Strain identifier
BacDive ID: 13803
Type strain: 
Species: Shimia aestuarii
Strain Designation: JC2049
Strain history: <- J Chun, Seoul Univ.
NCBI tax ID(s): 254406 (species)
version 8.1 (current version)
General
@ref: 5792
BacDive-ID: 13803
DSM-Number: 15283
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Shimia aestuarii JC2049 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample of getbol.
NCBI tax id
- NCBI tax id: 254406
- Matching level: species
strain history
| @ref | history |
|---|---|
| 5792 | <- J. Chun; JC2049 |
| 67770 | J. Chun JC2049. |
| 67771 | <- J Chun, Seoul Univ. |
doi: 10.13145/bacdive13803.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Rhodobacterales
- family: Roseobacteraceae
- genus: Shimia
- species: Shimia aestuarii
- full scientific name: Shimia aestuarii (Yi and Chun 2007) Wirth and Whitman 2018
synonyms
@ref synonym 20215 Thalassovita aestuarii 20215 Thalassobius aestuarii
@ref: 5792
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Shimia
species: Shimia aestuarii
full scientific name: Shimia aestuarii (Yi and Chun 2007) Wirth and Whitman 2018
strain designation: JC2049
type strain: yes
Morphology
cell morphology
| @ref | gram stain | confidence |
|---|---|---|
| 67771 | negative | |
| 69480 | negative | 99.997 |
Culture and growth conditions
culture medium
- @ref: 5792
- 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 |
|---|---|---|---|---|
| 5792 | positive | growth | 35 | mesophilic |
| 67770 | positive | growth | 30 | mesophilic |
| 67771 | positive | growth | 28 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.973 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 5792 | sediment sample of getbol | Korea, Ganghwa island | Republic of Korea | KOR | Asia |
| 67770 | Sediment sample of tidal flat | Ganghwa Island | Republic of Korea | KOR | Asia |
| 67771 | From a tidal flat sediment sample | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Sediment |
| #Environmental | #Terrestrial | #Tidal flat |
taxonmaps
- @ref: 69479
- File name: preview.99_119648.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_777;97_12843;98_35585;99_119648&stattab=map
- Last taxonomy: Shimia
- 16S sequence: AY442178
- Sequence Identity:
- Total samples: 389
- soil counts: 22
- aquatic counts: 348
- animal counts: 17
- plant counts: 2
Safety information
risk assessment
- @ref: 5792
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 20218
- description: Thalassobius aestuarii strain JC2049 16S ribosomal RNA gene, partial sequence
- accession: AY442178
- length: 1386
- database: ena
- NCBI tax ID: 254406
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Shimia aestuarii strain DSM 15283 | 254406.10 | wgs | patric | 254406 |
| 66792 | Shimia aestuarii DSM 15283 | 2616644822 | draft | img | 254406 |
| 67770 | Shimia aestuarii DSM 15283 | GCA_900114635 | contig | ncbi | 254406 |
GC content
- @ref: 67770
- GC-content: 61
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 64.571 | no |
| gram-positive | no | 98.44 | yes |
| anaerobic | no | 98.21 | yes |
| aerobic | yes | 87.74 | yes |
| halophile | yes | 76.806 | no |
| spore-forming | no | 96.158 | no |
| glucose-util | no | 65.603 | no |
| flagellated | no | 85.328 | no |
| thermophile | no | 95.937 | no |
| glucose-ferment | no | 90.841 | no |
External links
@ref: 5792
culture collection no.: DSM 15283, KCTC 12049, JCM 14332, IMSNU 14011
straininfo link
- @ref: 82981
- straininfo: 127389
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 16728953 | Thalassobius aestuarii sp. nov., isolated from tidal flat sediment. | Yi H, Chun J | J Microbiol | 2368 | 2006 | Fatty Acids/analysis/metabolism, Genotype, Hydroxybutyrates/metabolism, Nitrites/analysis/metabolism, Phenotype, Phylogeny, Polyesters/metabolism, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/*genetics/isolation & purification, Seawater/*microbiology, Sodium Chloride/metabolism, Ubiquinone/analysis/metabolism | Metabolism |
| Phylogeny | 19196784 | Tropicibacter naphthalenivorans gen. nov., sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium isolated from Semarang Port in Indonesia. | Harwati TU, Kasai Y, Kodama Y, Susilaningsih D, Watanabe K | Int J Syst Evol Microbiol | 10.1099/ijs.0.65821-0 | 2009 | Fatty Acids/analysis, Indonesia, Molecular Sequence Data, Phenotype, Phylogeny, Polycyclic Aromatic Hydrocarbons/*metabolism, RNA, Ribosomal, 16S, Rhodobacteraceae/chemistry/*classification/genetics/metabolism/ultrastructure, Seawater/*microbiology, Species Specificity | Genetics |
| Phylogeny | 22904216 | Epibacterium ulvae gen. nov., sp. nov., epibiotic bacteria isolated from the surface of a marine alga. | Penesyan A, Breider S, Schumann P, Tindall BJ, Egan S, Brinkhoff T | Int J Syst Evol Microbiol | 10.1099/ijs.0.042838-0 | 2012 | Australia, Bacterial Typing Techniques, Bacteriochlorophyll A/analysis, Base Composition, DNA, Bacterial/genetics, DNA, Ribosomal Spacer/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, *Phylogeny, RNA, Ribosomal, 16S/genetics, Roseobacter/*classification/genetics/isolation & purification, Seawater, Sequence Analysis, DNA, Ubiquinone/analysis, Ulva/*microbiology, Water Microbiology | Genetics |
| Phylogeny | 26554730 | Thalassobius abyssi sp. nov., a marine bacterium isolated from cold-seep sediment. | Nogi Y, Mori K, Makita H, Hatada Y | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000758 | 2015 | ||
| Phylogeny | 33886449 | Shimia sediminis sp. nov., a bacterium isolated from marine sediment in the East China Sea. | Zhu S, Chen C, Cheng Y, Guo C, Peng N, Zhang W, He S | Int J Syst Evol Microbiol | 10.1099/ijsem.0.004782 | 2021 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
| Phylogeny | 35333154 | Thiosulfatihalobacter marinus gen. nov. sp. nov., a novel member of the family Roseobacteraceae, isolated from the West Pacific Ocean. | Wu Y, Ren WT, Zhong YW, Guo LL, Zhou P, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005286 | 2022 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, *Fatty Acids/chemistry, Pacific Ocean, *Phospholipids/chemistry, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title | journal | pubmed |
|---|---|---|---|---|---|---|
| 5792 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15283) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15283 | |||
| 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 | |||
| 20218 | Verslyppe, B., De Smet, W., De Baets, B., De Vos, P., Dawyndt P. | 10.1016/j.syapm.2013.11.002 | StrainInfo introduces electronic passports for microorganisms. | Syst Appl Microbiol. 37: 42-50 2014 | 24321274 | |
| 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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 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 | |||
| 82981 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID127389.1 | StrainInfo: A central database for resolving microbial strain identifiers |