Strain identifier
BacDive ID: 5732
Type strain: 
Species: Joostella marina
Strain Designation: EN5
Strain history: <- ZX Quan, KRIBB
NCBI tax ID(s): 926559 (strain), 453852 (species)
version 8.1 (current version)
General
@ref: 8196
BacDive-ID: 5732
DSM-Number: 19592
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Joostella marina EN5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from coastal seawater in the East Sea of Korea, at a depth of 100 m.
NCBI tax id
| NCBI tax id | Matching level |
|---|---|
| 453852 | species |
| 926559 | strain |
strain history
| @ref | history |
|---|---|
| 8196 | <- S. W. Roh, Korea Res. Inst. of Biosci. and Biotechnol. (KRIBB); EN5 |
| 67771 | <- ZX Quan, KRIBB |
doi: 10.13145/bacdive5732.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/bacteroidota
- domain: Bacteria
- phylum: Bacteroidota
- class: Flavobacteriia
- order: Flavobacteriales
- family: Flavobacteriaceae
- genus: Joostella
- species: Joostella marina
- full scientific name: Joostella marina Quan et al. 2008
synonyms
- @ref: 20215
- synonym: Galbibacter orientalis
@ref: 8196
domain: Bacteria
phylum: Bacteroidetes
class: Flavobacteriia
order: Flavobacteriales
family: Flavobacteriaceae
genus: Joostella
species: Joostella marina
full scientific name: Joostella marina Quan et al. 2008 emend. Hahnke et al. 2016
strain designation: EN5
type strain: yes
Morphology
cell morphology
| @ref | gram stain | cell length | cell width | cell shape | motility | confidence |
|---|---|---|---|---|---|---|
| 32515 | negative | 1.5 µm | 0.25 µm | rod-shaped | no | |
| 67771 | negative | |||||
| 69480 | negative | 99.99 |
pigmentation
- @ref: 32515
- production: yes
multimedia
- @ref: 66793
- multimedia content: EM_DSM_19592_1.jpg
- caption: electron microscopic image
- intellectual property rights: © HZI/Manfred Rohde
Culture and growth conditions
culture medium
- @ref: 8196
- 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 |
|---|---|---|---|---|
| 8196 | positive | growth | 28 | mesophilic |
| 32515 | positive | growth | 10-37 | |
| 32515 | positive | optimum | 30 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
culture pH
| @ref | ability | type | pH | PH range |
|---|---|---|---|---|
| 32515 | positive | growth | 5.3-10.5 | alkaliphile |
| 32515 | positive | optimum | 6.45 |
Physiology and metabolism
oxygen tolerance
| @ref | oxygen tolerance |
|---|---|
| 32515 | aerobe |
| 67771 | aerobe |
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 32515 | no | |
| 69481 | no | 100 |
| 69480 | no | 99.994 |
halophily
| @ref | salt | growth | tested relation | concentration |
|---|---|---|---|---|
| 32515 | NaCl | positive | growth | 0-15 % |
| 32515 | NaCl | positive | optimum | 2 % |
observation
- @ref: 67771
- observation: quinones: MK-6
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 32515 | 22599 | arabinose | + | carbon source |
| 32515 | 17234 | glucose | + | carbon source |
| 32515 | 17306 | maltose | + | carbon source |
| 32515 | 37684 | mannose | + | carbon source |
| 32515 | 17992 | sucrose | + | carbon source |
| 32515 | 4853 | esculin | + | hydrolysis |
enzymes
| @ref | value | activity | ec |
|---|---|---|---|
| 32515 | acid phosphatase | + | 3.1.3.2 |
| 32515 | alkaline phosphatase | + | 3.1.3.1 |
| 32515 | catalase | + | 1.11.1.6 |
| 32515 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
| @ref | sample type | country | origin.country | continent | geographic location |
|---|---|---|---|---|---|
| 8196 | coastal seawater in the East Sea of Korea, at a depth of 100 m | Republic of Korea | KOR | Asia | |
| 67771 | From sea water | Republic of Korea | KOR | Asia | Goseong, East Sea |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_2632.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_230;96_1402;97_1673;98_2037;99_2632&stattab=map
- Last taxonomy: Joostella
- 16S sequence: EF660761
- Sequence Identity:
- Total samples: 4055
- soil counts: 134
- aquatic counts: 3235
- animal counts: 662
- plant counts: 24
Safety information
risk assessment
- @ref: 8196
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
| @ref | description | accession | length | database | NCBI tax ID |
|---|---|---|---|---|---|
| 8196 | Joostella marina DSM 19592 strain En5 16S ribosomal RNA gene, partial sequence | EF660761 | 1427 | ena | 926559 |
| 67771 | Venteria marina strain En5 16S ribosomal RNA gene, partial sequence | DQ097522 | 1427 | ena | 335971 |
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Galbibacter orientalis DSM 19592 | GCA_000260115 | scaffold | ncbi | 926559 |
| 66792 | Joostella marina DSM 19592 | 926559.3 | wgs | patric | 926559 |
| 66792 | Joostella marina DSM 19592 | 2509276026 | draft | img | 926559 |
GC content
| @ref | GC-content | method |
|---|---|---|
| 8196 | 30.1 | |
| 8196 | 33.6 | sequence analysis |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | no | 90.014 | yes |
| flagellated | no | 95.685 | yes |
| gram-positive | no | 97.727 | yes |
| anaerobic | no | 99.72 | no |
| aerobic | yes | 85.737 | yes |
| halophile | no | 63.777 | no |
| spore-forming | no | 95.87 | yes |
| glucose-util | yes | 89.59 | yes |
| thermophile | no | 98.329 | yes |
| glucose-ferment | no | 89.182 | no |
External links
@ref: 8196
culture collection no.: DSM 19592, CGMCC 1.6973, KCTC 12518
straininfo link
- @ref: 75212
- straininfo: 405879
literature
- topic: Phylogeny
- Pubmed-ID: 18523183
- title: Joostella marina gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the East Sea.
- authors: Quan ZX, Xiao YP, Roh SW, Nam YD, Chang HW, Shin KS, Rhee SK, Park YH, Bae JW
- journal: Int J Syst Evol Microbiol
- DOI: 10.1099/ijs.0.65611-0
- year: 2008
- mesh: Bacterial Typing Techniques, Base Composition, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Flavobacteriaceae/*classification/genetics/*isolation & purification, Genes, rRNA, Korea, Molecular Sequence Data, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Species Specificity
- topic2: Genetics
Reference
| @id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
|---|---|---|---|---|---|---|---|
| 8196 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19592) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19592 | ||||
| 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 | ||||
| 32515 | 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 | 28735 | 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) | ||||
| 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 | 28604660 | 35: 676-683 2017 | ||
| 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 | ||
| 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 | ||||
| 75212 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID405879.1 | StrainInfo: A central database for resolving microbial strain identifiers |