Strain identifier
BacDive ID: 130501
Type strain:
Species: Sinobacterium caligoides
Strain Designation: SCSWE24
Strain history: <- LMG <- J. Su, Xiamen Univ., China
NCBI tax ID(s): 933926 (species)
General
@ref: 22097
BacDive-ID: 130501
DSM-Number: 100316
keywords: genome sequence, 16S sequence, Bacteria, mesophilic, Gram-negative, rod-shaped
description: Sinobacterium caligoides SCSWE24 is a mesophilic, Gram-negative, rod-shaped bacterium that was isolated from seawater at 450m depth.
NCBI tax id
- NCBI tax id: 933926
- Matching level: species
strain history
- @ref: 22097
- history: <- LMG <- J. Su, Xiamen Univ., China
doi: 10.13145/bacdive130501.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Cellvibrionales
- family: Spongiibacteraceae
- genus: Sinobacterium
- species: Sinobacterium caligoides
- full scientific name: Sinobacterium caligoides Su et al. 2013
@ref: 22097
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Pseudomonadales
family: Spongiibacteraceae
genus: Sinobacterium
species: Sinobacterium caligoides
full scientific name: Sinobacterium caligoides Su et al. 2013 emend. Diéguez et al. 2015
strain designation: SCSWE24
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
30216 | negative | 2 µm | 0.6 µm | rod-shaped | no | |
69480 | negative | 99.981 |
colony morphology
- @ref: 22097
- incubation period: 2-3 days
pigmentation
- @ref: 30216
- production: no
Culture and growth conditions
culture medium
- @ref: 22097
- 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 |
---|---|---|---|---|
22097 | positive | growth | 28 | mesophilic |
30216 | positive | growth | 04-37 | |
30216 | positive | optimum | 25 | mesophilic |
Physiology and metabolism
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.949 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
30216 | NaCl | positive | growth | 1.5-4.5 % |
30216 | NaCl | positive | optimum | 3.25 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
30216 | 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 |
---|---|---|---|
30216 | acid phosphatase | + | 3.1.3.2 |
30216 | alkaline phosphatase | + | 3.1.3.1 |
30216 | alpha-galactosidase | + | 3.2.1.22 |
30216 | catalase | + | 1.11.1.6 |
30216 | cytochrome oxidase | + | 1.9.3.1 |
30216 | urease | + | 3.5.1.5 |
68369 | 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 | OX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
22097 | + | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + |
Isolation, sampling and environmental information
isolation
- @ref: 22097
- sample type: seawater at 450m depth
- geographic location: South China Sea
- country: China
- origin.country: CHN
- continent: Asia
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_61730.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16634;96_8001;97_9624;98_43789;99_61730&stattab=map
- Last taxonomy: Sinobacterium caligoides subclade
- 16S sequence: HQ686140
- Sequence Identity:
- Total samples: 398
- soil counts: 2
- aquatic counts: 378
- animal counts: 18
Safety information
risk assessment
- @ref: 22097
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 22097
- description: Sinobacterium caligoides strain SCSWE24 16S ribosomal RNA gene, partial sequence
- accession: HQ686140
- length: 1501
- database: ena
- NCBI tax ID: 933926
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Sinobacterium caligoides DSM 100316 | GCA_003752585 | scaffold | ncbi | 933926 |
66792 | Sinobacterium caligoides strain DSM 100316 | 933926.3 | wgs | patric | 933926 |
66792 | Sinobacterium caligoides DSM 100316 | 2788499881 | draft | img | 933926 |
GC content
@ref | GC-content | method |
---|---|---|
30216 | 58.8 | |
22097 | 54 | fluorimetric |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | no | 83.335 | yes |
flagellated | no | 57.575 | no |
gram-positive | no | 97.694 | yes |
anaerobic | no | 99.412 | no |
aerobic | yes | 77.251 | no |
halophile | yes | 65.645 | no |
spore-forming | no | 94.11 | no |
glucose-util | yes | 74.021 | no |
thermophile | no | 99.653 | yes |
glucose-ferment | no | 77.15 | no |
External links
@ref: 22097
culture collection no.: DSM 100316, CCTCC AB 209289, LMG 25705, MCCC 1F01088
straininfo link
- @ref: 89024
- straininfo: 369643
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 23087165 | Sinobacterium caligoides gen. nov., sp. nov., a new member of the family Oceanospirillaceae isolated from the South China Sea, and emended description of Amphritea japonica. | Su J, Zhou Y, Lai Q, Li X, Dong P, Yang X, Zhang B, Zhang J, Zheng X, Tian Y, Zheng T | Int J Syst Evol Microbiol | 10.1099/ijs.0.030965-0 | 2012 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Oceanospirillaceae/*classification/genetics/isolation & purification, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Water Microbiology | Genetics |
Phylogeny | 26267335 | Sinobacterium norvegicum sp. nov., isolated from great scallop (Pecten maximus) broodstock and emended description of Sinobacterium caligoides. | Dieguez AL, Jacobsen A, Magnesen T, Romalde JL | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0551-y | 2015 | Aerobiosis, Animals, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Gammaproteobacteria/*classification/genetics/*isolation & purification/physiology, Microscopy, Electron, Scanning, Molecular Sequence Data, Norway, Nucleic Acid Hybridization, Pecten/*microbiology, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Genetics |
Reference
@id | authors | title | doi/url | catalogue | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
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 | ||||
22097 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-100316 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 100316) | ||||
30216 | Barberan A, Caceres Velazquez H, Jones S, Fierer N. | Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information | 10.1128/mSphere.00237-17 | 26560 | 28776041 | ||
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 | 33211880 | Nucleic Acids Res. 49: D498-D508 2020 | ||
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 | ||||
89024 | 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-ID369643.1 |