Strain identifier

BacDive ID: 133543

Type strain: Yes

Species: Vagococcus penaei

Strain Designation: CD276, CD 276

Strain history: CIP <- 2008, E. Jaffrès, INRA, Nantes, France: strain CD 276

NCBI tax ID(s): 633807 (species)

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General

@ref: 29425

BacDive-ID: 133543

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-positive, coccus-shaped

description: Vagococcus penaei CD276 is a facultative anaerobe, Gram-positive, coccus-shaped bacterium that was isolated from Shelled shrimp cook.

NCBI tax id

  • NCBI tax id: 633807
  • Matching level: species

strain history

@refhistory
376932008, E. Jaffrès, INRA, Nantes, France: strain CD 276
121657CIP <- 2008, E. Jaffrès, INRA, Nantes, France: strain CD 276

doi: 10.13145/bacdive133543.20250331.9.3

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 penaei
  • full scientific name: Vagococcus penaei Jaffrès et al. 2010

@ref: 29425

domain: Bacteria

phylum: Firmicutes

class: Bacilli

order: Lactobacillales

family: Enterococcaceae

genus: Vagococcus

species: Vagococcus penaei

strain designation: CD276, CD 276

type strain: yes

Morphology

cell morphology

@refgram staincell widthcell shapemotility
29425positive0.5-1 µmcoccus-shapedno
121657positiveoval-shapedyes

pigmentation

  • @ref: 29425
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
37693MEDIUM 29- Brain heart agaryesDistilled water make up to (1000.000 ml);Brain heart infusion agar (52.000 g)
121657CIP Medium 29yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=29

culture temp

@refgrowthtypetemperature
29425positivegrowth10-30
29425positiveoptimum30
37693positivegrowth30

culture pH

@refabilitytypepH
29425positivegrowth7
29425positiveoptimum7

Physiology and metabolism

oxygen tolerance

@refoxygen toleranceconfidence
29425facultative anaerobe
121657facultative anaerobe
125439microaerophile92.6

spore formation

  • @ref: 29425
  • spore formation: no

observation

  • @ref: 29425
  • observation: aggregates in chains

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2942517306maltose+carbon source
2942516634raffinose+carbon source
2942533942ribose+carbon source
2942517992sucrose+carbon source
2942527082trehalose+carbon source
12165717632nitrate-reduction
12165716301nitrite-reduction

metabolite production

  • @ref: 121657
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
29425acid phosphatase+3.1.3.2
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
68382acid phosphatase+3.1.3.2
68382naphthol-AS-BI-phosphohydrolase+
68382alpha-chymotrypsin+3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase+3.4.11.3
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
121657oxidase-
121657catalase-1.11.1.6
121657urease-3.5.1.5
68382valine arylamidase-
68382alkaline phosphatase+3.1.3.1

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
121657-+++-+-+-+++-+-+----

Isolation, sampling and environmental information

isolation

  • @ref: 121657
  • sample type: Shelled shrimp cook
  • geographic location: Nantes
  • country: France
  • origin.country: FRA
  • continent: Europe
  • isolation date: 2006

taxonmaps

  • @ref: 69479
  • File name: preview.99_3624.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_13;96_1881;97_2259;98_2772;99_3624&stattab=map
  • Last taxonomy: Vagococcus penaei
  • 16S sequence: FJ360897
  • Sequence Identity:
  • Total samples: 1025
  • soil counts: 25
  • aquatic counts: 74
  • animal counts: 863
  • plant counts: 63

Safety information

risk assessment

  • @ref: 121657
  • biosafety level: 1
  • biosafety level comment: Risk group (French classification)

Sequence information

16S sequences

  • @ref: 29425
  • description: Vagococcus penaei strain CD 276 16S ribosomal RNA gene, complete sequence
  • accession: FJ360897
  • length: 1550
  • database: nuccore
  • NCBI tax ID: 633807

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vagococcus penaei LMG 24833GCA_003987515contigncbi633807
66792Vagococcus penaei CD276TGCA_001998885completencbi633807
66792Vagococcus penaei strain CD276633807.3completepatric633807
66792Vagococcus penaei strain LMG 24833633807.5wgspatric633807
66792Vagococcus penaei LMG 248332894095031draftimg633807

GC content

  • @ref: 29425
  • GC-content: 35.4

Genome-based predictions

predictions

@refmodeltraitdescriptionpredictionconfidencetraining_data
125438gram-positivegram-positivePositive reaction to Gram-stainingyes86.15yes
125438anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no87.715yes
125438aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no96.332yes
125438spore-formingspore-formingAbility to form endo- or exosporesno71.881yes
125438thermophilethermophilicAbility to grow at temperatures above or equal to 45°Cno95.677yes
125438motile2+flagellatedAbility to perform flagellated movementyes56.833no
125439BacteriaNetspore_formationAbility to form endo- or exosporesyes53.5
125439BacteriaNetmotilityAbility to perform movementno52.6
125439BacteriaNetgram_stainReaction to gram-stainingpositive84.5
125439BacteriaNetoxygen_toleranceOxygenic conditions needed for growthmicroaerophile92.6

External links

@ref: 29425

culture collection no.: LMG 24833, CIP 109914, CCM 8416

straininfo link

  • @ref: 91496
  • straininfo: 360632

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny19897618Vagococcus penaei sp. nov., isolated from spoilage microbiota of cooked shrimp (Penaeus vannamei).Jaffres E, Prevost H, Rossero A, Joffraud JJ, Dousset XInt J Syst Evol Microbiol10.1099/ijs.0.012872-02009Animals, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Enterococcaceae/*classification/genetics/*isolation & purification/metabolism, Fatty Acids/metabolism, Molecular Sequence Data, Penaeidae/*microbiology, Phylogeny, RNA, Ribosomal, 16S/geneticsMetabolism
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
Phylogeny28857031Vagococcus martis sp. nov., isolated from the small intestine of a marten, Martes flavigula.Tak EJ, Kim HS, Lee JY, Kang W, Hyun DW, Kim PS, Shin NR, Bae JWInt J Syst Evol Microbiol10.1099/ijsem.0.0021312017Animals, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/genetics, Enterococcaceae/*classification/genetics/isolation & purification, Fatty Acids/chemistry, Intestine, Small/*microbiology, Mustelidae/*microbiology, Peptidoglycan/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/chemistryTranscriptome
Phylogeny29306597Vagococcus teuberi sp. nov., isolated from the Malian artisanal sour milk fene.Wullschleger S, Jans C, Seifert C, Baumgartner S, Lacroix C, Bonfoh B, Stevens MJA, Meile LSyst Appl Microbiol10.1016/j.syapm.2017.11.0032017Animals, Bacterial Typing Techniques, Base Composition, Cattle/microbiology, Cultured Milk Products/*microbiology, DNA, Bacterial/genetics, Enterococcaceae/classification/*genetics/*isolation & purification, Fatty Acids/chemistry, Mali, Milk/*microbiology, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorstitledoi/urlID_cross_referencepubmedjournalcatalogue
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
29425Barberan A, Caceres Velazquez H, Jones S, Fierer N.Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information10.1128/mSphere.00237-172583128776041
37693Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/7711
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar SchomburgBRENDA, the ELIXIR core data resource in 2021: new developments and updates10.1093/nar/gkaa102533211880Nucleic Acids Res. 49: D498-D508 2020
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
91496Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.StrainInfo: A central database for resolving microbial strain identifiers10.60712/SI-ID360632.1
121657Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109914Collection of Institut Pasteur (CIP 109914)
125438Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg OvermannPredicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets10.1101/2024.08.12.607695
125439Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardydeepG: Deep Learning for Genome Sequence Data. R package version 0.3.1https://github.com/GenomeNet/deepG