Strain identifier
BacDive ID: 23232
Type strain:
Species: Shimia marina
Strain Designation: CL-TA03
Strain history: D. H. Choi CL-TA03.
NCBI tax ID(s): 321267 (species)
General
@ref: 19053
BacDive-ID: 23232
DSM-Number: 26895
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Shimia marina CL-TA03 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from from biofilm in a coastal fish farm.
NCBI tax id
- NCBI tax id: 321267
- Matching level: species
strain history
@ref | history |
---|---|
19053 | <- JCM <- D. H. Choi; CL-TA03 |
67770 | D. H. Choi CL-TA03. |
doi: 10.13145/bacdive23232.20230509.8.1
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 marina
- full scientific name: Shimia marina Choi and Cho 2006
@ref: 19053
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Rhodobacterales
family: Rhodobacteraceae
genus: Shimia
species: Shimia marina
full scientific name: Shimia marina Choi and Cho 2006
strain designation: CL-TA03
type strain: yes
Morphology
cell morphology
- @ref: 31768
- gram stain: negative
- cell length: 0.8-3.6 µm
- cell width: 0.3-0.6 µm
- cell shape: rod-shaped
- motility: yes
colony morphology
- @ref: 19053
- incubation period: 1-2 days
pigmentation
- @ref: 31768
- production: yes
Culture and growth conditions
culture medium
- @ref: 19053
- 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 |
---|---|---|---|---|
19053 | positive | growth | 30 | mesophilic |
31768 | positive | growth | 15-35 | |
31768 | positive | optimum | 30-35 | mesophilic |
67770 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31768 | positive | growth | 06-10 | alkaliphile |
31768 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31768
- oxygen tolerance: aerobe
spore formation
- @ref: 31768
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31768 | NaCl | positive | growth | 03-07 % |
31768 | NaCl | positive | optimum | 03-07 % |
observation
@ref | observation |
---|---|
31768 | aggregates in chains |
67770 | quinones: Q-10 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31768 | 16947 | citrate | + | carbon source |
31768 | 16236 | ethanol | + | carbon source |
31768 | 15428 | glycine | + | carbon source |
31768 | 28087 | glycogen | + | carbon source |
31768 | 25017 | leucine | + | carbon source |
31768 | 18257 | ornithine | + | carbon source |
31768 | 15361 | pyruvate | + | carbon source |
31768 | 16634 | raffinose | + | carbon source |
31768 | 30031 | succinate | + | carbon source |
31768 | 17632 | nitrate | + | reduction |
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 |
---|---|---|---|
19053 | catalase | + | 1.11.1.6 |
19053 | cytochrome-c oxidase | + | 1.9.3.1 |
31768 | alkaline phosphatase | + | 3.1.3.1 |
31768 | catalase | + | 1.11.1.6 |
31768 | gelatinase | + | |
31768 | cytochrome 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 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
19053 | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
19053 | from biofilm in a coastal fish farm | Tongyeong | Republic of Korea | KOR | Asia |
67770 | Biofilm in a coastal fish farm in Tongyeong | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Engineered | #Food production | #Aquaculture |
#Environmental | #Biofilm | |
#Host | #Fishes |
taxonmaps
- @ref: 69479
- File name: preview.99_8298.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_2271;97_2752;98_6038;99_8298&stattab=map
- Last taxonomy: Shimia marina
- 16S sequence: AY962292
- Sequence Identity:
- Total samples: 1630
- soil counts: 16
- aquatic counts: 1469
- animal counts: 141
- plant counts: 4
Safety information
risk assessment
- @ref: 19053
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19053
- description: Shimia marina strain CL-TA03 16S ribosomal RNA gene, partial sequence
- accession: AY962292
- length: 1382
- database: ena
- NCBI tax ID: 321267
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Shimia marina DSM 26895 | GCA_900112745 | scaffold | ncbi | 321267 |
66792 | Shimia marina strain DSM 26895 | 321267.13 | wgs | patric | 321267 |
66792 | Shimia marina DSM 26895 | 2619618961 | draft | img | 321267 |
GC content
@ref | GC-content | method |
---|---|---|
19053 | 57.2 | high performance liquid chromatography (HPLC) |
31768 | 57.2 |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | yes | 60.951 | no |
flagellated | no | 74.263 | no |
gram-positive | no | 98.797 | no |
anaerobic | no | 98.182 | no |
aerobic | yes | 88.616 | yes |
halophile | yes | 80.063 | no |
spore-forming | no | 97.215 | yes |
glucose-ferment | no | 91.876 | yes |
thermophile | no | 98.577 | yes |
glucose-util | yes | 55.884 | yes |
External links
@ref: 19053
culture collection no.: DSM 26895, JCM 13038, KCCM 42117, BCRC 80068, CIP 109331, NCIMB 14294
straininfo link
- @ref: 87458
- straininfo: 292325
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16902023 | Shimia marina gen. nov., sp. nov., a novel bacterium of the Roseobacter clade isolated from biofilm in a coastal fish farm. | Choi DH, Cho BC | Int J Syst Evol Microbiol | 10.1099/ijs.0.64235-0 | 2006 | Agar, Aquaculture, Base Composition, *Biofilms, Culture Media, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, *Marine Biology, Molecular Sequence Data, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Roseobacter/chemistry/*classification/isolation & purification/physiology, Salts, Sequence Homology, Nucleic Acid, Species Specificity, Temperature | Cultivation |
Phylogeny | 20453104 | Shimia isoporae sp. nov., isolated from the reef-building coral Isopora palifera. | Chen MH, Sheu SY, Chen CA, Wang JT, Chen WM | Int J Syst Evol Microbiol | 10.1099/ijs.0.022848-0 | 2010 | Aerobiosis, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Flagella/physiology, Locomotion, Molecular Sequence Data, Phylogeny, Pigments, Biological/metabolism, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/*isolation & purification/physiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Taiwan | Genetics |
Phylogeny | 23907225 | Shimia biformata sp. nov., isolated from surface seawater, and emended description of the genus Shimia Choi and Cho 2006. | Hameed A, Shahina M, Lin SY, Lai WA, Hsu YH, Liu YC, Huang YM, Young CC | Int J Syst Evol Microbiol | 10.1099/ijs.0.053553-0 | 2013 | Bacterial Typing Techniques, Base Composition, Cadaverine/chemistry, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Taiwan, Ubiquinone/chemistry | Genetics |
Genetics | 26852259 | Draft genome sequence of Shimia marina CECT 7688(T). | Rodrigo-Torres L, Pujalte MJ, Arahal DR | Mar Genomics | 10.1016/j.margen.2016.01.006 | 2016 | Base Composition, *Genome, Bacterial, Molecular Sequence Annotation, Republic of Korea, Rhodobacteraceae/*genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
19053 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26895) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26895 | ||||
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 | ||||
31768 | 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 | 28041 | 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/ | |||||
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. | https://microbeatlas.org/ | MicrobeAtlas 1.0 beta | ||||
87458 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID292325.1 | StrainInfo: A central database for resolving microbial strain identifiers |