10.1016/j.syapm.2016.04.0022016Alginates/metabolism, Animals, Anthozoa/*microbiology, Base Composition/genetics, Base Sequence, *Coral Reefs, DNA, Bacterial/genetics, Genes, Essential/genetics, Japan, Multilocus Sequence Typing, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, *Vibrio/classification/genetics/isolation & purificationTranscriptome

Reference

@idauthorscataloguedoi/urltitlejournalpubmedID_cross_reference
6542Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 16639)https://www.dsmz.de/collection/catalogue/details/culture/DSM-16639
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
29995Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2877604126361
33172Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5421
61146Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 56967)https://www.ccug.se/strain?id=56967
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)
68368Automatically annotated from API 20E
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
86299Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID97546.1StrainInfo: A central database for resolving microbial strain identifiers
119510Curators of the CIPCollection of Institut Pasteur (CIP 107863)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20107863