Strain identifier
BacDive ID: 17651
Type strain:
Species: Coraliomargarita akajimensis
Strain Designation: 04OKA010-24, 04OKA10-24
Strain history: <- JW Yoon, Tokyo Univ. <- M Yasumoto-Hirose, MBI
NCBI tax ID(s): 583355 (strain), 395922 (species)
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 id | Matching level |
---|---|
395922 | species |
583355 | strain |
strain history
@ref | history |
---|---|
15802 | <- JCM/RIKEN; JCM 23193 <- IAM; IAM 15411 <- J. Yoon et al.; 04OKA010-24 |
67770 | IAM 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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31982 | negative | 1.2 µm | 0.5 µm | coccus-shaped | no | |
67771 | coccus-shaped | no | ||||
67771 | negative | |||||
69480 | negative | 99.985 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
15802 | positive | growth | 25 | mesophilic |
31982 | positive | growth | 20-30 | |
31982 | positive | optimum | 25 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
67771 | positive | growth | 20-30 |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31982 | positive | growth | 07-09 | alkaliphile |
31982 | positive | optimum | 8 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31982 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
31982 | no | |
69481 | no | 100 |
69480 | no | 99.985 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31982 | NaCl | positive | growth | 0.1-5 % |
31982 | NaCl | positive | optimum | 2.5 % |
observation
@ref | observation |
---|---|
67770 | quinones: MK-7 |
67771 | quinones: MK-7 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31982 | 16808 | 2-dehydro-D-gluconate | + | carbon source |
31982 | 58143 | 5-dehydro-D-gluconate | + | carbon source |
31982 | 15963 | ribitol | + | carbon source |
31982 | 22599 | arabinose | + | carbon source |
31982 | 18403 | L-arabitol | + | carbon source |
31982 | 17057 | cellobiose | + | carbon source |
31982 | 28757 | fructose | + | carbon source |
31982 | 33984 | fucose | + | carbon source |
31982 | 28260 | galactose | + | carbon source |
31982 | 24265 | gluconate | + | carbon source |
31982 | 17234 | glucose | + | carbon source |
31982 | 28087 | glycogen | + | carbon source |
31982 | 17716 | lactose | + | carbon source |
31982 | 17306 | maltose | + | carbon source |
31982 | 29864 | mannitol | + | carbon source |
31982 | 37684 | mannose | + | carbon source |
31982 | 28053 | melibiose | + | carbon source |
31982 | 506227 | N-acetylglucosamine | + | carbon source |
31982 | 16634 | raffinose | + | carbon source |
31982 | 26546 | rhamnose | + | carbon source |
31982 | 33942 | ribose | + | carbon source |
31982 | 17814 | salicin | + | carbon source |
31982 | 30911 | sorbitol | + | carbon source |
31982 | 17992 | sucrose | + | carbon source |
31982 | 27082 | trehalose | + | carbon source |
31982 | 16199 | urea | + | carbon source |
31982 | 17151 | xylitol | + | carbon source |
31982 | 18222 | xylose | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31982 | cytochrome oxidase | + | 1.9.3.1 |
31982 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
15802 | seawater surrounding the hard coral x Galaxea fascicularis | Galaxea fascicularis | Majanohama, Akajima | Japan | JPN | Asia |
67770 | Seawater surrounding the hard coral Galaxea facicularis L. | Galaxea facicularis | Majanohama, Akajima | Japan | JPN | Asia |
67771 | From seawater | Okinawa | Japan | JPN | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Coraliomargarita akajimensis DSM 45221 | GCA_000025905 | complete | ncbi | 583355 |
66792 | Coraliomargarita akajimensis DSM 45221 | 583355.3 | complete | patric | 583355 |
66792 | Coraliomargarita akajimensis DSM 45221 | 646564524 | complete | img | 583355 |
GC content
@ref | GC-content | method |
---|---|---|
15802 | 53.9 | |
67770 | 53.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 92.76 | no |
flagellated | no | 96.963 | yes |
gram-positive | no | 98.201 | yes |
anaerobic | no | 96.735 | yes |
aerobic | yes | 71.779 | no |
halophile | no | 68.779 | no |
spore-forming | no | 97.49 | yes |
thermophile | no | 96.602 | yes |
glucose-util | yes | 85.361 | no |
glucose-ferment | no | 76.057 | no |
External links
@ref: 15802
culture collection no.: DSM 45221, IAM 15411, JCM 23193, KCTC 12865, MBIC 06463
straininfo link
- @ref: 86642
- straininfo: 308606
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 17473241 | Coraliomargarita 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 A | Int J Syst Evol Microbiol | 10.1099/ijs.0.64755-0 | 2007 | Bacteria/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/analysis | Genetics |
Genetics | 21304713 | Complete 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 NC | Stand Genomic Sci | 10.4056/sigs.952166 | 2010 | ||
Phylogeny | 30694173 | Coraliomargarita sinensis sp. nov., isolated from a marine solar saltern. | Zhou LY, Wang NN, Mu DS, Liu Y, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003205 | 2019 | Bacterial 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 Microbiology | Transcriptome |
Phylogeny | 32931410 | Oceanipulchritudo coccoides gen. nov., sp. nov., isolated from marine sediment within the family Puniceicoccaceae. | Feng X, Zou QH, Zhang XY, Ye MQ, Du ZJ | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004458 | 2020 | Bacterial 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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
15802 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 45221) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-45221 | ||||
20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | 10.1099/ijsem.0.004332 | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | ||||
31982 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | 10.1128/mSphere.00237-17 | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 28236 | 28776041 | ||
66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | 10.1093/nar/gkaa1025 | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | |||||
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | |||||
69479 | João 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 | ||||
69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | https://diaspora-project.de/progress.html#genomes | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | ||||
69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | 10.21203/rs.3.rs-2527258/v1 | Predictions based on the model GenomeNet Sporulation v. 1 | ||||
86642 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID308606.1 | StrainInfo: A central database for resolving microbial strain identifiers |