Strain identifier

BacDive ID: 17300

Type strain: Yes

Species: Vibrio chagasii

Strain Designation: R-3712

Strain history: <- CAIM

NCBI tax ID(s): 170679 (species)

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General

@ref: 6785

BacDive-ID: 17300

DSM-Number: 17138

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic

description: Vibrio chagasii R-3712 is an aerobe, mesophilic bacterium that was isolated from gut of turbot larvae .

NCBI tax id

  • NCBI tax id: 170679
  • Matching level: species

strain history

  • @ref: 6785
  • history: <- CAIM

doi: 10.13145/bacdive17300.20230509.8.1

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 chagasii
  • full scientific name: Vibrio chagasii Thompson et al. 2003

@ref: 6785

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio chagasii

full scientific name: Vibrio chagasii Thompson et al. 2003

strain designation: R-3712

type strain: yes

Culture and growth conditions

culture medium

  • @ref: 6785
  • name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514c
  • composition: Name: REACTIVATION WITH LIQUID MEDIUM 514 (DSMZ Medium 514c) Composition: NaCl 19.45 g/l Agar 18.0 g/l MgCl2 5.9 g/l Bacto peptone 5.0 g/l Na2SO4 3.24 g/l CaCl2 1.8 g/l Yeast extract 1.0 g/l KCl 0.55 g/l Na2CO3 0.16 g/l Fe(III) citrate 0.1 g/l KBr 0.08 g/l SrCl2 0.034 g/l H3BO3 0.022 g/l Na2HPO4 0.008 g/l Na-silicate 0.004 g/l NaF 0.0024 g/l (NH4)NO3 0.0016 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
6785positivegrowth28mesophilic
58269positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 58269
  • oxygen tolerance: aerobe

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate-assimilation
6836917306maltose+assimilation
6836959640N-acetylglucosamine+assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose-assimilation
6836930849L-arabinose-assimilation
6836917634D-glucose+assimilation
683695291gelatin+hydrolysis
683694853esculin-hydrolysis
6836916199urea-hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose+fermentation
6836927897tryptophan+energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: yes

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: +

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase+
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
6785+++---+++--+++---++-+

Isolation, sampling and environmental information

isolation

  • @ref: 6785
  • sample type: gut of turbot larvae (Scophthalmus maximus)
  • host species: Scophthalmus maximus
  • geographic location: Austevoll
  • country: Norway
  • origin.country: NOR
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Host#Fishes
#Host Body-Site#Gastrointestinal tract#Stomach

taxonmaps

  • @ref: 69479
  • File name: preview.99_3109.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_71;97_361;98_409;99_3109&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: HM771345
  • Sequence Identity:
  • Total samples: 140
  • soil counts: 3
  • aquatic counts: 134
  • animal counts: 3

Safety information

risk assessment

  • @ref: 6785
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

@refdescriptionaccessionlengthdatabaseNCBI tax ID
20218Vibrio chagasii 16S ribosomal RNA gene, partial sequenceHM7713451471ena170679
6785Vibrio sp. R-3712 16S rRNA gene, strain R-3712AJ3161991435ena170679

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio chagasii LMG 21353GCA_005281815scaffoldncbi170679
66792Vibrio chagasii CCUG 48643GCA_008801295contigncbi170679
66792Vibrio chagasii strain CCUG 48643170679.8wgspatric170679
66792Vibrio chagasii strain LMG 21353170679.6wgspatric170679
66792Vibrio chagasii CCUG 486432845273529draftimg170679
66792Vibrio chagasii LMG 213532844774916draftimg170679
66792Vibrio chagasii LMG 21353GCA_024347355completencbi170679

GC content

  • @ref: 6785
  • GC-content: 44.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedyes87.276no
gram-positiveno98.515no
anaerobicno96.33yes
aerobicyes77.617no
halophileyes61.513no
spore-formingno94.51no
motileyes90.741no
glucose-fermentyes86.463yes
thermophileno99.694no
glucose-utilyes91.911no

External links

@ref: 6785

culture collection no.: CIP 108276, DSM 17138, CAIM 431, CCUG 48643, LMG 21353

straininfo link

  • @ref: 86300
  • straininfo: 18084

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny12807197Vibrio kanaloae sp. nov., Vibrio pomeroyi sp. nov. and Vibrio chagasii sp. nov., from sea water and marine animals.Thompson FL, Thompson CC, Li Y, Gomez-Gil B, Vandenberghe J, Hoste B, Swings JInt J Syst Evol Microbiol10.1099/ijs.0.02490-02003Animals, Bacterial Typing Techniques, Base Composition, Bass/microbiology, DNA, Ribosomal/analysis, Flatfishes/microbiology, *Marine Biology, Molecular Sequence Data, Mollusca/microbiology, Nucleic Acid Hybridization, Penaeidae/microbiology, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Rotifera/microbiology, Seawater/*microbiology, Sequence Analysis, DNA, Vibrio/chemistry/*classification/geneticsGenetics
Phylogeny31172330Vibrio profundi sp. nov., isolated from a deep-sea seamount.Zhang NX, Zhang DC, Qiao NHAntonie Van Leeuwenhoek10.1007/s10482-019-01286-42019Genome, Bacterial, Geologic Sediments/*microbiology, Multilocus Sequence Typing, Pacific Ocean, Phenotype, Phylogeny, Seawater/*microbiology, Vibrio/chemistry/*classification/isolation & purification, Whole Genome SequencingGenetics

Reference

@idauthorscataloguedoi/urltitlejournalpubmed
6785Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17138)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17138
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
20218Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P.10.1016/j.syapm.2013.11.002StrainInfo introduces electronic passports for microorganisms.Syst Appl Microbiol. 37: 42-50 201424321274
58269Curators of the CCUGCulture Collection University of Gothenburg (CCUG) (CCUG 48643)https://www.ccug.se/strain?id=48643
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)
68369Automatically annotated from API 20NE
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
86300Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID18084.1StrainInfo: A central database for resolving microbial strain identifiers