Strain identifier

BacDive ID: 132167

Type strain: Yes

Species: Vibrio cortegadensis

Strain Designation: C 16.17

Strain history: CIP <- 2014, CECT <- 2006, JL Romalde, Santiago de Compostela Univ., Santiago de Compostela, Spain: strain C 16.17

NCBI tax ID(s): 1328770 (species)

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General

@ref: 23956

BacDive-ID: 132167

DSM-Number: 102805

keywords: genome sequence, 16S sequence, Bacteria, Gram-negative, motile, rod-shaped

description: Vibrio cortegadensis C 16.17 is a Gram-negative, motile, rod-shaped bacterium that was isolated from healthy Manila clam .

NCBI tax id

  • NCBI tax id: 1328770
  • Matching level: species

strain history

@refhistory
23956<- CECT <- A. Lasa, Centro de Investigaciones Biológicas, Universidad de Santiago de Compostela, Spain <- R. Beaz
118758CIP <- 2014, CECT <- 2006, JL Romalde, Santiago de Compostela Univ., Santiago de Compostela, Spain: strain C 16.17

doi: 10.13145/bacdive132167.20240916.9.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Gammaproteobacteria
  • order: Vibrionales
  • family: Vibrionaceae
  • genus: Vibrio
  • species: Vibrio cortegadensis
  • full scientific name: Vibrio cortegadensis Lasa et al. 2014

@ref: 23956

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio cortegadensis

full scientific name: Vibrio cortegadensis Lasa et al. 2014

strain designation: C 16.17

type strain: yes

Morphology

cell morphology

@refgram stainconfidencecell shapemotility
69480negative99.917
118758negativerod-shapedyes

Culture and growth conditions

culture medium

@refnamegrowthcompositionlink
41595Marine agar (MA)yesDistilled water make up to (1000.000 ml);Marine agar (55.100 g)
23956HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a)yesName: HALF STRENGTH BACTO MARINE BROTH (DSMZ Medium 514a) Composition: Agar 15.0 g/l NaCl 9.725 g/l MgCl2 2.95 g/l Bacto peptone 2.5 g/l Na2SO4 1.62 g/l CaCl2 0.9 g/l Yeast extract 0.5 g/l KCl 0.275 g/l NaHCO3 0.08 g/l Fe(III) citrate 0.05 g/l KBr 0.04 g/l SrCl2 0.017 g/l H3BO3 0.011 g/l Na2HPO4 0.004 g/l Na-silicate 0.002 g/l NaF 0.0012 g/l (NH4)NO3 0.0008 g/l Distilled waterhttps://mediadive.dsmz.de/medium/514a
118758CIP Medium 13yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13
118758CIP Medium 45yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=45

culture temp

@refgrowthtypetemperature
23956positivegrowth25
41595positivegrowth30

Physiology and metabolism

spore formation

  • @ref: 69480
  • spore formation: no
  • confidence: 90.734

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836830849L-arabinose-fermentation
6836827613amygdalin-fermentation
6836828053melibiose-fermentation
6836817992sucrose-fermentation
6836862345L-rhamnose-fermentation
6836830911sorbitol-fermentation
6836817268myo-inositol-fermentation
6836816899D-mannitol-fermentation
6836817634D-glucose+fermentation
683685291gelatin-hydrolysis
6836827897tryptophan+energy source
6836816199urea-hydrolysis
6836816947citrate-assimilation
6836818257ornithine-degradation
6836825094lysine-degradation
6836829016arginine+hydrolysis

metabolite production

@refChebi-IDmetaboliteproduction
6836815688acetoinno
6836835581indoleyes
6836816136hydrogen sulfideno

metabolite tests

@refChebi-IDmetabolitevoges-proskauer-testindole test
6836815688acetoin-
6836835581indole+

enzymes

@refvalueactivityec
68368cytochrome oxidase+1.9.3.1
68368gelatinase-
68368tryptophan deaminase-4.1.99.1
68368urease-3.5.1.5
68368ornithine decarboxylase-4.1.1.17
68368lysine decarboxylase-4.1.1.18
68368arginine dihydrolase+3.5.3.6
68368beta-galactosidase-3.2.1.23

API 20E

@refONPGADH ArgLDC LysODCCITH2SURETDA TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOX
23956-+------+--+--------+

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentisolation date
23956healthy Manila clam ( Venerupis philippinarum)Venerupis philippinarumCortegada Island, Carril, GaliciaSpainESPEurope
118758Healthy culture Manila clam, Ruditapes PhilippinarumCarril (A Coruna), SpainSpainESPEurope2005-01-03

isolation source categories

  • Cat1: #Host
  • Cat2: #Invertebrates (Other)
  • Cat3: #Mollusca

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
239561Risk group (German classification)
1187582Risk group (French classification)

Sequence information

16S sequences

  • @ref: 23956
  • description: Vibrio cortegadensis partial 16S rRNA gene, strain CECT 7227
  • accession: HF955037
  • length: 1417
  • database: nuccore
  • NCBI tax ID: 1328770

Genome sequences

  • @ref: 66792
  • description: Vibrio cortegadensis CECT 7227
  • accession: GCA_024347395
  • assembly level: complete
  • database: ncbi
  • NCBI tax ID: 1328770

Genome-based predictions

predictions

@reftraitmodeldescriptionpredictionconfidencetraining_data
69480gram-positivegram-positivePositive reaction to Gram-stainingno99.917no
69480anaerobicanaerobicAbility to grow under anoxygenic conditions (including facultative anaerobes)no95.372no
69480aerobicaerobicAbility to grow under oxygenic conditions (including facultative aerobes)no68.239no
69480spore-formingspore-formingAbility to form endo- or exosporesno90.734no
69480thermophilicthermophileAbility to grow at temperatures above or equal to 45°Cno98yes
69480flagellatedmotile2+Ability to perform flagellated movementyes87.446no

External links

@ref: 23956

culture collection no.: DSM 102805, CECT 7227, LMG 27474, CIP 110813, LMG 27475

straininfo link

  • @ref: 90522
  • straininfo: 376929

literature

  • topic: Phylogeny
  • Pubmed-ID: 24271473
  • title: Vibrio cortegadensis sp. nov., isolated from clams.
  • authors: Lasa A, Dieguez AL, Romalde JL
  • journal: Antonie Van Leeuwenhoek
  • DOI: 10.1007/s10482-013-0078-z
  • year: 2013
  • mesh: Animals, Bacterial Proteins/genetics, Bacterial Typing Techniques, Bivalvia/*microbiology, Cluster Analysis, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Spain, Vibrio/chemistry/*classification/genetics/*isolation & purification
  • topic2: Genetics

Reference

@idauthorstitledoi/urlcatalogue
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
23956Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-102805Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 102805)
41595Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/30626
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
68368Automatically annotated from API 20E
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
90522Reimer, 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-ID376929.1
118758Curators of the CIPhttps://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20110813Collection of Institut Pasteur (CIP 110813)