Strain identifier

BacDive ID: 5266

Type strain: Yes

Species: Vagococcus lutrae

Strain Designation: M1134/97/1

Strain history: CIP <- 1999, CCUG <- M.D. Collins, IFR, Reading, UK: strain M1134/97/1 <- G. Foster, Inverness, UK

NCBI tax ID(s): 81947 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 6093

BacDive-ID: 5266

DSM-Number: 15741

keywords: genome sequence, 16S sequence, Bacteria, microaerophile, mesophilic, Gram-positive, motile, coccus-shaped

description: Vagococcus lutrae M1134/97/1 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from otter blood, liver, lungs and spleen, post-mortem.

NCBI tax id

  • NCBI tax id: 81947
  • Matching level: species

strain history

@refhistory
6093<- CCUG <- M. D. Collins, IFR Reading <- G. Foster
120714CIP <- 1999, CCUG <- M.D. Collins, IFR, Reading, UK: strain M1134/97/1 <- G. Foster, Inverness, UK

doi: 10.13145/bacdive5266.20230509.8.1

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 lutrae
  • full scientific name: Vagococcus lutrae Lawson et al. 1999

@ref: 6093

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Vagococcus

species: Vagococcus lutrae

full scientific name: Vagococcus lutrae Lawson et al. 1999

strain designation: M1134/97/1

type strain: yes

Morphology

cell morphology

  • @ref: 120714
  • gram stain: positive
  • cell shape: coccus-shaped
  • motility: yes

colony morphology

  • @ref: 120714

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
6093TRYPTICASE 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
6093COLUMBIA BLOOD MEDIUM (DSMZ Medium 693)yeshttps://mediadive.dsmz.de/medium/693Name: COLUMBIA BLOOD MEDIUM (DSMZ Medium 693) Composition: Defibrinated sheep blood 50.0 g/l Columbia agar base
39477MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
120714CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
6093positivegrowth37mesophilic
39477positivegrowth37mesophilic
54693positivegrowth30-37mesophilic
120714positivegrowth10-45

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
6093microaerophile
54693aerobe
120714facultative anaerobe

halophily

  • @ref: 120714
  • salt: NaCl
  • growth: positive
  • tested relation: growth
  • concentration: 6.5 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
120714606565hippurate+hydrolysis
12071417632nitrate-reduction
12071416301nitrite-reduction

metabolite tests

  • @ref: 120714
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

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
120714oxidase-
120714beta-galactosidase-3.2.1.23
120714alcohol dehydrogenase-1.1.1.1
120714catalase-1.11.1.6
120714gamma-glutamyltransferase-2.3.2.2
120714lysine decarboxylase-4.1.1.18
120714ornithine decarboxylase-4.1.1.17

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120714---+-----+++++---+--

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinentsampling dategeographic locationisolation date
6093otter blood, liver, lungs and spleen, post-mortemUnited KingdomGBREurope
54693Otter blood,liver,lungs and spleen,post-mortemUnited KingdomGBREurope1996Scotland,Isle of Mull
120714Otter, bloodUnited KingdomGBREuropeIsle of Mull, Scotland1996

isolation source categories

Cat1Cat2Cat3
#Host#Mammals
#Host Body-Site#Organ
#Host Body Product#Fluids#Blood

taxonmaps

  • @ref: 69479
  • File name: preview.99_4956.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1881;97_2961;98_3706;99_4956&stattab=map
  • Last taxonomy: Vagococcus lutrae subclade
  • 16S sequence: Y17152
  • Sequence Identity:
  • Total samples: 6002
  • soil counts: 51
  • aquatic counts: 248
  • animal counts: 5650
  • plant counts: 53

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
60931Risk group (German classification)
1207141Risk group (French classification)

Sequence information

16S sequences

  • @ref: 6093
  • description: Vagococcus sp. CCUG39187 16S rRNA gene
  • accession: Y17152
  • length: 1463
  • database: ena
  • NCBI tax ID: 81947

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vagococcus lutrae CCUG 39187GCA_003987555contigncbi81947
66792Vagococcus lutrae strain CCUG 3918781947.4wgspatric81947

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno94.013no
flagellatedno98.125no
gram-positiveyes90.753no
anaerobicno90.801no
halophileyes90.391no
spore-formingno92.99no
thermophileno99.065yes
glucose-utilyes89.675no
aerobicno93.875no
glucose-fermentyes88.157no

External links

@ref: 6093

culture collection no.: DSM 15741, ATCC 70083, CCM 4937, CCUG 39187, CIP 106118, ATCC 700839

straininfo link

  • @ref: 74756
  • straininfo: 14205

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny10425788Vagococcus lutrae sp. nov., isolated from the common otter (Lutra lutra).Lawson PA, Foster G, Falsen E, Ohlen M, Collins MDInt J Syst Bacteriol10.1099/00207713-49-3-12511999Animals, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Gram-Positive Cocci/*classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, Otters/*microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNAGenetics
Phylogeny28304272Vagococcus humatus sp. nov., isolated from soil beneath a decomposing pig carcass.Sundararaman A, Srinivasan S, Lee SSInt J Syst Evol Microbiol10.1099/ijsem.0.0016252017Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Diaminopimelic Acid/chemistry, Enterococcaceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Sus scrofa/*microbiologyTranscriptome
Phylogeny32195646Vagococcus xieshaowenii sp. nov., isolated from snow finch (Montifringilla taczanowskii) cloacal content.Ge Y, Yang J, Lai XH, Zhang G, Jin D, Lu S, Wang B, Huang Y, Huang Y, Ren Z, Zhang X, Xu JInt J Syst Evol Microbiol10.1099/ijsem.0.0040612020Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, Cloaca/*microbiology, DNA, Bacterial/genetics, Enterococcaceae/*classification/isolation & purification, Fatty Acids/chemistry, Finches/*microbiology, Nucleic Acid Hybridization, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Tibet, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitle
6093Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15741)https://www.dsmz.de/collection/catalogue/details/culture/DSM-15741
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
39477Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/18214
54693Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 39187)https://www.ccug.se/strain?id=39187
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)
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
74756Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID14205.1StrainInfo: A central database for resolving microbial strain identifiers
120714Curators of the CIPCollection of Institut Pasteur (CIP 106118)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20106118