Strain identifier
BacDive ID: 17858
Type strain:
Species: Kordiimonas gwangyangensis
Strain Designation: GW14-5
Strain history: CIP <- 2005, JCM <- 2004, K.K. Kwon and S.J. Kim, Marine Biotechnol. Res. Cent., Ansan, Korea: strain GW14-5
NCBI tax ID(s): 1122137 (strain), 288022 (species)
General
@ref: 8014
BacDive-ID: 17858
DSM-Number: 19435
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped
description: Kordiimonas gwangyangensis GW14-5 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediments of Gwangyang Bay of the South Sea.
NCBI tax id
NCBI tax id | Matching level |
---|---|
288022 | species |
1122137 | strain |
strain history
@ref | history |
---|---|
8014 | <- JCM/RIKEN <- K. K. Kwon and S.-J. Kim, Korea Ocean Res. and Development Inst., Ansan; GW14-5 |
67770 | K. K. Kwon and S.-J. Kim GW14-5. |
119755 | CIP <- 2005, JCM <- 2004, K.K. Kwon and S.J. Kim, Marine Biotechnol. Res. Cent., Ansan, Korea: strain GW14-5 |
doi: 10.13145/bacdive17858.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Alphaproteobacteria
- order: Kordiimonadales
- family: Temperatibacteraceae
- genus: Kordiimonas
- species: Kordiimonas gwangyangensis
- full scientific name: Kordiimonas gwangyangensis Kwon et al. 2005
@ref: 8014
domain: Bacteria
phylum: Proteobacteria
class: Alphaproteobacteria
order: Kordiimonadales
family: Temperatibacteraceae
genus: Kordiimonas
species: Kordiimonas gwangyangensis
full scientific name: Kordiimonas gwangyangensis Kwon et al. 2005 emend. Yang et al. 2013
strain designation: GW14-5
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility | confidence |
---|---|---|---|---|---|---|
31494 | negative | 1.35 µm | 0.25 µm | rod-shaped | yes | |
69480 | yes | 90.405 | ||||
69480 | negative | 99.987 |
pigmentation
- @ref: 31494
- production: no
Culture and growth conditions
culture medium
@ref | name | growth | link | composition |
---|---|---|---|---|
8014 | 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 |
36070 | Marine agar (MA) | yes | Distilled water make up to (1000.000 ml);Marine agar (55.100 g) | |
119755 | CIP Medium 13 | yes | https://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=13 |
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
8014 | positive | growth | 35 | mesophilic |
31494 | positive | growth | 17-44 | |
31494 | positive | optimum | 38.5 | mesophilic |
36070 | positive | growth | 37 | mesophilic |
67770 | positive | growth | 35 | mesophilic |
culture pH
@ref | ability | type | pH | PH range |
---|---|---|---|---|
31494 | positive | growth | 6.0-8.5 | alkaliphile |
31494 | positive | optimum | 7 |
Physiology and metabolism
oxygen tolerance
- @ref: 31494
- oxygen tolerance: aerobe
spore formation
@ref | spore formation | confidence |
---|---|---|
69481 | no | 100 |
69480 | no | 99.995 |
halophily
@ref | salt | growth | tested relation | concentration |
---|---|---|---|---|
31494 | NaCl | positive | growth | 0.5-4 % |
31494 | NaCl | positive | optimum | 2 % |
observation
@ref | observation |
---|---|
31494 | aggregates in clumps |
67770 | quinones: MK-5, Q-10 |
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
31494 | 37054 | 3-hydroxybutyrate | + | carbon source |
31494 | 40585 | alpha-cyclodextrin | + | carbon source |
31494 | 35391 | aspartate | + | carbon source |
31494 | 17057 | cellobiose | + | carbon source |
31494 | 23652 | dextrin | + | carbon source |
31494 | 17234 | glucose | + | carbon source |
31494 | 29987 | glutamate | + | carbon source |
31494 | 15428 | glycine | + | carbon source |
31494 | 17306 | maltose | + | carbon source |
31494 | 51850 | methyl pyruvate | + | carbon source |
31494 | 506227 | N-acetylglucosamine | + | carbon source |
31494 | 17148 | putrescine | + | carbon source |
31494 | 26986 | threonine | + | carbon source |
31494 | 27082 | trehalose | + | carbon source |
31494 | 53423 | tween 40 | + | carbon source |
31494 | 53426 | tween 80 | + | carbon source |
enzymes
@ref | value | activity | ec |
---|---|---|---|
31494 | catalase | + | 1.11.1.6 |
31494 | cytochrome oxidase | + | 1.9.3.1 |
Isolation, sampling and environmental information
isolation
@ref | sample type | country | origin.country | continent | geographic location |
---|---|---|---|---|---|
8014 | sediments of Gwangyang Bay of the South Sea | Republic of Korea | KOR | Asia | |
67770 | Sediment of Gwangyang Bay | Republic of Korea | KOR | Asia | |
119755 | Environment, Estuarine sediment | Republic of Korea | KOR | Asia | Gwangyang bay |
isolation source categories
Cat1 | Cat2 | Cat3 |
---|---|---|
#Environmental | #Aquatic | #Marine |
#Environmental | #Aquatic | #Sediment |
taxonmaps
- @ref: 69479
- File name: preview.99_4222.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_16030;96_1039;97_2568;98_3182;99_4222&stattab=map
- Last taxonomy: Kordiimonas gwangyangensis subclade
- 16S sequence: AY682384
- Sequence Identity:
- Total samples: 115
- soil counts: 3
- aquatic counts: 90
- animal counts: 20
- plant counts: 2
Safety information
risk assessment
@ref | biosafety level | biosafety level comment |
---|---|---|
8014 | 1 | Risk group (German classification) |
119755 | 1 | Risk group (French classification) |
Sequence information
16S sequences
- @ref: 8014
- description: Kordiimonas gwangyangensis strain GW14-5 16S ribosomal RNA gene, partial sequence
- accession: AY682384
- length: 1448
- database: ena
- NCBI tax ID: 1122137
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Kordiimonas gwangyangensis DSM 19435 | 1122137.3 | wgs | patric | 1122137 |
66792 | Kordiimonas gwangyangensis JCM 12864 | 1236957.3 | wgs | patric | 1122137 |
66792 | Kordiimonas gwangyangensis DSM 19435 | 2517093004 | draft | img | 1122137 |
66792 | Kordiimonas gwangyangensis JCM 12864 | 2585427871 | draft | img | 1122137 |
67770 | Kordiimonas gwangyangensis DSM 19435 = JCM 12864 | GCA_000375545 | contig | ncbi | 1122137 |
67770 | Kordiimonas gwangyangensis DSM 19435 = JCM 12864 | GCA_000616065 | contig | ncbi | 1122137 |
GC content
@ref | GC-content | method |
---|---|---|
8014 | 58.0 | high performance liquid chromatography (HPLC) |
8014 | 39.3 | high performance liquid chromatography (HPLC) |
31494 | 39.3 | |
67770 | 55.3-55.9 | high performance liquid chromatography (HPLC) |
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
spore-forming | no | 100 | no |
motile | yes | 88.836 | yes |
flagellated | yes | 59.725 | no |
gram-positive | no | 98.717 | yes |
anaerobic | no | 99.174 | yes |
halophile | no | 66.343 | no |
spore-forming | no | 93.938 | no |
thermophile | no | 98.791 | no |
glucose-util | yes | 88.786 | yes |
aerobic | yes | 89.345 | yes |
glucose-ferment | no | 89.778 | no |
External links
@ref: 8014
culture collection no.: DSM 19435, CIP 109032, JCM 12864, KCCM 42021
straininfo link
- @ref: 86849
- straininfo: 265605
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 16166706 | Kordiimonas gwangyangensis gen. nov., sp. nov., a marine bacterium isolated from marine sediments that forms a distinct phyletic lineage (Kordiimonadales ord. nov.) in the 'Alphaproteobacteria'. | Kwon KK, Lee HS, Yang SH, Kim SJ | Int J Syst Evol Microbiol | 10.1099/ijs.0.63684-0 | 2005 | Alphaproteobacteria/chemistry/*classification/genetics/isolation & purification, Benzopyrenes/*metabolism, Biodegradation, Environmental, DNA, Bacterial/analysis, DNA, Ribosomal/genetics, Fatty Acids/analysis, Genes, rRNA, Geologic Sediments/*microbiology, Molecular Sequence Data, Phenotype, Phylogeny, Pyrenes/*metabolism, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA | Metabolism |
Phylogeny | 19187209 | Novel marine carbazole-degrading bacteria. | Maeda R, Nagashima H, Widada J, Iwata K, Omori T | FEMS Microbiol Lett | 10.1111/j.1574-6968.2009.01497.x | 2009 | Bacteria/*classification/isolation & purification/*metabolism, Bacterial Proteins/genetics, Biotransformation, Blotting, Southern, Carbazoles/*metabolism, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Genes, rRNA, Japan, Molecular Sequence Data, Oxidoreductases/genetics, Phylogeny, RNA, Bacterial/genetics, RNA, Ribosomal, 16S/genetics, Seawater/*microbiology, Sequence Analysis, DNA, Sequence Homology, Nucleic Acid, ortho-Aminobenzoates/metabolism | Metabolism |
Phylogeny | 22307506 | Kordiimonas aestuarii sp. nov., a marine bacterium isolated from a tidal flat. | Math RK, Jeong SH, Jin HM, Park MS, Kim JM, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.038943-0 | 2012 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
Phylogeny | 22427451 | Description of Kordiimonas aquimaris sp. nov., isolated from seawater, and emended descriptions of the genus Kordiimonas Kwon et al. 2005 emend. Xu et al. 2011 and of its existing species. | Yang SH, Kim MR, Seo HS, Lee SH, Lee JH, Kim SJ, Kwon KK | Int J Syst Evol Microbiol | 10.1099/ijs.0.038893-0 | 2012 | Alphaproteobacteria/*classification/genetics/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Glycolipids/analysis, Molecular Sequence Data, *Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Republic of Korea, Seawater/*microbiology, Sequence Analysis, DNA | Genetics |
Phylogeny | 23002050 | Eilatimonas milleporae gen. nov., sp. nov., a marine bacterium isolated from the hydrocoral Millepora dichotoma. | Paramasivam N, Ben-Dov E, Arotsker L, Kushmaro A | Int J Syst Evol Microbiol | 10.1099/ijs.0.043976-0 | 2012 | Alphaproteobacteria/*classification/genetics/isolation & purification, Animals, Anthozoa/*microbiology, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/analysis, Indian Ocean, Israel, Molecular Sequence Data, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Ubiquinone/analysis | Genetics |
Phylogeny | 25577204 | Emcibacter nanhaiensis gen. nov. sp. nov., isolated from sediment of the South China Sea. | Liu X, Li G, Lai Q, Sun F, Du Y, Shao Z | Antonie Van Leeuwenhoek | 10.1007/s10482-015-0381-y | 2015 | Aerobiosis, Alphaproteobacteria/*classification/genetics/*isolation & purification/physiology, Bacterial Typing Techniques, Base Composition, China, Cluster Analysis, Cytosol/chemistry, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/chemistry/genetics, Fatty Acids/analysis, Geologic Sediments/*microbiology, Glycolipids/analysis, Hydrogen-Ion Concentration, Molecular Sequence Data, Oceans and Seas, Phospholipids/analysis, Phylogeny, Quinones/analysis, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sodium Chloride/metabolism, Temperature | Genetics |
Phylogeny | 26936256 | Kordiimonas sediminis sp. nov., isolated from a sea cucumber culture pond. | Zhang HX, Zhao JX, Chen GJ, Du ZJ | Antonie Van Leeuwenhoek | 10.1007/s10482-016-0671-z | 2016 | Alphaproteobacteria/*classification/genetics/growth & development/*isolation & purification, Animals, Bacterial Typing Techniques, China, DNA, Bacterial/genetics, Genotype, Geologic Sediments/microbiology, Phenotype, Phylogeny, Ponds/*microbiology, RNA, Ribosomal, 16S/genetics, Sea Cucumbers/*microbiology, Seawater/*microbiology | Genetics |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed |
---|---|---|---|---|---|---|
8014 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 19435) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-19435 | |||
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 | |||
31494 | 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 | 27792 | 28776041 | |
36070 | Curators of the CIP | https://brclims.pasteur.fr/brcWeb/souche/detail/1/6729 | ||||
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) | |||
67770 | Curators of the JCM | https://jcm.brc.riken.jp/en/ | ||||
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 | |||
86849 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID265605.1 | StrainInfo: A central database for resolving microbial strain identifiers | |||
119755 | Curators of the CIP | Collection of Institut Pasteur (CIP 109032) | https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20109032 |