Strain identifier
BacDive ID: 132202
Type strain: 
Species: Agarivorans litoreus
Strain Designation: GJSW-6
Strain history: <- Jung-Hoon Yoon, Sungkyunkwan Univ.
NCBI tax ID(s): 1510455 (species)
version 8.1 (current version)
General
@ref: 23991
BacDive-ID: 132202
DSM-Number: 103824
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile
description: Agarivorans litoreus GJSW-6 is an aerobe, mesophilic, motile bacterium that was isolated from seawater.
NCBI tax id
- NCBI tax id: 1510455
- Matching level: species
strain history
| @ref | history |
|---|---|
| 23991 | <- KCTC <- S. Park and J.-H. Yoon, Department of Food Science and Biotechnology, Sungkyunkwan University, Suwon, South Korea; GJSW-6 |
| 67771 | <- Jung-Hoon Yoon, Sungkyunkwan Univ. |
doi: 10.13145/bacdive132202.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Alteromonadaceae
- genus: Agarivorans
- species: Agarivorans litoreus
- full scientific name: Agarivorans litoreus Park et al. 2015
@ref: 23991
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Alteromonadaceae
genus: Agarivorans
species: Agarivorans litoreus
full scientific name: Agarivorans litoreus Park et al. 2015
strain designation: GJSW-6
type strain: yes
Morphology
cell morphology
| @ref | motility | confidence | gram stain |
|---|---|---|---|
| 69480 | yes | 98.324 | |
| 69480 | 99.995 | negative |
Culture and growth conditions
culture medium
- @ref: 23991
- 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 |
|---|---|---|---|---|
| 23991 | positive | growth | 28 | mesophilic |
| 67771 | positive | growth | 30 | mesophilic |
Physiology and metabolism
oxygen tolerance
- @ref: 67771
- oxygen tolerance: aerobe
spore formation
| @ref | spore formation | confidence |
|---|---|---|
| 69481 | no | 100 |
| 69480 | no | 99.967 |
metabolite utilization
| @ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
|---|---|---|---|---|
| 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 |
|---|---|---|---|
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 23991 | + | - | + | - | - | + | + | + | - | + | - | - | - | + | + | - | + | + | + | - | + |
Isolation, sampling and environmental information
isolation
| @ref | sample type | geographic location | country | origin.country | continent |
|---|---|---|---|---|---|
| 23991 | seawater | South Sea near Geoje Island | Republic of Korea | KOR | Asia |
| 67771 | From seawater | Geojedo | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Environmental
- Cat2: #Aquatic
- Cat3: #Marine
taxonmaps
- @ref: 69479
- File name: preview.99_113090.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_361;96_2853;97_3509;98_4441;99_113090&stattab=map
- Last taxonomy: Agarivorans
- 16S sequence: KJ729029
- Sequence Identity:
- Total samples: 205
- aquatic counts: 201
- animal counts: 3
- plant counts: 1
Safety information
risk assessment
- @ref: 23991
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 23991
- description: Agarivorans litoreus strain GJSW-6 16S ribosomal RNA gene, partial sequence
- accession: KJ729029
- length: 1467
- database: ena
- NCBI tax ID: 1510455
Genome sequences
| @ref | description | accession | assembly level | database | NCBI tax ID |
|---|---|---|---|---|---|
| 66792 | Agarivorans litoreus NBRC 110444 | GCA_019649015 | contig | ncbi | 1510455 |
| 66792 | Agarivorans litoreus strain NBRC 110444 | 1510455.3 | wgs | patric | 1510455 |
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| spore-forming | no | 100 | no |
| motile | yes | 90.173 | no |
| gram-positive | no | 98.796 | no |
| anaerobic | no | 95.78 | yes |
| aerobic | yes | 85.569 | yes |
| halophile | yes | 81.889 | no |
| spore-forming | no | 95.888 | no |
| thermophile | no | 99.568 | yes |
| glucose-util | yes | 84.265 | yes |
| flagellated | yes | 91.299 | no |
| glucose-ferment | yes | 83.376 | yes |
External links
@ref: 23991
culture collection no.: DSM 103824, KCTC 42116, NBRC 110444
straininfo link
- @ref: 90555
- straininfo: 404420
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 25186952 | Agarivorans litoreus sp. nov., a novel gammaproteobacterium isolated from seawater and emended description of the genus Agarivorans. | Park S, Park JM, Jung YT, Yoon JH | Antonie Van Leeuwenhoek | 10.1007/s10482-014-0273-6 | 2014 | Aerobiosis, Alteromonadaceae/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Hydrogen-Ion Concentration, Korea, Locomotion, Molecular Sequence Data, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
| Phylogeny | 27189058 | Agarivorans aestuarii sp. nov., an agar-degrading bacterium isolated from a tidal flat. | Kim SG, Pheng S, Lee YJ, Eom MK, Shin DH | Int J Syst Evol Microbiol | 10.1099/ijsem.0.001155 | 2016 | Agar, Alteromonadaceae/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/microbiology, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | title | doi/url | catalogue |
|---|---|---|---|---|
| 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 | |
| 23991 | Curators of the DSMZ | https://www.dsmz.de/collection/catalogue/details/culture/DSM-103824 | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103824) | |
| 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 | |
| 67771 | Curators of the KCTC | https://kctc.kribb.re.kr/En/Kctc | ||
| 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 | |
| 90555 | 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-ID404420.1 |