Strain identifier
BacDive ID: 5595
Type strain:
Species: Aquimarina spongiae
Strain Designation: A6
Strain history: <- BJ Yoon, Jeju Natl. Univ
NCBI tax ID(s): 570521 (species)
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
@ref | history |
---|---|
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
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
29832 | negative | 4.75 µm | 0.3 µm | rod-shaped | ||
67771 | rod-shaped | no | ||||
67771 | negative | |||||
69480 | negative | 99.994 |
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
@ref | growth | type | temperature | range |
---|---|---|---|---|
16433 | positive | growth | 28 | mesophilic |
29832 | positive | growth | 10-35 | |
29832 | positive | optimum | 32.5 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
29832 | positive | growth | 06-11 | alkaliphile |
29832 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
29832 | aerobe |
67771 | aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.993 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
29832 | NaCl | positive | growth | 01-05 % |
29832 | NaCl | positive | optimum | 3 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
29832 | 17234 | glucose | + | carbon source |
29832 | 4853 | esculin | + | hydrolysis |
enzymes
@ref | value | activity | ec |
---|---|---|---|
29832 | acid phosphatase | + | 3.1.3.2 |
29832 | alkaline phosphatase | + | 3.1.3.1 |
29832 | catalase | + | 1.11.1.6 |
29832 | gelatinase | + | |
29832 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | host species | geographic location | country | origin.country | continent |
---|---|---|---|---|---|---|
16433 | marine sponge, Halichondria oshoro | Halichondria oshoro | Jeju, coastal area | Republic of Korea | KOR | Asia |
67771 | From marine sponge, `Halichondria oshoro` | the coast of Jeju Island | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#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
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Aquimarina spongiae DSM 22623 | GCA_900141785 | scaffold | ncbi | 570521 |
66792 | Aquimarina spongiae strain DSM 22623 | 570521.3 | wgs | patric | 570521 |
66792 | Aquimarina spongiae DSM 22623 | 2622736502 | draft | img | 570521 |
GC content
@ref | GC-content | method |
---|---|---|
16433 | 36.0 | thermal denaturation, midpoint method (Tm) |
29832 | 36 | |
67771 | 36.0 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 89.275 | no |
flagellated | no | 94.301 | yes |
gram-positive | no | 97.216 | no |
anaerobic | no | 99.592 | yes |
aerobic | yes | 92.589 | yes |
halophile | no | 51.502 | no |
spore-forming | no | 93.215 | no |
thermophile | no | 99.432 | yes |
glucose-util | yes | 86.431 | yes |
glucose-ferment | no | 90.604 | no |
External links
@ref: 16433
culture collection no.: DSM 22623, KCTC 22663
straininfo link
- @ref: 75077
- straininfo: 404718
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 20348323 | Aquimarina spongiae sp. nov., isolated from marine sponge Halichondria oshoro. | Yoon BJ, You HS, Lee DH, Oh DC | Int J Syst Evol Microbiol | 10.1099/ijs.0.022046-0 | 2010 | Animals, 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/analysis | Genetics |
Phylogeny | 36223175 | Aquimarina 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 B | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005607 | 2022 | Animals, *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/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
16433 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22623) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22623 | ||||
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 | ||||
29832 | 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 | 26208 | 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 | ||
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 | ||||
75077 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID404718.1 | StrainInfo: A central database for resolving microbial strain identifiers |