Strain identifier
BacDive ID: 5853
Type strain:
Species: Zooshikella ganghwensis
Strain Designation: JC2044
Strain history: CIP <- 2004, J. Chun, Seoul, Korea: strain JC2044
NCBI tax ID(s): 1123509 (strain), 202772 (species)
General
@ref: 5784
BacDive-ID: 5853
DSM-Number: 15267
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative
description: Zooshikella ganghwensis JC2044 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment sample of getbol.
NCBI tax id
NCBI tax id | Matching level |
---|---|
1123509 | strain |
202772 | species |
strain history
@ref | history |
---|---|
5784 | <- J. Chun; JC2044 |
37424 | 2004, J. Chun, Seoul, Korea: strain JC2044 |
67771 | <- J Chon, Seoul Nat. Univ. |
119531 | CIP <- 2004, J. Chun, Seoul, Korea: strain JC2044 |
doi: 10.13145/bacdive5853.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Oceanospirillales
- family: Zooshikellaceae
- genus: Zooshikella
- species: Zooshikella ganghwensis
- full scientific name: Zooshikella ganghwensis Yi et al. 2003
synonyms
@ref synonym 20215 Zooshikella ganghwensis subsp. marina 20215 Zooshikella marina
@ref: 5784
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Oceanospirillales
family: Hahellaceae
genus: Zooshikella
species: Zooshikella ganghwensis
full scientific name: Zooshikella ganghwensis Yi et al. 2003
strain designation: JC2044
type strain: yes
Morphology
cell morphology
@ref | gram stain | motility | confidence | cell shape |
---|---|---|---|---|
67771 | negative | |||
69480 | yes | 94.947 | ||
69480 | negative | 99.897 | ||
119531 | negative | yes | rod-shaped |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_15267_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15267_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15267_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15267_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_15267_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
5784 | BACTO MARINE BROTH (DIFCO 2216) (DSMZ Medium 514) | yes | https://mediadive.dsmz.de/medium/514 | 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 |
37424 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
119531 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
5784 | positive | growth | 30 | mesophilic |
37424 | positive | growth | 30 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
119531 | positive | growth | 22-37 | |
119531 | no | growth | 5 | psychrophilic |
119531 | no | growth | 15 | psychrophilic |
119531 | no | growth | 41 | thermophilic |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
67771 | aerobe |
119531 | obligate aerobe |
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 94 |
69480 | no | 99.843 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
119531 | NaCl | positive | growth | 2-4 % |
119531 | NaCl | no | growth | 0 % |
119531 | NaCl | no | growth | 6 % |
119531 | NaCl | no | growth | 8 % |
119531 | NaCl | no | growth | 10 % |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
119531 | 4853 | esculin | - | hydrolysis |
119531 | 17632 | nitrate | - | builds gas from |
119531 | 17632 | nitrate | - | reduction |
119531 | 16301 | nitrite | - | builds gas from |
119531 | 16301 | nitrite | - | reduction |
metabolite production
- @ref: 119531
- Chebi-ID: 35581
- metabolite: indole
- production: no
enzymes
@ref | value | activity | ec |
---|---|---|---|
68382 | alpha-fucosidase | - | 3.2.1.51 |
68382 | alpha-mannosidase | - | 3.2.1.24 |
68382 | N-acetyl-beta-glucosaminidase | - | 3.2.1.52 |
68382 | beta-glucosidase | - | 3.2.1.21 |
68382 | alpha-glucosidase | - | 3.2.1.20 |
68382 | beta-glucuronidase | - | 3.2.1.31 |
68382 | beta-galactosidase | - | 3.2.1.23 |
68382 | alpha-galactosidase | - | 3.2.1.22 |
68382 | naphthol-AS-BI-phosphohydrolase | - | |
68382 | acid phosphatase | + | 3.1.3.2 |
68382 | alpha-chymotrypsin | - | 3.4.21.1 |
68382 | trypsin | - | 3.4.21.4 |
68382 | cystine arylamidase | - | 3.4.11.3 |
68382 | valine arylamidase | + | |
68382 | leucine arylamidase | + | 3.4.11.1 |
68382 | lipase (C 14) | - | |
68382 | esterase lipase (C 8) | + | |
68382 | esterase (C 4) | + | |
68382 | alkaline phosphatase | + | 3.1.3.1 |
119531 | oxidase | + | |
119531 | beta-galactosidase | - | 3.2.1.23 |
119531 | alcohol dehydrogenase | - | 1.1.1.1 |
119531 | gelatinase | + | |
119531 | amylase | + | |
119531 | caseinase | + | 3.4.21.50 |
119531 | catalase | + | 1.11.1.6 |
119531 | tween esterase | + | |
119531 | gamma-glutamyltransferase | + | 2.3.2.2 |
119531 | lecithinase | + | |
119531 | lipase | + | |
119531 | lysine decarboxylase | - | 4.1.1.18 |
119531 | ornithine decarboxylase | - | 4.1.1.17 |
119531 | phenylalanine ammonia-lyase | - | 4.3.1.24 |
119531 | protease | - | |
119531 | tryptophan deaminase | - | |
119531 | urease | - | 3.5.1.5 |
API zym
@ref | Control | Alkaline phosphatase | Esterase | Esterase Lipase | Lipase | Leucine arylamidase | Valine arylamidase | Cystine arylamidase | Trypsin | alpha- Chymotrypsin | Acid phosphatase | Naphthol-AS-BI-phosphohydrolase | alpha- Galactosidase | beta- Galactosidase | beta- Glucuronidase | alpha- Glucosidase | beta- Glucosidase | N-acetyl-beta- glucosaminidase | alpha- Mannosidase | alpha- Fucosidase |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119531 | - | + | + | + | - | + | + | - | - | - | + | - | - | - | - | - | - | - | - | - |
API biotype100
@ref | GLU | FRU | GAL | TRE | MNE | SBE | MEL | SAC | RAF | MTE | MAL | LAC | LTE | MbGa | MaGa | CEL | GEN | MbGu | ESC | RIB | ARA | XYL | PLE | RHA | FUC | MLZ | DARL | LARL | XLT | DUL | TAG | GLY | INO | MAN | MTL | TUR | SOR | ADO | HBG | LYX | ERY | MDG | 3MDG | SAT | MUC | LTAT | DTAT | MTAT | DMLT | LMLT | CATE | TATE | TTE | CIT | GRT | GAT | 2KG | 5KG | TRY | NAG | GNT | PAC | PAT | pOBE | QAT | GTE | mOBE | BAT | PPAT | CMT | TGE | BET | PCE | ABT | HIN | LAT | CAP | CYT | HIS | SUC | FUM | GRE | GYT | AVT | ETN | TTN | GLN | ITA | 3OBU | APT | GTT | PRO | DALA | LALA | SER | MNT | PROP | TYR | 2KT |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
119531 | + | + | - | + | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | + | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | - | + | + | - | - | - | - | - | - | - | - | - | + | + | - | + | - | - | - | + | - |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
5784 | sediment sample of getbol | Korea, Ganghwa island | Republic of Korea | KOR | Asia |
67771 | From Sediment sample of getbol | Ganghwa island | Republic of Korea | KOR | Asia |
119531 | Environment, Sediment sample of getbol | Republic of Korea | KOR | Asia |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Sediment |
#Environmental | #Terrestrial | #Tidal flat |
taxonmaps
- @ref: 69479
- File name: preview.99_6836.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_202;96_3219;97_3951;98_5036;99_6836&stattab=map
- Last taxonomy: Zooshikella
- 16S sequence: AY130994
- Sequence Identity:
- Total samples: 1619
- soil counts: 143
- aquatic counts: 1307
- animal counts: 154
- plant counts: 15
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
5784 | 1 | Risk group (German classification) |
119531 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 5784
- description: Zooshikella ganghwensis strain JC2044 16S ribosomal RNA gene, partial sequence
- accession: AY130994
- length: 1462
- database: ena
- NCBI tax ID: 202772
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Zooshikella ganghwensis DSM 15267 | GCA_000428585 | scaffold | ncbi | 1123509 |
66792 | Zooshikella ganghwensis DSM 15267 | 1123509.3 | wgs | patric | 1123509 |
66792 | Zooshikella ganghwensis DSM 15267 | 2524614643 | draft | img | 1123509 |
GC content
- @ref: 5784
- GC-content: 42
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 94 | no |
motile | yes | 88.657 | no |
flagellated | yes | 82.559 | no |
gram-positive | no | 98.562 | yes |
anaerobic | no | 96.223 | yes |
aerobic | yes | 78.939 | yes |
halophile | no | 76.523 | no |
spore-forming | no | 89.235 | no |
glucose-util | yes | 89.409 | no |
thermophile | no | 98.527 | no |
glucose-ferment | no | 77.906 | no |
External links
@ref: 5784
culture collection no.: DSM 15267, KCTC 12044, IMSNU 14003, CIP 108300
straininfo link
- @ref: 75334
- straininfo: 113586
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 26409875 | Zooshikella marina sp. nov. a cycloprodigiosin- and prodigiosin-producing marine bacterium isolated from beach sand. | Ramaprasad EVV, Bharti D, Sasikala C, Ramana CV | Int J Syst Evol Microbiol | 10.1099/ijsem.0.000630 | 2015 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Gammaproteobacteria/*classification/genetics/isolation & purification, India, Indoles/*metabolism, Molecular Sequence Data, Nucleic Acid Hybridization/genetics, Phospholipids/chemistry, *Phylogeny, Pigmentation, Prodigiosin/*metabolism, Pyrroles/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Metabolism |
Phylogeny | 34705624 | Proposal of Zooshikellaceae fam. nov. to accommodate the genera Zooshikella and Spartinivicinus and reclassification of Zooshikella marina as a later heterotypic synonym of Zooshikella ganghwensis based on whole genome sequence analysis. | Huang Z, Su P, Lai Q | Int J Syst Evol Microbiol | 10.1099/ijsem.0.005055 | 2021 | Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, *Gammaproteobacteria/classification/isolation & purification, Nucleic Acid Hybridization, *Phylogeny, Pigmentation, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | journal | pubmed |
---|---|---|---|---|---|---|
5784 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 15267) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-15267 | |||
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 | |||
37424 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/5908 | ||||
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) | |||
66793 | Mukherjee et al. | 10.1038/nbt.3886 | GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life | 35: 676-683 2017 | 28604660 | |
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 | Nucleic Acids Res. 49: D498-D508 2020 | 33211880 | |
67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||||
68382 | Automatically annotated from API zym | |||||
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 | |||
75334 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID113586.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119531 | Curators of the CIP | Collection of Institut Pasteur (CIP 108300) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108300 |