Strain identifier
BacDive ID: 5261
Type strain:
Species: Vagococcus salmoninarum
Strain Designation: OS1-68
Strain history: CIP <- 1996, NCFB <- Fryer, Oregon, USA
NCBI tax ID(s): 2739 (species)
General
@ref: 2639
BacDive-ID: 5261
DSM-Number: 6633
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-positive, ovoid-shaped, animal pathogen
description: Vagococcus salmoninarum OS1-68 is a facultative anaerobe, mesophilic, Gram-positive animal pathogen that was isolated from rainbow trout.
NCBI tax id
- NCBI tax id: 2739
- Matching level: species
strain history
@ref | history |
---|---|
2639 | <- NCFB <- J.L. Fryer <- R.A. Holt, OS1-68 |
122402 | CIP <- 1996, NCFB <- Fryer, Oregon, USA |
doi: 10.13145/bacdive5261.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacillota
- domain: Bacteria
- phylum: Bacillota
- class: Bacilli
- order: Lactobacillales
- family: Enterococcaceae
- genus: Vagococcus
- species: Vagococcus salmoninarum
- full scientific name: Vagococcus salmoninarum Wallbanks et al. 1990
@ref: 2639
domain: Bacteria
phylum: Firmicutes
class: Bacilli
order: Lactobacillales
family: Enterococcaceae
genus: Vagococcus
species: Vagococcus salmoninarum
full scientific name: Vagococcus salmoninarum Wallbanks et al. 1990
strain designation: OS1-68
type strain: yes
Morphology
cell morphology
- @ref: 122402
- gram stain: positive
- cell shape: ovoid-shaped
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
2639 | TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) | yes | https://mediadive.dsmz.de/medium/92 | Name: TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Yeast extract 3.0 g/l Distilled water |
41271 | MEDIUM 6 - Columbia agar with 10 % horse blood | yes | Distilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml) | |
122402 | CIP Medium 6 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
2639 | positive | growth | 30 | mesophilic |
41271 | positive | growth | 30 | mesophilic |
51497 | positive | growth | 22 | psychrophilic |
51497 | positive | growth | 20-30 | |
122402 | positive | growth | 5 | psychrophilic |
122402 | no | growth | 37 | mesophilic |
122402 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 122402
- oxygen tolerance: facultative anaerobe
murein
- @ref: 2639
- murein short key: A11.42
- type: A4alpha L-Lys-Gly-D-Asp
metabolite utilization
@ref | metabolite | utilization activity | kind of utilization tested | Chebi-ID |
---|---|---|---|---|
68371 | Potassium 5-ketogluconate | - | builds acid from | |
68371 | Potassium 2-ketogluconate | - | builds acid from | |
68371 | L-arabitol | - | builds acid from | 18403 |
68371 | D-arabitol | - | builds acid from | 18333 |
68371 | L-fucose | - | builds acid from | 18287 |
68371 | D-fucose | - | builds acid from | 28847 |
68371 | D-tagatose | - | builds acid from | 16443 |
68371 | D-lyxose | - | builds acid from | 62318 |
68371 | xylitol | - | builds acid from | 17151 |
68371 | raffinose | - | builds acid from | 16634 |
68371 | melezitose | - | builds acid from | 6731 |
68371 | inulin | - | builds acid from | 15443 |
68371 | melibiose | - | builds acid from | 28053 |
68371 | lactose | - | builds acid from | 17716 |
68371 | methyl alpha-D-glucopyranoside | - | builds acid from | 320061 |
68371 | methyl alpha-D-mannoside | - | builds acid from | 43943 |
68371 | D-sorbitol | - | builds acid from | 17924 |
68371 | D-mannitol | - | builds acid from | 16899 |
68371 | myo-inositol | - | builds acid from | 17268 |
68371 | galactitol | - | builds acid from | 16813 |
68371 | L-rhamnose | - | builds acid from | 62345 |
68371 | L-sorbose | - | builds acid from | 17266 |
68371 | D-galactose | - | builds acid from | 12936 |
68371 | methyl beta-D-xylopyranoside | - | builds acid from | 74863 |
68371 | ribitol | - | builds acid from | 15963 |
68371 | L-xylose | - | builds acid from | 65328 |
68371 | D-xylose | - | builds acid from | 65327 |
68371 | L-arabinose | - | builds acid from | 30849 |
68371 | D-arabinose | - | builds acid from | 17108 |
68371 | erythritol | - | builds acid from | 17113 |
68371 | glycerol | - | builds acid from | 17754 |
122402 | esculin | + | hydrolysis | 4853 |
122402 | glucose | + | fermentation | 17234 |
122402 | lactose | + | fermentation | 17716 |
122402 | nitrate | - | reduction | 17632 |
122402 | nitrite | - | reduction | 16301 |
122402 | sodium thiosulfate | - | builds gas from | 132112 |
metabolite production
- @ref: 122402
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | + | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | + | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | - | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
122402 | beta-galactosidase | - | 3.2.1.23 |
122402 | alcohol dehydrogenase | - | 1.1.1.1 |
122402 | gelatinase | - | |
122402 | amylase | - | |
122402 | DNase | - | |
122402 | caseinase | - | 3.4.21.50 |
122402 | catalase | - | 1.11.1.6 |
122402 | tween esterase | - | |
122402 | lecithinase | - | |
122402 | lysine decarboxylase | - | 4.1.1.18 |
122402 | ornithine decarboxylase | - | 4.1.1.17 |
122402 | urease | - | 3.5.1.5 |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122402 | - | + | + | + | - | + | - | - | - | + | + | - | - | - | - | + | - | - | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122402 | - | - | - | - | +/- | - | - | - | - | - | +/- | +/- | +/- | - | - | - | - | - | - | - | - | +/- | +/- | +/- | +/- | +/- | +/- | +/- | - | - | +/- | +/- | - | - | - | +/- | +/- | - | +/- | +/- | - | - | - | - | - | - | +/- | - | - |
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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
122402 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | sampling date | isolation date |
---|---|---|---|---|---|---|---|
2639 | rainbow trout | Oregon, Oak Spring Hatchery | USA | USA | North America | ||
51497 | Rainbow trout,diseased adult (Oncorhynchus mykiss) | Oregon,Oak Spring Hatchery | USA | USA | North America | 1968 | |
122402 | Rainbow brood trout diseased in hatchery | Oak Springs, Arizona | United States of America | USA | North America | 1968 |
isolation source categories
- Cat1: #Host
- Cat2: #Fishes
- Cat3: #Salmonidae
taxonmaps
- @ref: 69479
- File name: preview.99_27328.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_13545;97_16490;98_20458;99_27328&stattab=map
- Last taxonomy: Vagococcus salmoninarum subclade
- 16S sequence: Y18097
- Sequence Identity:
- Total samples: 1279
- soil counts: 21
- aquatic counts: 211
- animal counts: 1023
- plant counts: 24
Safety information
risk assessment
@ref | pathogenicity animal | biosafety level | biosafety level comment |
---|---|---|---|
2639 | yes | 1 | Risk group (German classification) |
122402 | 1 | Risk group (French classification) |
Sequence information
16S sequences
@ref | description | accession | length | database | NCBI tax ID |
---|---|---|---|---|---|
20218 | Vagococcus salmoninarum strain ATCC 51200 16S ribosomal RNA gene, partial sequence | AY577824 | 539 | ena | 2739 |
20218 | Vagococcus salmoninarum 16S rRNA gene | Y18097 | 1465 | ena | 2739 |
20218 | Vagococcus salmoninarum partial 16S rRNA | X54272 | 1491 | ena | 2739 |
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Vagococcus salmoninarum NCFB 2777 | GCA_003987495 | contig | ncbi | 2739 |
66792 | Vagococcus salmoninarum strain NCFB 2777 | 2739.3 | wgs | patric | 2739 |
66792 | Vagococcus salmoninarum NCFB 2777 | 2894100150 | draft | img | 2739 |
GC content
- @ref: 2639
- GC-content: 36.0
- method: thermal denaturation, midpoint method (Tm)
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 59.667 | no |
gram-positive | yes | 87.059 | no |
anaerobic | no | 93.888 | no |
halophile | yes | 70.119 | no |
spore-forming | no | 76.822 | no |
glucose-util | yes | 86.419 | no |
aerobic | no | 91.575 | no |
flagellated | no | 80.693 | no |
thermophile | no | 99.435 | no |
glucose-ferment | yes | 81.958 | no |
External links
@ref: 2639
culture collection no.: DSM 6633, ATCC 51200, NCFB 2777, CCUG 33394, LMG 11491, CCM 4305, CIP 104684, NCIMB 13133
straininfo link
- @ref: 74751
- straininfo: 5034
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 1697764 | 16S rRNA sequence determination for members of the genus Carnobacterium and related lactic acid bacteria and description of Vagococcus salmoninarum sp. nov. | Wallbanks S, Martinez-Murcia AJ, Fryer JL, Phillips BA, Collins MD | Int J Syst Bacteriol | 10.1099/00207713-40-3-224 | 1990 | Animals, Base Sequence, DNA, Bacterial, Fatty Acids/metabolism, Gram-Positive Asporogenous Rods/*classification/genetics/metabolism, Gram-Positive Bacteria/classification/genetics/metabolism, Lactates, Lactic Acid, Lactobacillus/classification/genetics/metabolism, Molecular Sequence Data, RNA, Bacterial/*genetics, RNA, Ribosomal/*genetics, RNA, Ribosomal, 16S/*genetics, Sequence Homology, Nucleic Acid, Trout/microbiology | Metabolism |
Enzymology | 7961194 | Characteristics of Vagococcus salmoninarum isolated from diseased salmonid fish. | Schmidtke LM, Carson J | J Appl Bacteriol | 10.1111/j.1365-2672.1994.tb03068.x | 1994 | Animals, Bacterial Proteins/analysis, Electrophoresis, Polyacrylamide Gel, Fish Diseases/etiology/*microbiology, Gram-Positive Bacterial Infections/*veterinary, Gram-Positive Cocci/*isolation & purification, Microbial Sensitivity Tests, Oncorhynchus mykiss/microbiology, Peritonitis/*veterinary, Salmon/microbiology, Salmonidae/*microbiology, Trout/microbiology | Phylogeny |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
2639 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6633) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-6633 | |||
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 | |
41271 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/16619 | ||||
51497 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 33394) | https://www.ccug.se/strain?id=33394 | |||
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) | |||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
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 | |||
74751 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID5034.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
122402 | Curators of the CIP | Collection of Institut Pasteur (CIP 104684) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104684 |