Strain identifier
BacDive ID: 5593
Type strain: 
Species: Aquimarina intermedia
Strain history: KMM 6258 <-- O. I. Nedashkovskaya.
NCBI tax ID(s): 350814 (species)
version 8.1 (current version)
General
@ref: 7043
BacDive-ID: 5593
DSM-Number: 17527
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Aquimarina intermedia DSM 17527 is a mesophilic, Gram-negative bacterium that was isolated from sea urchin Strongylocentrotus intermedius.
NCBI tax id
- NCBI tax id: 350814
- Matching level: species
strain history
| @ref | history |
|---|---|
| 7043 | <- O. I. Nedashkovskaya, RAS, Pacific Inst. Bioorg. Chem.; KMM 6258 |
| 67770 | KMM 6258 <-- O. I. Nedashkovskaya. |
doi: 10.13145/bacdive5593.20230509.8.1
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 intermedia
- full scientific name: Aquimarina intermedia Nedashkovskaya et al. 2006
@ref: 7043
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Aquimarina
species: Aquimarina intermedia
full scientific name: Aquimarina intermedia Nedashkovskaya et al. 2006
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.993
Culture and growth conditions
culture medium
- @ref: 7043
- 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 |
|---|---|---|---|---|
| 7043 | positive | growth | 28 | mesophilic |
| 67770 | positive | growth | 25 | mesophilic |
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.993 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | host species | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|---|
| 7043 | sea urchin Strongylocentrotus intermedius | Strongylocentrotus intermedius | Sea of Japan, Peter the Great Gulf, Troitsa Bay | Russia | RUS | Asia |
| 67770 | Sea urchin Strongylocentrotus intermedius collected in Troitsa Bay | Strongylocentrotus intermedius | Gulf of Peter the Great |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Host | #Invertebrates (Other) | #Echinodermata |
| #Environmental | #Aquatic | #Marine |
taxonmaps
- @ref: 69479
- File name: preview.99_63231.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_52;96_3439;97_34708;98_44764;99_63231&stattab=map
- Last taxonomy: Aquimarina intermedia subclade
- 16S sequence: AM113977
- Sequence Identity:
- Total samples: 1986
- soil counts: 31
- aquatic counts: 1900
- animal counts: 38
- plant counts: 17
Safety information
risk assessment
- @ref: 7043
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7043
- description: Aquimarina intermedia 16S rRNA gene, type strain LMG 23204T
- accession: AM113977
- length: 1476
- database: ena
- NCBI tax ID: 350814
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Aquimarina intermedia strain DSM 17527 | 350814.3 | wgs | patric | 350814 |
| 66792 | Aquimarina intermedia DSM 17527 | 2693429858 | draft | img | 350814 |
| 67770 | Aquimarina intermedia DSM 17527 | GCA_008124785 | contig | ncbi | 350814 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 7043 | 37.1 | |
| 67770 | 37.1 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| gram-positive | no | 97.76 | no |
| anaerobic | no | 99.354 | no |
| halophile | yes | 50.565 | no |
| spore-forming | no | 93.889 | no |
| glucose-util | yes | 76.547 | no |
| motile | no | 87.25 | no |
| flagellated | no | 93.389 | no |
| aerobic | yes | 93.191 | no |
| thermophile | no | 98.976 | yes |
| glucose-ferment | no | 92.017 | no |
External links
@ref: 7043
culture collection no.: DSM 17527, JCM 13506, LMG 23204, KMM 6258, BCRC 80195, KCTC 22830, NCIMB 14286
straininfo link
- @ref: 75075
- straininfo: 138878
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16957096 | Aquimarina intermedia sp. nov., reclassification of Stanierella latercula (Lewin 1969) as Aquimarina latercula comb. nov. and Gaetbulimicrobium brevivitae Yoon et al. 2006 as Aquimarina brevivitae comb. nov. and emended description of the genus Aquimarina. | Nedashkovskaya OI, Vancanneyt M, Christiaens L, Kalinovskaya NI, Mikhailov VV, Swings J | Int J Syst Evol Microbiol | 10.1099/ijs.0.64155-0 | 2006 | Bacterial Typing Techniques, DNA, Bacterial/*analysis, Flavobacteriaceae/*classification/genetics, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/*analysis/genetics, Sequence Analysis, DNA, Terminology as Topic | Genetics |
| 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 | 20799083 | Aquimarina litoralis sp. nov., isolated from a coastal seawater. | Oh YS, Kahng HY, Lee YS, Yoon BJ, Lim SB, Jung JS, Oh DC, Lee DH | J Microbiol | 10.1007/s12275-010-0088-8 | 2010 | DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Flavobacteriaceae/classification/genetics/*isolation & purification, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology | Genetics |
| Phylogeny | 22771683 | Aquimarina longa sp. nov., isolated from seawater, and emended description of Aquimarina muelleri. | Yu T, Yin Q, Song X, Zhao R, Shi X, Zhang XH | Int J Syst Evol Microbiol | 10.1099/ijs.0.041509-0 | 2012 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/isolation & purification, Molecular Sequence Data, Pacific Ocean, Phosphatidylethanolamines/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Vitamin K 2/analogs & derivatives/analysis, Water Microbiology | Genetics |
| Phylogeny | 25253586 | Aquimarina penaei sp. nov., isolated from intestinal tract contents of Pacific white shrimp, Penaeus vannamei. | Li X, Wang L, Huang H, Lai Q, Shao Z | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0292-3 | 2014 | Animals, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification, Gastrointestinal Tract/microbiology, Hydrogen-Ion Concentration, Molecular Sequence Data, Penaeidae/*microbiology, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Salts/metabolism, Sequence Analysis, DNA, Temperature | Genetics |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7043 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17527) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17527 | |
| 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 | |
| 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) | |
| 67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||
| 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 | |
| 75075 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID138878.1 | StrainInfo: A central database for resolving microbial strain identifiers |