Strain identifier

BacDive ID: 5268

Type strain: Yes

Species: Vagococcus elongatus

Strain Designation: PPC9

Strain history: CIP <- CCUG 2007 <- 2005, T. Whitehead, USDA, Peoria, IL, USA: strain PPC9

NCBI tax ID(s): 180344 (species)

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General

@ref: 15731

BacDive-ID: 5268

DSM-Number: 21480

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

description: Vagococcus elongatus PPC9 is a microaerophile, mesophilic, Gram-positive bacterium that was isolated from swine-manure storage pit.

NCBI tax id

  • NCBI tax id: 180344
  • Matching level: species

strain history

@refhistory
15731<- CCUG <- T. R. Whitehead, USDA, Peoria, IL, USA; PPC9
119019CIP <- CCUG 2007 <- 2005, T. Whitehead, USDA, Peoria, IL, USA: strain PPC9

doi: 10.13145/bacdive5268.20230509.8.1

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 elongatus
  • full scientific name: Vagococcus elongatus Lawson et al. 2007

@ref: 15731

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Vagococcus

species: Vagococcus elongatus

full scientific name: Vagococcus elongatus Lawson et al. 2007

strain designation: PPC9

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotilityconfidence
31968positivecoccus-shapedno
69480no93.05
69480positive100
119019positivecoccus-shapedno

pigmentation

  • @ref: 31968
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
15731TRYPTICASE 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
37767MEDIUM 6 - Columbia agar with 10 % horse bloodyesDistilled water make up to (1000.000 ml);Columbia agar (39.000 g);Horseblood (100.000 ml)
119019CIP Medium 6yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=6

culture temp

@refgrowthtypetemperaturerange
15731positivegrowth37mesophilic
31968positiveoptimum37mesophilic
37767positivegrowth37mesophilic
59187positivegrowth37mesophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
15731microaerophile
15731aerobe
31968anaerobe
59187microaerophile

spore formation

@refspore formationconfidence
31968no
69481no99
69480no99.821

observation

  • @ref: 31968
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
319684853esculin+hydrolysis
11901917632nitrate-reduction
11901916301nitrite-reduction
6838016199urea-hydrolysis
6838029016arginine-hydrolysis
6838016024D-mannose+fermentation
6838016634raffinose+fermentation
6838029985L-glutamate-degradation
6838017632nitrate-reduction
6838027897tryptophan-energy source

metabolite production

@refChebi-IDmetaboliteproduction
11901935581indoleno
6838035581indoleno

metabolite tests

  • @ref: 68380
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
31968alkaline phosphatase+3.1.3.1
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
68380serine arylamidase-
68380glutamyl-glutamate arylamidase-
68380histidine arylamidase-
68380glycin arylamidase-
68380alanine arylamidase-3.4.11.2
68380tyrosine arylamidase+
68380pyrrolidonyl arylamidase-3.4.19.3
68380leucine arylamidase-3.4.11.1
68380phenylalanine arylamidase+
68380leucyl glycin arylamidase-3.4.11.1
68380proline-arylamidase-3.4.11.5
68380L-arginine arylamidase-
68380alkaline phosphatase-3.1.3.1
68380tryptophan deaminase-4.1.99.1
68380alpha-fucosidase-3.2.1.51
68380glutamate decarboxylase-4.1.1.15
68380N-acetyl-beta-glucosaminidase+3.2.1.52
68380beta-glucuronidase-3.2.1.31
68380alpha-arabinosidase-3.2.1.55
68380beta-glucosidase+3.2.1.21
68380alpha-glucosidase+3.2.1.20
68380beta-Galactosidase 6-phosphate-
68380beta-galactosidase-3.2.1.23
68380alpha-galactosidase+3.2.1.22
68380arginine dihydrolase-3.5.3.6
68380urease-3.5.1.5
119019oxidase-
119019catalase-1.11.1.6
119019urease-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
119019-+++-+----++---++---

API rID32A

@refUREADH Argalpha GALbeta GALbeta GPalpha GLUbeta GLUalpha ARAbeta GURbeta NAGMNERAFGDCalpha FUCNITINDPALArgAProALGAPheALeuAPyrATyrAAlaAGlyAHisAGGASerA
15731--+--++--+++--------+--+-----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinentsampling dateisolation date
15731swine-manure storage pitPeoriaUSAUSANorth America
59187Stored swine manureIL,PeoriaUSAUSANorth America1998
119019Stored swine manurePeoria, IllinoisUnited States of AmericaUSANorth America1998

isolation source categories

Cat1Cat2Cat3
#Engineered#Built environment#Container (Reservoir)
#Host#Mammals#Suidae (Pig,Swine)
#Host Body Product#Gastrointestinal tract#Feces (Stool)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
157311Risk group (German classification)
1190191Risk group (French classification)

Sequence information

16S sequences

  • @ref: 15731
  • description: UNVERIFIED: Vagococcus elongatus strain PPC9 16S ribosomal RNA gene, partial sequence
  • accession: AF445297
  • length: 1554
  • database: ena
  • NCBI tax ID: 180344

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vagococcus elongatus CCUG 51432GCA_003987645contigncbi180344
66792Vagococcus elongatus strain CCUG 51432180344.3wgspatric180344
66792Vagococcus elongatus CCUG 514322894097338draftimg180344

GC content

  • @ref: 15731
  • GC-content: 44.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno99no
motileno94.788yes
gram-positiveyes93.054no
anaerobicno86.313no
aerobicno97.595no
halophileyes65.212no
spore-formingno88.538no
glucose-utilyes89.003no
flagellatedno97.006yes
thermophileno95.505yes
glucose-fermentyes81.298no

External links

@ref: 15731

culture collection no.: DSM 21480, CCUG 51432, NRRL B-41357, CIP 109559, CCM 8415

straininfo link

  • @ref: 74758
  • straininfo: 296138

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17392200Vagococcus elongatus sp. nov., isolated from a swine-manure storage pit.Lawson PA, Falsen E, Cotta MA, Whitehead TRInt J Syst Evol Microbiol10.1099/ijs.0.64730-02007Anaerobiosis, Animals, Bacillus/*classification/genetics/isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Manure/*microbiology, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Swine/*microbiologyGenetics
Phylogeny20543153Vagococcus acidifermentans sp. nov., isolated from an acidogenic fermentation bioreactor.Wang L, Cui YS, Kwon CS, Lee ST, Lee JS, Im WTInt J Syst Evol Microbiol10.1099/ijs.0.022087-02010Acids/*metabolism, Bioreactors/*microbiology, DNA, Bacterial/genetics, Enterococcaceae/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, *Fermentation, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Waste Disposal, FluidMetabolism
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
Phylogeny33355894Vagococcus zengguangii sp. nov., isolated from yak faeces.Ge Y, Jin D, Lai XH, Yang J, Lu S, Huang Y, Zheng H, Zhang X, Xu JJ Microbiol10.1007/s12275-021-0406-32020Animals, Bacterial Typing Techniques, Base Composition, Cattle, DNA, Bacterial/genetics, Enterococcaceae/classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Feces/*microbiology, Genome, Bacterial, RNA, Ribosomal, 16S/geneticsMetabolism

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15731Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 21480)https://www.dsmz.de/collection/catalogue/details/culture/DSM-21480
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
31968Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2822328776041
37767Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7316
59187Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 51432)https://www.ccug.se/strain?id=51432
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 updates33211880Nucleic Acids Res. 49: D498-D508 2020
68380Automatically annotated from API rID32A
68382Automatically annotated from API zym
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
74758Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID296138.1StrainInfo: A central database for resolving microbial strain identifiers
119019Curators of the CIPCollection of Institut Pasteur (CIP 109559)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109559