Strain identifier
BacDive ID: 485
Type strain: 
Species: Marinobacter koreensis
Strain Designation: DD-M3
Strain history: <- S.-W. Kwon; DD-M3 <- B.-Y. Kim et al.
NCBI tax ID(s): 335974 (species)
version 8.1 (current version)
General
@ref: 7250
BacDive-ID: 485
DSM-Number: 17924
keywords: genome sequence, 16S sequence, Bacteria, mesophilic
description: Marinobacter koreensis DD-M3 is a mesophilic bacterium that was isolated from sea sand.
NCBI tax id
- NCBI tax id: 335974
- Matching level: species
strain history
- @ref: 7250
- history: <- S.-W. Kwon; DD-M3 <- B.-Y. Kim et al.
doi: 10.13145/bacdive485.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Gammaproteobacteria
- order: Alteromonadales
- family: Alteromonadaceae
- genus: Marinobacter
- species: Marinobacter koreensis
- full scientific name: Marinobacter koreensis Kim et al. 2006
@ref: 7250
domain: Bacteria
phylum: Proteobacteria
class: Gammaproteobacteria
order: Alteromonadales
family: Alteromonadaceae
genus: Marinobacter
species: Marinobacter koreensis
full scientific name: Marinobacter koreensis Kim et al. 2006
strain designation: DD-M3
type strain: yes
Culture and growth conditions
culture medium
- @ref: 7250
- 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: 7250
- growth: positive
- type: growth
- temperature: 28
- range: mesophilic
Isolation, sampling and environmental information
isolation
- @ref: 7250
- sample type: sea sand
- geographic location: Pohang, Homo Cape
- country: Republic of Korea
- origin.country: KOR
- continent: Asia
isolation source categories
| Cat1 | Cat2 | Cat3 |
|---|---|---|
| #Environmental | #Aquatic | #Marine |
| #Environmental | #Terrestrial | #Sandy |
taxonmaps
- @ref: 69479
- File name: preview.99_3505.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_89;96_693;97_2189;98_2686;99_3505&stattab=map
- Last taxonomy: Marinobacter
- 16S sequence: DQ325514
- Sequence Identity:
- Total samples: 562
- soil counts: 33
- aquatic counts: 499
- animal counts: 18
- plant counts: 12
Safety information
risk assessment
- @ref: 7250
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7250
- description: Marinobacter koreensis strain DD-M3 16S ribosomal RNA gene, partial sequence
- accession: DQ325514
- length: 1463
- database: ena
- NCBI tax ID: 335974
Genome sequences
- @ref: 66792
- description: Marinobacter koreensis DSM 17924
- accession: GCA_023156285
- assembly level: contig
- database: ncbi
- NCBI tax ID: 335974
GC content
- @ref: 7250
- GC-content: 54.1
- method: high performance liquid chromatography (HPLC)
Genome-based predictions
predictions
| trait | prediction | confidence | training_data |
|---|---|---|---|
| flagellated | yes | 83.816 | no |
| gram-positive | no | 99.168 | no |
| anaerobic | no | 96.15 | no |
| aerobic | yes | 61.488 | no |
| halophile | yes | 88.288 | no |
| spore-forming | no | 96.208 | no |
| motile | yes | 88.743 | no |
| glucose-ferment | no | 88.323 | no |
| thermophile | no | 99.366 | yes |
| glucose-util | no | 58.719 | no |
External links
@ref: 7250
culture collection no.: DSM 17924, KACC 11513
straininfo link
- @ref: 70164
- straininfo: 400114
literature
| topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
|---|---|---|---|---|---|---|---|---|
| Phylogeny | 17082406 | Marinobacter koreensis sp. nov., isolated from sea sand in Korea. | Kim BY, Weon HY, Yoo SH, Kim JS, Kwon SW, Stackebrandt E, Go SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.64231-0 | 2006 | Amino Acids/metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Enzymes/metabolism, Fatty Acids/analysis/chemistry, Genes, rRNA, Geologic Sediments/*microbiology, Korea, Marinobacter/*classification/cytology/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phylogeny, Quinones/analysis/chemistry, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, Silicon Dioxide | Metabolism |
| Phylogeny | 18319470 | Marinobacter pelagius sp. nov., a moderately halophilic bacterium. | Xu XW, Wu YH, Wang CS, Yang JY, Oren A, Wu M | Int J Syst Evol Microbiol | 10.1099/ijs.0.65390-0 | 2008 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/analysis, DNA, Ribosomal/analysis, Fatty Acids/analysis, Genes, rRNA, Genotype, Marinobacter/*classification/genetics/isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride, Species Specificity | Genetics |
| Phylogeny | 19060077 | Marinobacter mobilis sp. nov. and Marinobacter zhejiangensis sp. nov., halophilic bacteria isolated from the East China Sea. | Huo YY, Wang CS, Yang JY, Wu M, Xu XW | Int J Syst Evol Microbiol | 10.1099/ijs.0.2008/000786-0 | 2008 | China, Geologic Sediments/*microbiology, Marinobacter/*classification/genetics/*physiology, Molecular Sequence Data, Oceans and Seas, Phylogeny, RNA, Ribosomal, 16S/genetics, Species Specificity | Genetics |
| Phylogeny | 19329625 | Marinobacter santoriniensis sp. nov., an arsenate-respiring and arsenite-oxidizing bacterium isolated from hydrothermal sediment. | Handley KM, Hery M, Lloyd JR | Int J Syst Evol Microbiol | 10.1099/ijs.0.003145-0 | 2009 | Aerobiosis, Anaerobiosis, Arsenates/*metabolism, Arsenites/*metabolism, Bacterial Typing Techniques, Base Composition, Carbohydrate Metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Greece, Hot Springs/*microbiology, Locomotion, Marinobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nucleic Acid Hybridization, Oxidation-Reduction, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid | Metabolism |
| Phylogeny | 20935087 | Marinobacter oulmenensis sp. nov., a moderately halophilic bacterium isolated from brine of a salt concentrator. | Kharroub K, Aguilera M, Jimenez-Pranteda ML, Gonzalez-Paredes A, Ramos-Cormenzana A, Monteoliva-Sanchez M | Int J Syst Evol Microbiol | 10.1099/ijs.0.027284-0 | 2010 | Algeria, Bacterial Typing Techniques, Base Composition, Carbon/metabolism, Cluster Analysis, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Heterotrophic Processes, Hydrogen-Ion Concentration, Marinobacter/*classification/genetics/*isolation & purification/physiology, Molecular Sequence Data, Nitrogen/metabolism, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Metabolism |
| Phylogeny | 21800628 | [Identification and characterization of a novel hydrocarbon-degrading Marinobacter sp. PY97S]. | Li Q, Cui Z, Zhao A, Gao W, Zheng L | Wei Sheng Wu Xue Bao | 2011 | Anti-Bacterial Agents/pharmacology, Base Composition, Base Sequence, Biodegradation, Environmental, Carbon/metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Hydrocarbons/*metabolism, Hydrogen-Ion Concentration, Marinobacter/*classification/drug effects/genetics/*physiology, Microbial Sensitivity Tests, Molecular Sequence Data, Phenotype, Phylogeny, Quinones/chemistry, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sodium Chloride/pharmacology, Temperature | Metabolism | |
| Phylogeny | 30231958 | Marinobacter bohaiensis sp. nov., a moderate halophile isolated from benthic sediment of the Bohai Sea. | Xu S, Wang D, Wei Y, Cui Q, Li W | Int J Syst Evol Microbiol | 10.1099/ijsem.0.003025 | 2018 | Bacterial Typing Techniques, Base Composition, China, DNA, Bacterial/genetics, Fatty Acids/chemistry, Geologic Sediments/*microbiology, Marinobacter/*classification/genetics/isolation & purification, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry | Transcriptome |
Reference
| @id | authors | catalogue | doi/url | title |
|---|---|---|---|---|
| 7250 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17924) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17924 | |
| 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 | |
| 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) | |
| 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 | |
| 70164 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID400114.1 | StrainInfo: A central database for resolving microbial strain identifiers |