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BacDive ID 133543
Type strain
Strain Designation CD276, CD 276
Culture col. no. LMG 24833 CIP 109914 CD276 CCM 8416 CD 276
NCBI tax ID(s) 633807
Links
For citation purpose refer to the digital object identifier (doi) of the current version.

Archive

version 9.3 (current version):
version 9.3 (current version)

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

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