Strain identifier
BacDive ID: 17313
Type strain:
Species: Vibrio gigantis
Strain history: CIP <- 2005, M. Gay, IFREMER, La Tremblaye, France: strain LGP 13
NCBI tax ID(s): 296199 (species)
General
@ref: 7582
BacDive-ID: 17313
DSM-Number: 18531
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, animal pathogen
description: Vibrio gigantis DSM 18531 is a facultative anaerobe, mesophilic, Gram-negative animal pathogen that was isolated from haemolymph of oysters .
NCBI tax id
- NCBI tax id: 296199
- Matching level: species
strain history
@ref | history |
---|---|
7582 | <- CIP <- M. Gay, IFREMER; LGP 13 |
40048 | 2005, M. Gay, IFREMER, La Tremblaye, France: strain LGP 13 |
119615 | CIP <- 2005, M. Gay, IFREMER, La Tremblaye, France: strain LGP 13 |
doi: 10.13145/bacdive17313.20230509.8.1
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 gigantis
- full scientific name: Vibrio gigantis Le Roux et al. 2005
@ref: 7582
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio gigantis
full scientific name: Vibrio gigantis Le Roux et al. 2005
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | motility | cell shape |
---|---|---|---|---|---|
31486 | negative | 2.5 µm | 1 µm | yes | |
119615 | negative | yes | rod-shaped |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
7582 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | Name: 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 |
40048 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
119615 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7582 | positive | growth | 25 | mesophilic |
31486 | positive | optimum | 4 | psychrophilic |
40048 | positive | growth | 22 | psychrophilic |
61148 | positive | growth | 30 | mesophilic |
119615 | positive | growth | 5-30 | |
119615 | no | growth | 37 | mesophilic |
119615 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31486 | facultative anaerobe |
61148 | aerobe |
119615 | facultative anaerobe |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31486 | NaCl | positive | growth | 01-07 % |
31486 | NaCl | positive | optimum | 4 % |
119615 | NaCl | positive | growth | 2-8 % |
119615 | NaCl | no | growth | 0 % |
119615 | NaCl | no | growth | 10 % |
observation
- @ref: 31486
- observation: aggregates in clumps
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31486 | 17057 | cellobiose | + | carbon source |
31486 | 28757 | fructose | + | carbon source |
31486 | 28260 | galactose | + | carbon source |
31486 | 17234 | glucose | + | carbon source |
31486 | 17754 | glycerol | + | carbon source |
31486 | 28087 | glycogen | + | carbon source |
31486 | 29864 | mannitol | + | carbon source |
31486 | 37684 | mannose | + | carbon source |
31486 | 28053 | melibiose | + | carbon source |
31486 | 506227 | N-acetylglucosamine | + | carbon source |
31486 | 33942 | ribose | + | carbon source |
31486 | 27082 | trehalose | + | carbon source |
31486 | 4853 | esculin | + | hydrolysis |
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | 24265 | gluconate | + | builds acid from |
68371 | 18403 | L-arabitol | - | builds acid from |
68371 | 18333 | D-arabitol | - | builds acid from |
68371 | 18287 | L-fucose | - | builds acid from |
68371 | 28847 | D-fucose | - | builds acid from |
68371 | 16443 | D-tagatose | - | builds acid from |
68371 | 62318 | D-lyxose | - | builds acid from |
68371 | 32528 | turanose | - | builds acid from |
68371 | 28066 | gentiobiose | - | builds acid from |
68371 | 17151 | xylitol | - | builds acid from |
68371 | 28087 | glycogen | + | builds acid from |
68371 | 28017 | starch | + | builds acid from |
68371 | 16634 | raffinose | - | builds acid from |
68371 | 6731 | melezitose | - | builds acid from |
68371 | 15443 | inulin | - | builds acid from |
68371 | 27082 | trehalose | + | builds acid from |
68371 | 28053 | melibiose | + | builds acid from |
68371 | 17716 | lactose | - | builds acid from |
68371 | 17306 | maltose | + | builds acid from |
68371 | 17057 | cellobiose | + | builds acid from |
68371 | 17814 | salicin | - | builds acid from |
68371 | 18305 | arbutin | - | builds acid from |
68371 | 27613 | amygdalin | - | builds acid from |
68371 | 59640 | N-acetylglucosamine | + | builds acid from |
68371 | 320061 | methyl alpha-D-glucopyranoside | - | builds acid from |
68371 | 43943 | methyl alpha-D-mannoside | - | builds acid from |
68371 | 17924 | D-sorbitol | - | builds acid from |
68371 | 16899 | D-mannitol | + | builds acid from |
68371 | 17268 | myo-inositol | - | builds acid from |
68371 | 16813 | galactitol | - | builds acid from |
68371 | 62345 | L-rhamnose | - | builds acid from |
68371 | 17266 | L-sorbose | - | builds acid from |
68371 | 16024 | D-mannose | + | builds acid from |
68371 | 15824 | D-fructose | + | builds acid from |
68371 | 17634 | D-glucose | + | builds acid from |
68371 | 12936 | D-galactose | + | builds acid from |
68371 | 74863 | methyl beta-D-xylopyranoside | - | builds acid from |
68371 | 15963 | ribitol | - | builds acid from |
68371 | 65328 | L-xylose | - | builds acid from |
68371 | 65327 | D-xylose | - | builds acid from |
68371 | 16988 | D-ribose | + | builds acid from |
68371 | 30849 | L-arabinose | - | builds acid from |
68371 | 17108 | D-arabinose | - | builds acid from |
68371 | 17113 | erythritol | - | builds acid from |
68371 | 17754 | glycerol | + | builds acid from |
68369 | 25115 | malate | + | assimilation |
68369 | 17128 | adipate | - | assimilation |
68369 | 27689 | decanoate | + | assimilation |
68369 | 24265 | gluconate | + | assimilation |
68369 | 17306 | maltose | + | assimilation |
68369 | 59640 | N-acetylglucosamine | + | assimilation |
68369 | 16899 | D-mannitol | + | assimilation |
68369 | 16024 | D-mannose | + | assimilation |
68369 | 30849 | L-arabinose | - | assimilation |
68369 | 17634 | D-glucose | + | assimilation |
68369 | 5291 | gelatin | + | hydrolysis |
68369 | 4853 | esculin | + | hydrolysis |
68369 | 16199 | urea | - | hydrolysis |
68369 | 29016 | arginine | - | hydrolysis |
68369 | 17634 | D-glucose | + | fermentation |
68369 | 27897 | tryptophan | + | energy source |
68369 | 17632 | nitrate | + | reduction |
119615 | 16947 | citrate | - | carbon source |
119615 | 4853 | esculin | + | hydrolysis |
119615 | 17234 | glucose | + | fermentation |
119615 | 17716 | lactose | - | fermentation |
119615 | 17632 | nitrate | + | reduction |
119615 | 16301 | nitrite | - | reduction |
119615 | 132112 | sodium thiosulfate | - | builds gas from |
119615 | 17234 | glucose | + | degradation |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
68369 | 35581 | indole | yes |
119615 | 35581 | indole | no |
metabolite tests
@ref | Chebi-ID | metabolite | indole test | voges-proskauer-test | methylred-test |
---|---|---|---|---|---|
68369 | 35581 | indole | + | ||
119615 | 15688 | acetoin | - | ||
119615 | 17234 | glucose | - |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31486 | catalase | + | 1.11.1.6 |
31486 | gelatinase | + | |
31486 | cytochrome oxidase | + | 1.9.3.1 |
68369 | cytochrome oxidase | + | 1.9.3.1 |
68369 | gelatinase | + | |
68369 | beta-glucosidase | + | 3.2.1.21 |
68369 | urease | - | 3.5.1.5 |
68369 | arginine dihydrolase | - | 3.5.3.6 |
119615 | oxidase | + | |
119615 | beta-galactosidase | - | 3.2.1.23 |
119615 | alcohol dehydrogenase | - | 1.1.1.1 |
119615 | gelatinase | + | |
119615 | amylase | + | |
119615 | caseinase | + | 3.4.21.50 |
119615 | catalase | + | 1.11.1.6 |
119615 | tween esterase | + | |
119615 | gamma-glutamyltransferase | - | 2.3.2.2 |
119615 | lecithinase | - | |
119615 | lipase | + | |
119615 | lysine decarboxylase | - | 4.1.1.18 |
119615 | ornithine decarboxylase | - | 4.1.1.17 |
119615 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
119615 | protease | + | |
119615 | tryptophan deaminase | - | |
119615 | urease | - | 3.5.1.5 |
68382 | alkaline phosphatase | + | 3.1.3.1 |
68382 | esterase (C 4) | + | |
68382 | esterase lipase (C 8) | + | |
68382 | lipase (C 14) | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | valine arylamidase | - | |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | trypsin | + | 3.4.21.4 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | naphthol-AS-BI-phosphohydrolase | + | |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | alpha-fucosidase | - | 3.2.1.51 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119615 | - | + | + | + | - | + | - | - | + | - | + | + | - | - | - | - | - | - | - | - |
API 20NE
@ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
7582 | + | + | + | - | - | + | + | + | + | - | + | + | + | + | + | + | - | + | + | - | + |
API 50CHac
@ref | GLY | ERY | DARA | LARA | RIB | DXYL | LXYL | ADO | MDX | GAL | GLU | FRU | MNE | SBE | RHA | DUL | INO | MAN | SOR | MDM | MDG | NAG | AMY | ARB | ESC | SAL | CEL | MAL | LAC | MEL | SAC | TRE | INU | MLZ | RAF | AMD | GLYG | XLT | GEN | TUR | LYX | TAG | DFUC | LFUC | DARL | LARL | GNT | 2KG | 5KG |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119615 | + | - | - | - | + | - | - | - | - | + | + | + | + | - | - | - | - | + | - | - | - | + | - | - | +/- | - | + | + | - | + | +/- | + | - | - | - | + | + | - | - | - | - | - | - | - | - | - | + | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119615 | + | + | + | + | + | - | + | - | - | + | + | - | - | - | + | + | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | + | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | + | + | - | - | + | - | - | - | - | - | - | + | - | + | - | + | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | country | origin.country | continent | geographic location | isolation date |
---|---|---|---|---|---|---|---|
7582 | haemolymph of oysters (Crassostrea gigas) | Crassostrea gigas | France | FRA | Europe | ||
61148 | Haemolymph of oyster (Crassostrea gigas) | France | FRA | Europe | |||
119615 | Japanese oyster, C. Gigas | France | FRA | Europe | La Tremblaye | 2001 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Invertebrates (Other) | #Mollusca |
#Host Body Product | #Fluids |
taxonmaps
- @ref: 69479
- File name: preview.99_929.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_361;98_409;99_929&stattab=map
- Last taxonomy: Vibrio
- 16S sequence: AJ582810
- Sequence Identity:
- Total samples: 6265
- soil counts: 160
- aquatic counts: 5115
- animal counts: 960
- plant counts: 30
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
7582 | yes | 1 | Risk group (German classification) |
119615 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Vibrio gigantis strain CAIM 25 16S ribosomal RNA gene, partial sequence | EF094888 | 1498 | ena | 296199 |
7582 | Vibrio gigantis partial 16S rRNA gene, type strain LGP 13 | AJ582810 | 1202 | ena | 296199 |
Genome sequences
- @ref: 66792
- description: Vibrio gigantis LMG 22741
- accession: GCA_024347515
- assembly level: complete
- database: ncbi
- NCBI tax ID: 296199
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | yes | 89.556 | no |
gram-positive | no | 98.855 | yes |
anaerobic | no | 97.416 | yes |
aerobic | yes | 87.611 | no |
halophile | yes | 52.621 | no |
spore-forming | no | 94.575 | no |
motile | yes | 90.249 | yes |
glucose-ferment | yes | 86.553 | no |
thermophile | no | 99.688 | yes |
glucose-util | yes | 91.614 | yes |
External links
@ref: 7582
culture collection no.: DSM 18531, CIP 108656, LMG 22741, CCUG 56969, LGP 13
straininfo link
- @ref: 86313
- straininfo: 281472
literature
- topic: Phylogeny
- Pubmed-ID: 16280478
- title: Vibrio gigantis sp. nov., isolated from the haemolymph of cultured oysters (Crassostrea gigas).
- authors: Roux FL, Goubet A, Thompson FL, Faury N, Gay M, Swings J, Saulnier D
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.63666-0
- year: 2005
- mesh: Animals, Crassostrea/*microbiology, DNA Gyrase/*genetics, DNA, Bacterial/analysis/chemistry, Phylogeny, RNA, Ribosomal, 16S/analysis/genetics, Sequence Analysis, DNA, Vibrio/*classification/isolation & purification
- topic2: Transcriptome
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
7582 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18531) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-18531 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | ||
31486 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28776041 | 27784 | ||
40048 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6309 | |||||
61148 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 56969) | https://www.ccug.se/strain?id=56969 | ||||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
68369 | Automatically annotated from API 20NE | ||||||
68371 | Automatically annotated from API 50CH acid | ||||||
68382 | Automatically annotated from API zym | ||||||
69479 | João 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 | ||||
86313 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID281472.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
119615 | Curators of the CIP | Collection of Institut Pasteur (CIP 108656) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108656 |