Strain identifier

BacDive ID: 5595

Type strain: Yes

Species: Aquimarina spongiae

Strain Designation: A6

Strain history: <- BJ Yoon, Jeju Natl. Univ

NCBI tax ID(s): 570521 (species)

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General

@ref: 16433

BacDive-ID: 5595

DSM-Number: 22623

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

description: Aquimarina spongiae A6 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from marine sponge, Halichondria oshoro.

NCBI tax id

  • NCBI tax id: 570521
  • Matching level: species

strain history

@refhistory
16433<- B.-J. Yoon, Jeju National Univ., Rep. of Korea; A6
67771<- BJ Yoon, Jeju Natl. Univ

doi: 10.13145/bacdive5595.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/bacteroidota
  • domain: Bacteria
  • phylum: Bacteroidota
  • class: Flavobacteriia
  • order: Flavobacteriales
  • family: Flavobacteriaceae
  • genus: Aquimarina
  • species: Aquimarina spongiae
  • full scientific name: Aquimarina spongiae Yoon et al. 2011

@ref: 16433

domain: Bacteria

phylum: Bacteroidetes

class: Flavobacteriia

order: Flavobacteriales

family: Flavobacteriaceae

genus: Aquimarina

species: Aquimarina spongiae

full scientific name: Aquimarina spongiae Yoon et al. 2011 emend. Park et al. 2013

strain designation: A6

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
29832negative4.75 µm0.3 µmrod-shaped
67771rod-shapedno
67771negative
69480negative99.994

pigmentation

  • @ref: 29832
  • production: yes

Culture and growth conditions

culture medium

  • @ref: 16433
  • 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
16433positivegrowth28mesophilic
29832positivegrowth10-35
29832positiveoptimum32.5mesophilic
67771positivegrowth30mesophilic

culture pH

@refabilitytypepHPH range
29832positivegrowth06-11alkaliphile
29832positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
29832aerobe
67771aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
29832NaClpositivegrowth01-05 %
29832NaClpositiveoptimum3 %

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
2983217234glucose+carbon source
298324853esculin+hydrolysis

enzymes

@refvalueactivityec
29832acid phosphatase+3.1.3.2
29832alkaline phosphatase+3.1.3.1
29832catalase+1.11.1.6
29832gelatinase+
29832cytochrome oxidase+1.9.3.1

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
16433marine sponge, Halichondria oshoroHalichondria oshoroJeju, coastal areaRepublic of KoreaKORAsia
67771From marine sponge, `Halichondria oshoro`the coast of Jeju IslandRepublic of KoreaKORAsia

isolation source categories

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

taxonmaps

  • @ref: 69479
  • File name: preview.99_17298.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_8899;97_10694;98_13108;99_17298&stattab=map
  • Last taxonomy: Aquimarina spongiae subclade
  • 16S sequence: FJ348470
  • Sequence Identity:
  • Total samples: 725
  • soil counts: 30
  • aquatic counts: 587
  • animal counts: 101
  • plant counts: 7

Safety information

risk assessment

  • @ref: 16433
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 16433
  • description: Aquimarina spongiae strain A6 16S ribosomal RNA gene, partial sequence
  • accession: FJ348470
  • length: 1420
  • database: ena
  • NCBI tax ID: 570521

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Aquimarina spongiae DSM 22623GCA_900141785scaffoldncbi570521
66792Aquimarina spongiae strain DSM 22623570521.3wgspatric570521
66792Aquimarina spongiae DSM 226232622736502draftimg570521

GC content

@refGC-contentmethod
1643336.0thermal denaturation, midpoint method (Tm)
2983236
6777136.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno89.275no
flagellatedno94.301yes
gram-positiveno97.216no
anaerobicno99.592yes
aerobicyes92.589yes
halophileno51.502no
spore-formingno93.215no
thermophileno99.432yes
glucose-utilyes86.431yes
glucose-fermentno90.604no

External links

@ref: 16433

culture collection no.: DSM 22623, KCTC 22663

straininfo link

  • @ref: 75077
  • straininfo: 404718

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny20348323Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro.Yoon BJ, You HS, Lee DH, Oh DCInt J Syst Evol Microbiol10.1099/ijs.0.022046-02010Animals, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Phenotype, *Phylogeny, Porifera/*microbiology, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysisGenetics
Phylogeny36223175Aquimarina acroporae sp. nov., isolated from seawater surrounding scleractinian coral Acropora digitifera.Sun H, Rao C, Yang X, Xie Z, Chen B, Zheng H, Liao B, Xiao BInt J Syst Evol Microbiol10.1099/ijsem.0.0056072022Animals, *Anthozoa, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Flavobacteriaceae, Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sequence Analysis, DNA, Sodium Chloride, Vitamin K 2/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
16433Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22623)https://www.dsmz.de/collection/catalogue/details/culture/DSM-22623
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
29832Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2620828776041
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
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
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
75077Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID404718.1StrainInfo: A central database for resolving microbial strain identifiers