Strain identifier
BacDive ID: 17233
Type strain:
Species: Photobacterium ganghwense
Strain Designation: FR1311
Strain history: <- J Chun, Seoul National Univ.
NCBI tax ID(s): 320778 (species)
General
@ref: 16632
BacDive-ID: 17233
DSM-Number: 22954
keywords: genome sequence, 16S sequence, Bacteria, facultative anaerobe, mesophilic, Gram-negative, motile, ovoid-shaped
description: Photobacterium ganghwense FR1311 is a facultative anaerobe, mesophilic, Gram-negative bacterium that was isolated from sea water.
NCBI tax id
- NCBI tax id: 320778
- Matching level: species
strain history
@ref | history |
---|---|
16632 | <- KCTC <- J. Chun, Seoul Natl. Univ., Republic of Korea |
67770 | J. Chun FR1311. |
67771 | <- J Chun, Seoul National Univ. |
doi: 10.13145/bacdive17233.20230509.8.1
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 ganghwense
- full scientific name: Photobacterium ganghwense Park et al. 2006
@ref: 16632
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Vibrionales, not validated
family: Vibrionaceae
genus: Photobacterium
species: Photobacterium ganghwense
full scientific name: Photobacterium ganghwense Park et al. 2006
strain designation: FR1311
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
31562 | negative | 1.3-2 µm | 0.8-1.2 µm | ovoid-shaped | yes |
67771 | negative |
pigmentation
- @ref: 31562
- production: yes
multimedia
- @ref: 16632
- multimedia content: https://www.dsmz.de/microorganisms/photos/DSM_22954.jpg
- intellectual property rights: © Leibniz-Institut DSMZ
Culture and growth conditions
culture medium
- @ref: 16632
- name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535)
- growth: yes
- link: https://mediadive.dsmz.de/medium/535
- composition: Name: TRYPTICASE SOY BROTH AGAR (DSMZ Medium 535) Composition: Trypticase soy broth 30.0 g/l Agar 15.0 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
16632 | positive | growth | 28 | mesophilic |
31562 | positive | growth | 10-45 | |
31562 | positive | optimum | 35 | mesophilic |
67770 | positive | growth | 25 | mesophilic |
67771 | positive | growth | 30 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31562 | positive | growth | 05-11 | alkaliphile |
31562 | positive | optimum | 08-09 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
31562 | facultative anaerobe |
67771 | aerobe |
spore formation
- @ref: 31562
- spore formation: no
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31562 | NaCl | positive | growth | 01-07 % |
31562 | NaCl | positive | optimum | 2 % |
observation
@ref | observation |
---|---|
31562 | aggregates in chains |
67770 | quinones: Q-8 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31562 | 17128 | adipate | + | carbon source |
31562 | 27689 | decanoate | + | carbon source |
31562 | 16947 | citrate | + | carbon source |
31562 | 24265 | gluconate | + | carbon source |
31562 | 17234 | glucose | + | carbon source |
31562 | 25115 | malate | + | carbon source |
31562 | 29864 | mannitol | + | carbon source |
31562 | 37684 | mannose | + | carbon source |
31562 | 506227 | N-acetylglucosamine | + | carbon source |
31562 | 18401 | phenylacetate | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31562 | catalase | + | 1.11.1.6 |
31562 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent | latitude | longitude |
---|---|---|---|---|---|---|---|
16632 | sea water | Ganghwa Island (37°35'39.1'' N 126°27'24.5'' E) | Republic of Korea | KOR | Asia | 37.5942 | 126.457 |
67770 | Seawater | Ganghwa Island | Republic of Korea | KOR | Asia | ||
67771 | From seawater | Kangwha | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_5078.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_14;96_2475;97_3023;98_3791;99_5078&stattab=map
- Last taxonomy: Photobacterium ganghwense subclade
- 16S sequence: AY960847
- Sequence Identity:
- Total samples: 382
- soil counts: 44
- aquatic counts: 241
- animal counts: 93
- plant counts: 4
Safety information
risk assessment
- @ref: 16632
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 16632
- description: Photobacterium ganghwense strain FR1311 16S ribosomal RNA gene, partial sequence
- accession: AY960847
- length: 1474
- database: ena
- NCBI tax ID: 320778
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Photobacterium ganghwense JCM 12487 | GCA_003025595 | contig | ncbi | 320778 |
66792 | Photobacterium ganghwense DSM 22954 | GCA_001029455 | contig | ncbi | 320778 |
66792 | Photobacterium ganghwense strain DSM 22954 | 320778.3 | wgs | patric | 320778 |
66792 | Photobacterium ganghwense strain JCM 12487 | 320778.6 | wgs | patric | 320778 |
66792 | Photobacterium ganghwense DSM 22954 | 2713896764 | draft | img | 320778 |
66792 | Photobacterium ganghwense JCM 12487 | 2868869919 | draft | img | 320778 |
GC content
@ref | GC-content | method |
---|---|---|
16632 | 44.0 | |
31562 | 44 | |
67770 | 44 | thermal denaturation, midpoint method (Tm) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
gram-positive | no | 98.794 | yes |
anaerobic | no | 96.561 | yes |
halophile | no | 63.888 | no |
spore-forming | no | 93.663 | yes |
glucose-util | yes | 93.161 | yes |
motile | yes | 91.498 | yes |
flagellated | yes | 91.303 | no |
thermophile | no | 99.744 | yes |
aerobic | yes | 73.358 | no |
glucose-ferment | yes | 85.378 | no |
External links
@ref: 16632
culture collection no.: DSM 22954, IMSNU 60287, JCM 12487, KCTC 12328, CIP 109254, DSM 22358, NCIMB 14495
straininfo link
- @ref: 86232
- straininfo: 232818
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16585687 | Photobacterium ganghwense sp. nov., a halophilic bacterium isolated from sea water. | Park YD, Baik KS, Seong CN, Bae KS, Kim S, Chun J | Int J Syst Evol Microbiol | 10.1099/ijs.0.63811-0 | 2006 | DNA, Bacterial/analysis, Fatty Acids/analysis, Molecular Sequence Data, Photobacterium/*classification/enzymology/genetics/*isolation & purification, RNA, Ribosomal, 16S/analysis/genetics, Seawater/*microbiology, Sodium Chloride/metabolism | Genetics |
Pathogenicity | 28659560 | Environmental Impact of Tributyltin-Resistant Marine Bacteria in the Indigenous Microbial Population of Tributyltin-Polluted Surface Sediments. | Mimura H, Yagi M, Yoshida K | Biocontrol Sci | 10.4265/bio.22.89 | 2017 | DNA, Ribosomal, *Drug Resistance, Microbial, Geologic Sediments/*microbiology, Photobacterium/*drug effects/growth & development, Trialkyltin Compounds/*pharmacology, Water Microbiology, Water Pollutants, Chemical/pharmacology |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
16632 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 22954) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-22954 | ||||
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 | ||||
31562 | 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 | 27852 | 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/ | |||||
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 | ||||
86232 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID232818.1 | StrainInfo: A central database for resolving microbial strain identifiers |