Strain identifier

BacDive ID: 139783

Type strain: Yes

Species: Vibrio aphrogenes

Strain Designation: CA-1004

Strain history: T. Sawabe; Fac. of Fish. Sci., Hokkaido Univ., Japan; CA-1004.

NCBI tax ID(s): 1891186 (species)

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General

@ref: 42391

BacDive-ID: 139783

DSM-Number: 103759

keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative

description: Vibrio aphrogenes CA-1004 is a mesophilic, Gram-negative bacterium that was isolated from surface of seaweed.

NCBI tax id

  • NCBI tax id: 1891186
  • Matching level: species

strain history

@refhistory
42391<- T. Sawabe, Hokkaido University, Japan; CA-1004 <- T. Araki, Iga Research Institute of Mie University, Iga, Japan
67770T. Sawabe; Fac. of Fish. Sci., Hokkaido Univ., Japan; CA-1004.

doi: 10.13145/bacdive139783.20230509.8.1

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 aphrogenes
  • full scientific name: Vibrio aphrogenes Tanaka et al. 2018

@ref: 42391

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio aphrogenes

full scientific name: Vibrio aphrogenes Tanaka et al. 2018

strain designation: CA-1004

type strain: yes

Morphology

cell morphology

  • @ref: 69480
  • gram stain: negative
  • confidence: 99.874

Culture and growth conditions

culture medium

  • @ref: 42391
  • name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/514
  • composition: Name: BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) Composition: NaCl 19.45 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 NaHCO3 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
42391positivegrowth28mesophilic
67770positivegrowth25mesophilic

Physiology and metabolism

spore formation

@refspore formationconfidence
69481no100
69480no99.953

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836817632nitrate+reduction
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
6836817997dinitrogenno
6836816301nitriteyes
6836815688acetoinno
6836835581indoleno
6836816136hydrogen sulfideyes

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 TrpINDVPGELGLUMANINOSorRHASACMELAMYARAOXNO2N2
42391-+---+-----++-----+-++-

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
42391surface of seaweedMie PrefectureJapanJPNAsia
67770Surface of seaweed collected on the coast of Mie Pref.JapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Host#Algae
#Host#Plants#Aquatic plant
#Host Body-Site#Plant#Leaf (Phyllosphere)

taxonmaps

  • @ref: 69479
  • File name: preview.99_132185.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_982;97_1142;98_88410;99_132185&stattab=map
  • Last taxonomy: Vibrio
  • 16S sequence: KX713151
  • Sequence Identity:
  • Total samples: 152
  • soil counts: 5
  • aquatic counts: 74
  • animal counts: 66
  • plant counts: 7

Sequence information

16S sequences

  • @ref: 42391
  • description: Vibrio aphrogenes strain CA-1004 16S ribosomal RNA gene, partial sequence
  • accession: KX713151
  • length: 1477
  • database: ena
  • NCBI tax ID: 1891186

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio aphrogenes CA-10042791355440draftimg1891186
67770Vibrio aphrogenes CA-1004GCA_002157735completencbi1891186

GC content

  • @ref: 67770
  • GC-content: 42.1
  • method: genome sequence analysis

Genome-based predictions

predictions

  • trait: spore-forming
  • prediction: no
  • confidence: 100
  • training_data: no

External links

@ref: 42391

culture collection no.: DSM 103759, JCM 31643

straininfo link

  • @ref: 96226
  • straininfo: 405660

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny28662104Vibrio aphrogenes sp. nov., in the Rumoiensis clade isolated from a seaweed.Tanaka M, Endo S, Kotake F, Al-Saari N, Amin AKMR, Feng G, Mino S, Doi H, Ogura Y, Hayashi T, Suda W, Hattori M, Yumoto I, Sawabe T, Sawabe T, Araki TPLoS One10.1371/journal.pone.01800532017DNA, Bacterial/genetics, Genes, Bacterial, Nucleic Acid Hybridization, Phylogeny, RNA, Ribosomal, 16S/genetics, Seaweed/*microbiology, Vibrio/classification/*genetics
Phylogeny29676719Vibrio gangliei sp. nov., a novel member of Vibrionaceae isolated from sawdust in a pigpen.Meng YC, Liu HC, Zhou YG, Cai M, Kang YInt J Syst Evol Microbiol10.1099/ijsem.0.0027792018Animals, Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Housing, Animal, Multilocus Sequence Typing, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Swine, Vibrio/*classification/genetics/isolation & purificationTranscriptome

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
42391Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103759Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103759)
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
68368Automatically annotated from API 20E
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/
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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
96226Reimer, 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-ID405660.1