Strain identifier
BacDive ID: 131300
Type strain: 
Species: Shimia gijangensis
Strain Designation: YSS-7
Strain history: <- KCTC <- J.-H. Yoon <- Y.-O. Kim; YSS-7
NCBI tax ID(s): 1470563 (species)
version 8.1 (current version)
General
@ref: 22527
BacDive-ID: 131300
DSM-Number: 100564
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative
description: Shimia gijangensis YSS-7 is a mesophilic, Gram-negative bacterium that was isolated from sea squirt Halocynthia roretzi.
NCBI tax id
- NCBI tax id: 1470563
- Matching level: species
strain history
- @ref: 22527
- history: <- KCTC <- J.-H. Yoon <- Y.-O. Kim; YSS-7
doi: 10.13145/bacdive131300.20230509.8.1
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 gijangensis
- full scientific name: Shimia gijangensis (Kim et al. 2014) Arahal et al. 2019
synonyms
- @ref: 20215
- synonym: Pseudopelagicola gijangensis
@ref: 22527
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Shimia
species: Shimia gijangensis
full scientific name: Shimia gijangensis (Kim et al. 2014) Arahal et al. 2019
strain designation: YSS-7
type strain: yes
Morphology
cell morphology
- @ref: 69480
- gram stain: negative
- confidence: 99.998
colony morphology
- @ref: 22527
- incubation period: 3-7 days
Culture and growth conditions
culture medium
- @ref: 22527
- 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: 22527
- growth: positive
- type: growth
- temperature: 25
- range: mesophilic
Physiology and metabolism
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.995 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 68369 | 25115 | malate | - | assimilation |
| 68369 | 17128 | adipate | - | assimilation |
| 68369 | 27689 | decanoate | - | assimilation |
| 68369 | 24265 | gluconate | - | assimilation |
| 68369 | 17306 | maltose | - | assimilation |
| 68369 | 59640 | N-acetylglucosamine | - | assimilation |
| 68369 | 16899 | D-mannitol | - | assimilation |
| 68369 | 16024 | D-mannose | - | assimilation |
| 68369 | 30849 | L-arabinose | - | assimilation |
| 68369 | 17634 | D-glucose | - | assimilation |
| 68369 | 5291 | gelatin | - | hydrolysis |
| 68369 | 4853 | esculin | - | hydrolysis |
| 68369 | 16199 | urea | - | hydrolysis |
| 68369 | 29016 | arginine | - | hydrolysis |
| 68369 | 17634 | D-glucose | - | fermentation |
| 68369 | 27897 | tryptophan | - | energy source |
| 68369 | 17632 | nitrate | - | reduction |
metabolite production
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- production: no
metabolite tests
- @ref: 68369
- Chebi-ID: 35581
- metabolite: indole
- indole test: -
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 22527 | catalase | + | 1.11.1.6 |
| 22527 | cytochrome-c oxidase | + | 1.9.3.1 |
| 68369 | gelatinase | - | |
| 68369 | beta-glucosidase | - | 3.2.1.21 |
| 68369 | urease | - | 3.5.1.5 |
| 68369 | arginine dihydrolase | - | 3.5.3.6 |
API 20NE
| @ref | NO3 | TRP | GLU_ Ferm | ADH Arg | URE | ESC | GEL | PNPG | GLU_ Assim | ARA | MNE | MAN | NAG | MAL | GNT | CAP | ADI | MLT | CIT | PAC |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 22527 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
- @ref: 22527
- sample type: sea squirt Halocynthia roretzi
- host species: Halocynthia roretzi
- geographic location: South Sea
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
- Cat1: #Host
- Cat2: #Invertebrates (Other)
- Cat3: #Tunicata
taxonmaps
- @ref: 69479
- File name: preview.99_7833.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2657;97_3338;98_5723;99_7833&stattab=map
- Last taxonomy: Shimia gijangensis subclade
- 16S sequence: KF977839
- Sequence Identity:
- Total samples: 540
- soil counts: 13
- aquatic counts: 505
- animal counts: 22
Safety information
risk assessment
- @ref: 22527
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22527
- description: Pseudopelagicola gijangensis strain YSS-7 16S ribosomal RNA gene, partial sequence
- accession: KF977839
- length: 1392
- database: ena
- NCBI tax ID: 1470563
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Shimia gijangensis DSM 100564 | GCA_900142085 | contig | ncbi | 1470563 |
| 66792 | Pseudopelagicola gijangensis strain DSM 100564 | 1470563.3 | wgs | patric | 1470563 |
| 66792 | Shimia gijangensis DSM 100564 | 2700988697 | draft | img | 1470563 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 88.249 | no |
| gram-positive | no | 98.44 | no |
| anaerobic | no | 97.579 | no |
| aerobic | yes | 82.769 | no |
| halophile | yes | 70.733 | no |
| spore-forming | no | 96.31 | no |
| thermophile | no | 97.494 | yes |
| glucose-util | no | 61.179 | no |
| flagellated | no | 93.376 | no |
| glucose-ferment | no | 93.048 | yes |
External links
@ref: 22527
culture collection no.: DSM 100564, CECT 8540, KCTC 42049
straininfo link
- @ref: 89743
- straininfo: 394465
literature
- topic: Phylogeny
- Pubmed-ID: 25048211
- title: Pseudopelagicola gijangensis gen. nov., sp. nov., isolated from the sea squirt Halocynthia roretzi.
- authors: Kim YO, Park S, Nam BH, Kim DG, Yoon JH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.062067-0
- year: 2014
- mesh: Animals, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Rhodobacteraceae/*classification/genetics/isolation & purification, Sequence Analysis, DNA, Ubiquinone/analogs & derivatives/chemistry, Urochordata/*microbiology
- topic2: Genetics
Reference
| @id | authors | title | doi/url | catalogue | journal | pubmed |
|---|---|---|---|---|---|---|
| 20215 | Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M. | List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ | 10.1099/ijsem.0.004332 | |||
| 22527 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100564 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100564) | |||
| 66792 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 66794 | Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg | BRENDA, the ELIXIR core data resource in 2021: new developments and updates | 10.1093/nar/gkaa1025 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
| 68369 | Automatically annotated from API 20NE | |||||
| 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. | MicrobeAtlas 1.0 beta | https://microbeatlas.org/ | |||
| 69480 | Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann | Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) | https://diaspora-project.de/progress.html#genomes | |||
| 69481 | Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. Münch | Predictions based on the model GenomeNet Sporulation v. 1 | 10.21203/rs.3.rs-2527258/v1 | |||
| 89743 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | StrainInfo: A central database for resolving microbial strain identifiers | 10.60712/SI-ID394465.1 |