Strain identifier

BacDive ID: 5261

Type strain: Yes

Species: Vagococcus salmoninarum

Strain Designation: OS1-68

Strain history: CIP <- 1996, NCFB <- Fryer, Oregon, USA

NCBI tax ID(s): 2739 (species)

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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

@refhistory
2639<- NCFB <- J.L. Fryer <- R.A. Holt, OS1-68
122402CIP <- 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

@refnamegrowthlinkcomposition
2639TRYPTICASE SOY YEAST EXTRACT MEDIUM (DSMZ Medium 92)yeshttps://mediadive.dsmz.de/medium/92Name: 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
41271MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
122402CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
2639positivegrowth30mesophilic
41271positivegrowth30mesophilic
51497positivegrowth22psychrophilic
51497positivegrowth20-30
122402positivegrowth5psychrophilic
122402nogrowth37mesophilic
122402nogrowth41thermophilic

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

@refmetaboliteutilization activitykind of utilization testedChebi-ID
68371Potassium 5-ketogluconate-builds acid from
68371Potassium 2-ketogluconate-builds acid from
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
68371xylitol-builds acid from17151
68371raffinose-builds acid from16634
68371melezitose-builds acid from6731
68371inulin-builds acid from15443
68371melibiose-builds acid from28053
68371lactose-builds acid from17716
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-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
68371L-arabinose-builds acid from30849
68371D-arabinose-builds acid from17108
68371erythritol-builds acid from17113
68371glycerol-builds acid from17754
122402esculin+hydrolysis4853
122402glucose+fermentation17234
122402lactose+fermentation17716
122402nitrate-reduction17632
122402nitrite-reduction16301
122402sodium thiosulfate-builds gas from132112

metabolite production

  • @ref: 122402
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase+3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase-
68382acid phosphatase+3.1.3.2
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase+3.1.3.1
122402beta-galactosidase-3.2.1.23
122402alcohol dehydrogenase-1.1.1.1
122402gelatinase-
122402amylase-
122402DNase-
122402caseinase-3.4.21.50
122402catalase-1.11.1.6
122402tween esterase-
122402lecithinase-
122402lysine decarboxylase-4.1.1.18
122402ornithine decarboxylase-4.1.1.17
122402urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
122402-+++-+---++----+----

API 50CHac

@refGLYERYDARALARARIBDXYLLXYLADOMDXGALGLUFRUMNESBERHADULINOMANSORMDMMDGNAGAMYARBESCSALCELMALLACMELSACTREINUMLZRAFAMDGLYGXLTGENTURLYXTAGDFUCLFUCDARLLARLGNT2KG5KG
122402----+/------+/-+/-+/---------+/-+/-+/-+/-+/-+/-+/---+/-+/----+/-+/--+/-+/-------+/---

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUC
122402------------------+-------------------------------------------------------------

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
2639rainbow troutOregon, Oak Spring HatcheryUSAUSANorth America
51497Rainbow trout,diseased adult (Oncorhynchus mykiss)Oregon,Oak Spring HatcheryUSAUSANorth America1968
122402Rainbow brood trout diseased in hatcheryOak Springs, ArizonaUnited States of AmericaUSANorth America1968

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

@refpathogenicity animalbiosafety levelbiosafety level comment
2639yes1Risk group (German classification)
1224021Risk group (French classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vagococcus salmoninarum strain ATCC 51200 16S ribosomal RNA gene, partial sequenceAY577824539ena2739
20218Vagococcus salmoninarum 16S rRNA geneY180971465ena2739
20218Vagococcus salmoninarum partial 16S rRNAX542721491ena2739

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vagococcus salmoninarum NCFB 2777GCA_003987495contigncbi2739
66792Vagococcus salmoninarum strain NCFB 27772739.3wgspatric2739
66792Vagococcus salmoninarum NCFB 27772894100150draftimg2739

GC content

  • @ref: 2639
  • GC-content: 36.0
  • method: thermal denaturation, midpoint method (Tm)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno59.667no
gram-positiveyes87.059no
anaerobicno93.888no
halophileyes70.119no
spore-formingno76.822no
glucose-utilyes86.419no
aerobicno91.575no
flagellatedno80.693no
thermophileno99.435no
glucose-fermentyes81.958no

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

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny169776416S 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 MDInt J Syst Bacteriol10.1099/00207713-40-3-2241990Animals, 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/microbiologyMetabolism
Enzymology7961194Characteristics of Vagococcus salmoninarum isolated from diseased salmonid fish.Schmidtke LM, Carson JJ Appl Bacteriol10.1111/j.1365-2672.1994.tb03068.x1994Animals, 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/microbiologyPhylogeny

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
2639Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 6633)https://www.dsmz.de/collection/catalogue/details/culture/DSM-6633
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
41271Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/16619
51497Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 33394)https://www.ccug.se/strain?id=33394
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updatesNucleic Acids Res. 49: D498-D508 202033211880
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
74751Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID5034.1StrainInfo: A central database for resolving microbial strain identifiers
122402Curators of the CIPCollection of Institut Pasteur (CIP 104684)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20104684