Strain identifier

BacDive ID: 23228

Type strain: Yes

Species: Pseudovibrio axinellae

Strain Designation: Ad2

Strain history: <- J. O'Halloran, University College Cork, Microbiology, Ireland; Ad2

NCBI tax ID(s): 989403 (species)

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General

@ref: 19203

BacDive-ID: 23228

DSM-Number: 24994

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

description: Pseudovibrio axinellae Ad2 is an anaerobe, psychrophilic, Gram-negative bacterium that was isolated from marine sponge Axinella dissimilis from a marine lake.

NCBI tax id

  • NCBI tax id: 989403
  • Matching level: species

strain history

  • @ref: 19203
  • history: <- J. O'Halloran, University College Cork, Microbiology, Ireland; Ad2

doi: 10.13145/bacdive23228.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Stappiaceae
  • genus: Pseudovibrio
  • species: Pseudovibrio axinellae
  • full scientific name: Pseudovibrio axinellae O'Halloran et al. 2013

@ref: 19203

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Stappiaceae

genus: Pseudovibrio

species: Pseudovibrio axinellae

full scientific name: Pseudovibrio axinellae O'Halloran et al. 2013

strain designation: Ad2

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
30618negative2.75 µm0.85 µmrod-shapedyes
69480yes92.544
69480negative99.897

colony morphology

  • @ref: 19203
  • incubation period: 2-3 days

pigmentation

  • @ref: 30618
  • production: yes

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
19203SYP - SW MEDIUM (DSMZ Medium 1348)yeshttps://mediadive.dsmz.de/medium/1348Name: SYP - SW MEDIUM (DSMZ Medium 1348) Composition: Artificial Sea Salt 33.3 g/l Agar 20.0 g/l Starch 10.0 g/l Yeast extract 4.0 g/l Peptone 2.0 g/l Distilled water
19203BACTO 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
19203positivegrowth24psychrophilic
30618positivegrowth10-30
30618positiveoptimum24psychrophilic
19203positivegrowth25mesophilic

culture pH

@refabilitytypepHPH range
30618positivegrowth06-09alkaliphile
30618positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 30618
  • oxygen tolerance: anaerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

halophily

@refsaltgrowthtested relationconcentration
30618NaClpositivegrowth02-04 %
30618NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3061816000ethanolamine+carbon source
3061816449alanine+carbon source
3061822653asparagine+carbon source
3061835391aspartate+carbon source
3061823652dextrin+carbon source
3061833984fucose+carbon source
3061824265gluconate+carbon source
3061817234glucose+carbon source
3061829987glutamate+carbon source
3061817754glycerol+carbon source
30618182404-hydroxy-L-proline+carbon source
3061817596inosine+carbon source
3061824996lactate+carbon source
3061817306maltose+carbon source
3061837684mannose+carbon source
3061817268myo-inositol+carbon source
3061826271proline+carbon source
3061815361pyruvate+carbon source
3061816634raffinose+carbon source
3061817822serine+carbon source
3061830031succinate+carbon source
3061817992sucrose+carbon source
3061817748thymidine+carbon source
3061827082trehalose+carbon source
3061853423tween 40+carbon source
3061853426tween 80+carbon source
3061816704uridine+carbon source
306184853esculin+hydrolysis
3061817632nitrate+reduction

enzymes

@refvalueactivityec
30618acid phosphatase+3.1.3.2
30618alkaline phosphatase+3.1.3.1
30618catalase+1.11.1.6
30618gelatinase+
30618cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

  • @ref: 19203
  • sample type: marine sponge Axinella dissimilis from a marine lake
  • host species: Axinella dissimilis
  • geographic location: Cork, Lough Hyne
  • country: Ireland
  • origin.country: IRL
  • continent: Europe

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Lake (large)
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Porifera (Sponges)

taxonmaps

  • @ref: 69479
  • File name: preview.99_917.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_5;96_441;97_504;98_579;99_917&stattab=map
  • Last taxonomy: Pseudovibrio axinellae
  • 16S sequence: JN167515
  • Sequence Identity:
  • Total samples: 181
  • soil counts: 34
  • aquatic counts: 146
  • animal counts: 1

Safety information

risk assessment

  • @ref: 19203
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 19203
  • description: Pseudovibrio axinellae strain Ad2 16S ribosomal RNA gene, partial sequence
  • accession: JN167515
  • length: 1446
  • database: ena
  • NCBI tax ID: 989403

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Pseudovibrio axinellae DSM 24994GCA_900110875scaffoldncbi989403
66792Pseudovibrio axinellae Ad2GCA_001623255contigncbi989403
66792Pseudovibrio axinellae strain DSM 24994989403.4wgspatric989403
66792Pseudovibrio axinellae DSM 249942684622848draftimg989403
66792Pseudovibrio axinellae Ad22744054490draftimg989403

GC content

@refGC-contentmethod
1920350.5high performance liquid chromatography (HPLC)
3061850.5

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
glucose-fermentno85.24no
motileyes90.846yes
flagellatedyes59.754no
gram-positiveno98.11yes
anaerobicno97.544no
aerobicyes75.441yes
halophileyes63.42no
spore-formingno93.982no
thermophileno96.238yes
glucose-utilyes90.283yes

External links

@ref: 19203

culture collection no.: DSM 24994, NCIMB 14761

straininfo link

  • @ref: 87454
  • straininfo: 400895

literature

  • topic: Phylogeny
  • Pubmed-ID: 22368168
  • title: Pseudovibrio axinellae sp. nov., isolated from an Irish marine sponge.
  • authors: O'Halloran JA, Barbosa TM, Morrissey JP, Kennedy J, Dobson ADW, O'Gara F
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijs.0.040196-0
  • year: 2012
  • mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Ireland, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA
  • topic2: Genetics

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
19203Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 24994)https://www.dsmz.de/collection/catalogue/details/culture/DSM-24994
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
30618Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2694928776041
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)
66794Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg10.1093/nar/gkaa1025BRENDA, the ELIXIR core data resource in 2021: new developments and updates33211880Nucleic Acids Res. 49: D498-D508 2020
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
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch10.21203/rs.3.rs-2527258/v1Predictions based on the model GenomeNet Sporulation v. 1
87454Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID400895.1StrainInfo: A central database for resolving microbial strain identifiers