Strain identifier

BacDive ID: 17651

Type strain: Yes

Species: Coraliomargarita akajimensis

Strain Designation: 04OKA010-24, 04OKA10-24

Strain history: <- JW Yoon, Tokyo Univ. <- M Yasumoto-Hirose, MBI

For citation purpose refer to the digital object identifier (doi) of the current version.
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General

@ref: 15802

BacDive-ID: 17651

DSM-Number: 45221

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

description: Coraliomargarita akajimensis 04OKA010-24 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from seawater surrounding the hard coral x Galaxea fascicularis.

NCBI tax id

NCBI tax idMatching level
395922species
583355strain

strain history

@refhistory
15802<- JCM/RIKEN; JCM 23193 <- IAM; IAM 15411 <- J. Yoon et al.; 04OKA010-24
67770IAM 15411 <-- J. Yoon et al. 04OKA010-24.
67771<- JW Yoon, Tokyo Univ. <- M Yasumoto-Hirose, MBI

doi: 10.13145/bacdive17651.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/verrucomicrobiota
  • domain: Bacteria
  • phylum: Verrucomicrobiota
  • class: Opitutia
  • order: Puniceicoccales
  • family: Puniceicoccaceae
  • genus: Coraliomargarita
  • species: Coraliomargarita akajimensis
  • full scientific name: Coraliomargarita akajimensis Yoon et al. 2007

@ref: 15802

domain: Bacteria

phylum: Verrucomicrobia

class: Opitutae

order: Puniceicoccales

family: Puniceicoccaceae

genus: Coraliomargarita

species: Coraliomargarita akajimensis

full scientific name: Coraliomargarita akajimensis Yoon et al. 2007

strain designation: 04OKA010-24, 04OKA10-24

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityconfidence
31982negative1.2 µm0.5 µmcoccus-shapedno
67771coccus-shapedno
67771negative
69480negative99.985

pigmentation

  • @ref: 31982
  • production: no

multimedia

  • @ref: 15802
  • multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_45221.jpg
  • caption: Medium 514 25°C
  • intellectual property rights: © Leibniz-Institut DSMZ

Culture and growth conditions

culture medium

  • @ref: 15802
  • 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
15802positivegrowth25mesophilic
31982positivegrowth20-30
31982positiveoptimum25mesophilic
67770positivegrowth25mesophilic
67771positivegrowth20-30

culture pH

@refabilitytypepHPH range
31982positivegrowth07-09alkaliphile
31982positiveoptimum8

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
31982aerobe
67771aerobe

spore formation

@refspore formationconfidence
31982no
69481no100
69480no99.985

halophily

@refsaltgrowthtested relationconcentration
31982NaClpositivegrowth0.1-5 %
31982NaClpositiveoptimum2.5 %

observation

@refobservation
67770quinones: MK-7
67771quinones: MK-7

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
31982168082-dehydro-D-gluconate+carbon source
31982581435-dehydro-D-gluconate+carbon source
3198215963ribitol+carbon source
3198222599arabinose+carbon source
3198218403L-arabitol+carbon source
3198217057cellobiose+carbon source
3198228757fructose+carbon source
3198233984fucose+carbon source
3198228260galactose+carbon source
3198224265gluconate+carbon source
3198217234glucose+carbon source
3198228087glycogen+carbon source
3198217716lactose+carbon source
3198217306maltose+carbon source
3198229864mannitol+carbon source
3198237684mannose+carbon source
3198228053melibiose+carbon source
31982506227N-acetylglucosamine+carbon source
3198216634raffinose+carbon source
3198226546rhamnose+carbon source
3198233942ribose+carbon source
3198217814salicin+carbon source
3198230911sorbitol+carbon source
3198217992sucrose+carbon source
3198227082trehalose+carbon source
3198216199urea+carbon source
3198217151xylitol+carbon source
3198218222xylose+carbon source

enzymes

@refvalueactivityec
31982cytochrome oxidase+1.9.3.1
31982urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typehost speciesgeographic locationcountryorigin.countrycontinent
15802seawater surrounding the hard coral x Galaxea fascicularisGalaxea fascicularisMajanohama, AkajimaJapanJPNAsia
67770Seawater surrounding the hard coral Galaxea facicularis L.Galaxea facicularisMajanohama, AkajimaJapanJPNAsia
67771From seawaterOkinawaJapanJPNAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Host#Invertebrates (Other)#Cnidaria (Corals)

taxonmaps

  • @ref: 69479
  • File name: preview.99_5544.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_529;96_2679;97_3287;98_4137;99_5544&stattab=map
  • Last taxonomy: Coraliomargarita akajimensis subclade
  • 16S sequence: AB266750
  • Sequence Identity:
  • Total samples: 5147
  • soil counts: 570
  • aquatic counts: 4409
  • animal counts: 119
  • plant counts: 49

Safety information

risk assessment

  • @ref: 15802
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 15802
  • description: Coraliomargarita akajimensis gene for 16S rRNA, partial sequence
  • accession: AB266750
  • length: 1457
  • database: ena
  • NCBI tax ID: 583355

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Coraliomargarita akajimensis DSM 45221GCA_000025905completencbi583355
66792Coraliomargarita akajimensis DSM 45221583355.3completepatric583355
66792Coraliomargarita akajimensis DSM 45221646564524completeimg583355

GC content

@refGC-contentmethod
1580253.9
6777053.9high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
motileno92.76no
flagellatedno96.963yes
gram-positiveno98.201yes
anaerobicno96.735yes
aerobicyes71.779no
halophileno68.779no
spore-formingno97.49yes
thermophileno96.602yes
glucose-utilyes85.361no
glucose-fermentno76.057no

External links

@ref: 15802

culture collection no.: DSM 45221, IAM 15411, JCM 23193, KCTC 12865, MBIC 06463

straininfo link

  • @ref: 86642
  • straininfo: 308606

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny17473241Coraliomargarita akajimensis gen. nov., sp. nov., a novel member of the phylum 'Verrucomicrobia' isolated from seawater in Japan.Yoon J, Yasumoto-Hirose M, Katsuta A, Sekiguchi H, Matsuda S, Kasai H, Yokota AInt J Syst Evol Microbiol10.1099/ijs.0.64755-02007Bacteria/chemistry/*classification/genetics/*isolation & purification, Bacterial Physiological Phenomena, Bacterial Typing Techniques, Base Composition, Cell Wall/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Diaminopimelic Acid/analysis, Fatty Acids/analysis, Genes, rRNA/genetics, Japan, Microscopy, Electron, Transmission, Molecular Sequence Data, Movement, Muramic Acids/analysis, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Spores, Bacterial, Vitamin K 2/analysisGenetics
Genetics21304713Complete genome sequence of Coraliomargarita akajimensis type strain (04OKA010-24).Mavromatis K, Abt B, Brambilla E, Lapidus A, Copeland A, Deshpande S, Nolan M, Lucas S, Tice H, Cheng JF, Han C, Detter JC, Woyke T, Goodwin L, Pitluck S, Held B, Brettin T, Tapia R, Ivanova N, Mikhailova N, Pati A, Liolios K, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CD, Rohde M, Goker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Klenk HP, Kyrpides NCStand Genomic Sci10.4056/sigs.9521662010
Phylogeny30694173Coraliomargarita sinensis sp. nov., isolated from a marine solar saltern.Zhou LY, Wang NN, Mu DS, Liu Y, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0032052019Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, *Saline Waters, Sequence Analysis, DNA, Verrucomicrobia/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistry, *Water MicrobiologyTranscriptome
Phylogeny32931410Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae.Feng X, Zou QH, Zhang XY, Ye MQ, Du ZJInt J Syst Evol Microbiol10.1099/ijsem.0.0044582020Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Islands, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Verrucomicrobia/*classification/isolation & purification, Vitamin K 2/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
15802Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45221)https://www.dsmz.de/collection/catalogue/details/culture/DSM-45221
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
31982Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2823628776041
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
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
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
86642Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID308606.1StrainInfo: A central database for resolving microbial strain identifiers