Strain identifier

BacDive ID: 132596

Type strain: Yes

Species: Vibrio algivorus

Strain Designation: SA2

Strain history: <- H. Doi, Ajinomoto Co., Inc, Kawasaki-shi, Japan; SA2

NCBI tax ID(s): 1667024 (species)

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General

@ref: 24385

BacDive-ID: 132596

DSM-Number: 29824

keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, Gram-negative, rod-shaped, colony-forming

description: Vibrio algivorus SA2 is a facultative anaerobe, Gram-negative, rod-shaped bacterium that forms circular colonies and was isolated from gut from a turban shell sea snail .

NCBI tax id

  • NCBI tax id: 1667024
  • Matching level: species

strain history

  • @ref: 24385
  • history: <- H. Doi, Ajinomoto Co., Inc, Kawasaki-shi, Japan; SA2

doi: 10.13145/bacdive132596.20230509.8.1

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 algivorus
  • full scientific name: Vibrio algivorus Doi et al. 2016

@ref: 24385

domain: Bacteria

phylum: Proteobacteria

class: Gammaproteobacteria

order: Vibrionales, not validated

family: Vibrionaceae

genus: Vibrio

species: Vibrio algivorus

full scientific name: Vibrio algivorus Doi et al. 2016

strain designation: SA2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
43598negative1.5-2.5 µm0.7-0.8 µmrod-shapedno
69480negative99.979

colony morphology

  • @ref: 43598
  • colony size: 2-3 mm
  • colony color: Pale yellow
  • colony shape: circular
  • incubation period: 1 day
  • medium used: Marine broth 2216 plates

multimedia

  • @ref: 24385
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_29824.jpg
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
43598Marine broth 2216 platesyes
24385BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514)yeshttps://mediadive.dsmz.de/medium/514Name: 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
43598positivegrowth4-40
43598positiveoptimum25-30mesophilic
24385positivegrowth28mesophilic

culture pH

@refabilitytypepHPH range
43598positivegrowth5.5-9.5alkaliphile
43598positiveoptimum7-8

Physiology and metabolism

oxygen tolerance

  • @ref: 43598
  • oxygen tolerance: facultative anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.998

halophily

@refsaltgrowthtested relationconcentrationhalophily level
43598NaClpositivegrowth1-14 %
43598NaClnogrowth0 %non-halophilic
43598NaClnogrowth15 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4359817128adipate-carbon source
4359822599arabinose-carbon source
4359827689decanoate-carbon source
4359816947citrate-carbon source
4359817306maltose-carbon source
4359829864mannitol-carbon source
4359837684mannose-carbon source
43598506227N-acetylglucosamine-carbon source
4359817128adipate-energy source
4359822599arabinose-energy source
4359827689decanoate-energy source
4359816947citrate-energy source
4359817306maltose-energy source
4359829864mannitol-energy source
4359837684mannose-energy source
43598506227N-acetylglucosamine-energy source
4359825115malate+carbon source
4359824265gluconate+carbon source
4359817234glucose+carbon source
4359825115malate+energy source
4359824265gluconate+energy source
4359817234glucose+energy source
4359817632nitrate+reduction

metabolite production

  • @ref: 43598
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

enzymes

@refvalueactivityec
43598catalase+1.11.1.6
43598cytochrome oxidase+1.9.3.1
43598alkaline phosphatase+3.1.3.1
43598esterase (C 4)+
43598leucine arylamidase+3.4.11.1
43598valine arylamidase+
43598acid phosphatase+3.1.3.2
43598naphthol-AS-BI-phosphohydrolase+
43598beta-galactosidase+3.2.1.23
43598N-acetyl-beta-glucosaminidase+3.2.1.52
43598esterase Lipase (C 8)-
43598arginine dihydrolase-3.5.3.6
43598lipase (C 14)-
43598cystine arylamidase-3.4.11.3
43598trypsin-3.4.21.4
43598chymotrypsin-3.4.4.5
43598alpha-galactosidase-3.2.1.22
43598beta-glucuronidase-3.2.1.31
43598alpha-glucosidase-3.2.1.20
43598beta-glucosidase-3.2.1.21
43598alpha-mannosidase-3.2.1.24
43598alpha-fucosidase-3.2.1.51

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinentlatitudelongitude
24385gut from a turban shell sea snail (Turbo cornutus)Turbo cornutusIshikawa Prefecture, near Noto Peninsula (37° 09' N 137° 05''E)JapanJPNAsia37.15137.083
43598live turban shell caught near the Noto IslandNoto IslandJapanJPNAsia37.15137.083

isolation source categories

Cat1Cat2Cat3
#Host Body-Site#Gastrointestinal tract
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Mollusca

taxonmaps

  • @ref: 69479
  • File name: preview.99_13390.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_982;97_1142;98_1364;99_13390&stattab=map
  • Last taxonomy: Vibrio rumoiensis
  • 16S sequence: LC060680
  • Sequence Identity:
  • Total samples: 330
  • soil counts: 16
  • aquatic counts: 229
  • animal counts: 63
  • plant counts: 22

Safety information

risk assessment

  • @ref: 24385
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 24385
  • description: Vibrio algivorus gene for 16S ribosomal RNA, partial sequence, strain: SA2
  • accession: LC060680
  • length: 1492
  • database: ena
  • NCBI tax ID: 1667024

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Vibrio algivorus NBRC 111146GCA_002218005scaffoldncbi1667024
66792Vibrio algivorus strain NBRC1111461667024.3wgspatric1667024

GC content

@refGC-contentmethod
4359840.7
2438540.7sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno69.249yes
gram-positiveno98.811yes
anaerobicno99.34yes
aerobicyes83.124no
halophileyes83.051no
spore-formingno96.802no
thermophileno99.607yes
glucose-utilyes91.806yes
flagellatedno80.05yes
glucose-fermentyes87.537no

External links

@ref: 24385

culture collection no.: DSM 29824, NBRC 111146

straininfo link

  • @ref: 90913
  • straininfo: 399526

literature

  • topic: Phylogeny
  • Pubmed-ID: 27199227
  • title: Vibrio algivorus sp. nov., an alginate- and agarose-assimilating bacterium isolated from the gut flora of a turban shell marine snail.
  • authors: Doi H, Chinen A, Fukuda H, Usuda Y
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001165
  • year: 2016
  • mesh: Alginates, Animals, Aquatic Organisms/microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gastrointestinal Microbiome, Glucuronic Acid, Hexuronic Acids, Japan, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sepharose, Sequence Analysis, DNA, Snails/*microbiology, Ubiquinone/chemistry, Vibrio/*classification/genetics/isolation & purification
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urlcataloguejournalpubmed
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
24385Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-29824Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 29824)
43598Hidetaka Doi, Akito Chinen, Hiroo Fukuda, Yoshihiro UsudaVibrio algivorus sp. nov., an alginate- and agarose-assimilating bacterium isolated from the gut flora of a turban shell marine snail10.1099/ijsem.0.001165IJSEM 66: 3164-3169 201627199227
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
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
90913Reimer, 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-ID399526.1