Strain identifier
BacDive ID: 23340
Type strain: 
Species: Photobacterium gaetbulicola
Strain Designation: Gung47
Strain history: <- JH Yoon, KRIBB
NCBI tax ID(s): 1295392 (species)
version 8.1 (current version)
General
@ref: 19109
BacDive-ID: 23340
DSM-Number: 26887
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Photobacterium gaetbulicola Gung47 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from tidal flat sediment.
NCBI tax id
- NCBI tax id: 1295392
- Matching level: species
strain history
| @ref | history |
|---|---|
| 19109 | <- CCUG <- Y.-H. Yoon, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea |
| 67771 | <- JH Yoon, KRIBB |
doi: 10.13145/bacdive23340.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Vibrionales
- family: Vibrionaceae
- genus: Photobacterium
- species: Photobacterium gaetbulicola
- full scientific name: Photobacterium gaetbulicola Kim et al. 2010
@ref: 19109
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Photobacterium
species: Photobacterium gaetbulicola
full scientific name: Photobacterium gaetbulicola Kim et al. 2010
strain designation: Gung47
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 29610 | negative | 01-05 µm | 0.4-1 µm | rod-shaped | yes | |
| 67771 | negative | |||||
| 69480 | yes | 92.816 | ||||
| 69480 | negative | 99.973 |
colony morphology
- @ref: 61678
- incubation period: 1 day
pigmentation
- @ref: 29610
- production: yes
multimedia
- @ref: 19109
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_26887.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 19109
- 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 |
|---|---|---|---|---|
| 19109 | positive | growth | 28 | mesophilic |
| 29610 | positive | growth | 10-40 | |
| 29610 | positive | optimum | 30 | mesophilic |
| 61678 | positive | growth | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH |
|---|---|---|---|
| 29610 | positive | growth | 05-08 |
| 29610 | positive | optimum | 07-08 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 29610 | aerobe |
| 61678 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 29610 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.814 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 29610 | NaCl | positive | growth | 0-8 % |
| 29610 | NaCl | positive | optimum | 02-05 % |
observation
- @ref: 29610
- observation: aggregates in chains
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 29610 | 30089 | acetate | + | carbon source |
| 29610 | 17057 | cellobiose | + | carbon source |
| 29610 | 37684 | mannose | + | carbon source |
| 29610 | 17992 | sucrose | + | carbon source |
| 29610 | 17632 | nitrate | + | reduction |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 29610 | catalase | + | 1.11.1.6 |
| 29610 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent | sampling date |
|---|---|---|---|---|---|---|
| 19109 | tidal flat sediment | Gung harbour | Republic of Korea | KOR | Asia | |
| 61678 | Tidal flat sediment | Gung harbour | Republic of Korea | KOR | Asia | 2008 |
| 67771 | From tidal flat | Gung Haber, Yellow Sea | Republic of Korea | KOR | Asia |
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Terrestrial | #Tidal flat |
| #Environmental | #Terrestrial | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_6793.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_3204;97_3933;98_5007;99_6793&stattab=map
- Last taxonomy: Photobacterium gaetbulicola subclade
- 16S sequence: GQ260188
- Sequence Identity:
- Total samples: 309
- soil counts: 18
- aquatic counts: 268
- animal counts: 19
- plant counts: 4
Safety information
risk assessment
- @ref: 19109
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 19109
- description: Photobacterium gaetbulicola Gung47 16S ribosomal RNA gene, partial sequence
- accession: GQ260188
- length: 1474
- database: ena
- NCBI tax ID: 658445
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Photobacterium gaetbulicola Gung47 | GCA_000940995 | complete | ncbi | 658445 |
| 66792 | Photobacterium gaetbulicola DSM 26887 | GCA_003025515 | contig | ncbi | 1295392 |
| 66792 | Photobacterium gaetbulicola Gung47 | 658445.3 | complete | patric | 658445 |
| 66792 | Photobacterium gaetbulicola strain DSM 26887 | 1295392.6 | wgs | patric | 1295392 |
| 66792 | Photobacterium gaetbulicola DSM 26887 | 2905573978 | draft | img | 1295392 |
| 66792 | Photobacterium gaetbulicola Gung47 | 2645727918 | complete | img | 658445 |
GC content
- @ref: 29610
- GC-content: 50.6
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 87.78 | no |
| flagellated | yes | 85.863 | no |
| gram-positive | no | 98.96 | yes |
| anaerobic | no | 95.523 | no |
| aerobic | yes | 84.987 | yes |
| halophile | no | 64.147 | no |
| spore-forming | no | 94.755 | no |
| glucose-util | yes | 90.465 | no |
| thermophile | no | 99.644 | yes |
| glucose-ferment | yes | 85.791 | no |
External links
@ref: 19109
culture collection no.: DSM 26887, CCUG 58399, KCTC 22804
straininfo link
- @ref: 87557
- straininfo: 401265
literature
- topic: Phylogeny
- Pubmed-ID: 20023056
- title: Photobacterium gaetbulicola sp. nov., a lipolytic bacterium isolated from a tidal flat sediment.
- authors: Kim YO, Kim KK, Park S, Kang SJ, Lee JH, Lee SJ, Oh TK, Yoon JH
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.016923-0
- year: 2009
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Geologic Sediments/microbiology, Molecular Sequence Data, Photobacterium/*classification/genetics/*isolation & purification/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/microbiology, Sodium Chloride/metabolism
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
|---|---|---|---|---|---|---|
| 19109 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 26887) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-26887 | |||
| 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 | |||
| 29610 | 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 | 26000 | 28776041 | |
| 61678 | Curators of the CCUG | Culture Collection University of Gothenburg (CCUG) (CCUG 58399) | https://www.ccug.se/strain?id=58399 | |||
| 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) | |||
| 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 | |||
| 87557 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID401265.1 | StrainInfo: A central database for resolving microbial strain identifiers |