Strain identifier
BacDive ID: 17342
Type strain:
Species: Vibrio rarus
Strain Designation: RW22
Strain history: CIP <- 2007, NBRC <- 2006, T. Sawabe, Hokkaido Univ., Hokkaido, Japan: strain RW22
NCBI tax ID(s): 1219063 (strain), 413403 (species)
General
@ref: 8239
BacDive-ID: 17342
DSM-Number: 19662
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, rod-shaped
description: Vibrio rarus RW22 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from gut of abalone Haliotis rufescens.
NCBI tax id
NCBI tax id | Matching level |
---|---|
413403 | species |
1219063 | strain |
strain history
@ref | history |
---|---|
8239 | <- T. Sawabe, Faculty of Fisheries Sciences, Hokkaido; RW22 |
122140 | CIP <- 2007, NBRC <- 2006, T. Sawabe, Hokkaido Univ., Hokkaido, Japan: strain RW22 |
doi: 10.13145/bacdive17342.20230509.8.1
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 rarus
- full scientific name: Vibrio rarus Sawabe et al. 2007
@ref: 8239
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Vibrio
species: Vibrio rarus
full scientific name: Vibrio rarus Sawabe et al. 2007
strain designation: RW22
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
32001 | negative | 1.5 µm | 0.75 µm | rod-shaped | no |
122140 | negative | rod-shaped | no |
pigmentation
- @ref: 32001
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8239 | 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 |
37653 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
122140 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8239 | positive | growth | 28 | mesophilic |
32001 | positive | growth | 15-30 | |
37653 | positive | growth | 20 | psychrophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 32001
- oxygen tolerance: facultative anaerobe
spore formation
- @ref: 32001
- spore formation: no
halophily
- @ref: 32001
- salt: NaCl
- growth: positive
- tested relation: growth
- concentration: <6 %
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32001 | 30089 | acetate | + | carbon source |
32001 | 17057 | cellobiose | + | carbon source |
32001 | 24265 | gluconate | + | carbon source |
32001 | 17234 | glucose | + | carbon source |
32001 | 29987 | glutamate | + | carbon source |
32001 | 17306 | maltose | + | carbon source |
32001 | 29864 | mannitol | + | carbon source |
32001 | 37684 | mannose | + | carbon source |
32001 | 506227 | N-acetylglucosamine | + | carbon source |
32001 | 26271 | proline | + | carbon source |
32001 | 15361 | pyruvate | + | carbon source |
32001 | 30911 | sorbitol | + | carbon source |
32001 | 30031 | succinate | + | carbon source |
32001 | 17992 | sucrose | + | carbon source |
32001 | 18222 | xylose | + | carbon source |
32001 | 17632 | nitrate | + | reduction |
122140 | 17632 | nitrate | + | reduction |
122140 | 16301 | nitrite | - | reduction |
metabolite production
@ref | Chebi-ID | metabolite | production |
---|---|---|---|
32001 | 35581 | indole | yes |
122140 | 35581 | indole | no |
metabolite tests
- @ref: 32001
- Chebi-ID: 35581
- metabolite: indole
- indole test: +
enzymes
@ref | value | activity | ec |
---|---|---|---|
32001 | catalase | + | 1.11.1.6 |
32001 | cytochrome oxidase | + | 1.9.3.1 |
122140 | oxidase | + | |
122140 | catalase | + | 1.11.1.6 |
122140 | 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122140 | - | + | + | - | - | + | - | - | - | - | - | + | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent | isolation date |
---|---|---|---|---|---|---|---|
8239 | gut of abalone Haliotis rufescens | Haliotis rufescens | La Jolla | USA | USA | North America | |
122140 | Gut, Californian abalone Haliotis rufescence | La Jolla, California | United States of America | USA | North America | 2005 |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Host | #Invertebrates (Other) | #Mollusca |
#Host Body-Site | #Gastrointestinal tract | #Stomach |
taxonmaps
- @ref: 69479
- File name: preview.99_75043.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_40270;98_52471;99_75043&stattab=map
- Last taxonomy: Vibrio rarus subclade
- 16S sequence: AB681696
- Sequence Identity:
- Total samples: 386
- soil counts: 6
- aquatic counts: 141
- animal counts: 233
- plant counts: 6
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8239 | 1 | Risk group (German classification) |
122140 | 2 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Vibrio rarus gene for 16S rRNA, partial sequence, strain: NBRC 102084 | AB681696 | 1495 | ena | 413403 |
8239 | Vibrio rarus strain RW22 16S ribosomal RNA gene, partial sequence | DQ914239 | 1403 | ena | 413403 |
Genome sequences
- @ref: 66792
- description: Vibrio rarus LMG 23674
- accession: GCA_024347075
- assembly level: complete
- database: ncbi
- NCBI tax ID: 413403
GC content
- @ref: 32001
- GC-content: 43.8
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
flagellated | no | 90.518 | yes |
gram-positive | no | 98.338 | yes |
anaerobic | no | 95.984 | yes |
aerobic | yes | 51.512 | yes |
halophile | yes | 86.104 | yes |
spore-forming | no | 96.252 | yes |
motile | no | 86.451 | yes |
glucose-ferment | yes | 83.39 | no |
thermophile | no | 99.335 | no |
glucose-util | yes | 88.161 | yes |
External links
@ref: 8239
culture collection no.: DSM 19662, LMG 23674, NBRC 102084, CIP 109638
straininfo link
- @ref: 86342
- straininfo: 307807
literature
- topic: Phylogeny
- Pubmed-ID: 17473233
- title: Vibrio comitans sp. nov., Vibrio rarus sp. nov. and Vibrio inusitatus sp. nov., from the gut of the abalones Haliotis discus discus, H. gigantea, H. madaka and H. rufescens.
- authors: Sawabe T, Fujimura Y, Niwa K, Aono H
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.64789-0
- year: 2007
- mesh: Adhesins, Bacterial/genetics, Aerobiosis, Alginates/metabolism, Anaerobiosis, Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Gastrointestinal Tract/microbiology, Gastropoda/*microbiology, Genes, rRNA/genetics, Glucuronic Acid/metabolism, Hexuronic Acids/metabolism, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Vibrio/*classification/*isolation & purification/metabolism
- topic2: Metabolism
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed | ID_cross_reference |
---|---|---|---|---|---|---|---|
8239 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19662) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19662 | ||||
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 | ||
32001 | 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 | 28255 | ||
37653 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/7404 | |||||
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) | ||||
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 | ||||
86342 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID307807.1 | StrainInfo: A central database for resolving microbial strain identifiers | ||||
122140 | Curators of the CIP | Collection of Institut Pasteur (CIP 109638) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109638 |