Strain identifier
BacDive ID: 3027
Type strain:
Species: Caenimonas koreensis
Strain Designation: EMB320
Strain history: <- CO Jeon, Gyungsang Univ.
NCBI tax ID(s): 1121255 (strain), 367474 (species)
General
@ref: 7314
BacDive-ID: 3027
DSM-Number: 17982
keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, rod-shaped
description: Caenimonas koreensis EMB320 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.
NCBI tax id
NCBI tax id | Matching level |
---|---|
367474 | species |
1121255 | strain |
strain history
@ref | history |
---|---|
7314 | <- C. O. Jeon; EMB320 |
67771 | <- CO Jeon, Gyungsang Univ. |
doi: 10.13145/bacdive3027.20230509.8.1
Name and taxonomic classification
LPSN
- @ref: 20215
- description: domain/bacteria
- keyword: phylum/pseudomonadota
- domain: Bacteria
- phylum: Pseudomonadota
- class: Betaproteobacteria
- order: Burkholderiales
- family: Comamonadaceae
- genus: Caenimonas
- species: Caenimonas koreensis
- full scientific name: Caenimonas koreensis Ryu et al. 2008
@ref: 7314
domain: Bacteria
phylum: Proteobacteria
class: Betaproteobacteria
order: Burkholderiales
family: Comamonadaceae
genus: Caenimonas
species: Caenimonas koreensis
full scientific name: Caenimonas koreensis Ryu et al. 2008
strain designation: EMB320
type strain: yes
Morphology
cell morphology
@ref | gram stain | cell length | cell width | cell shape | motility |
---|---|---|---|---|---|
32387 | negative | 1.4 µm | 0.5 µm | rod-shaped | no |
67771 | negative |
multimedia
@ref | multimedia content | caption | intellectual property rights |
---|---|---|---|
66793 | EM_DSM_17982_1.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17982_2.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17982_3.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17982_4.jpg | electron microscopic image | © HZI/Manfred Rohde |
66793 | EM_DSM_17982_5.jpg | electron microscopic image | © HZI/Manfred Rohde |
Culture and growth conditions
culture medium
- @ref: 7314
- name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)
- growth: yes
- link: https://mediadive.dsmz.de/medium/830c
- composition: Name: REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c) Composition: Agar 15.0 g/l Yeast extract 0.5 g/l Proteose peptone 0.5 g/l Casamino acids 0.5 g/l Glucose 0.5 g/l Starch 0.5 g/l K2HPO4 0.3 g/l Na-pyruvate 0.3 g/l MgSO4 x 7 H2O 0.05 g/l Distilled water
culture temp
@ref | growth | type | temperature | range |
---|---|---|---|---|
7314 | positive | growth | 28 | mesophilic |
32387 | positive | optimum | 30 | mesophilic |
67771 | positive | growth | 28 | mesophilic |
culture pH
@ref | ability | type | pH |
---|---|---|---|
32387 | positive | growth | 07-08 |
32387 | positive | optimum | 7.5 |
Physiology and metabolism
oxygen tolerance
@ref | oxygen tolerance |
---|---|
32387 | aerobe |
67771 | aerobe |
observation
- @ref: 67771
- observation: quinones: Q-8
metabolite utilization
@ref | Chebi-ID | metabolite | utilization activity | kind of utilization tested |
---|---|---|---|---|
32387 | 28757 | fructose | + | carbon source |
32387 | 17234 | glucose | + | carbon source |
32387 | 15792 | malonate | + | carbon source |
32387 | 17632 | nitrate | + | reduction |
enzymes
@ref | value | activity | ec |
---|---|---|---|
32387 | alkaline phosphatase | + | 3.1.3.1 |
32387 | catalase | + | 1.11.1.6 |
32387 | gelatinase | + | |
32387 | cytochrome oxidase | + | 1.9.3.1 |
32387 | urease | + | 3.5.1.5 |
Isolation, sampling and environmental information
isolation
@ref | sample type | geographic location | country | origin.country | continent |
---|---|---|---|---|---|
7314 | activated sludge | Pohang | Republic of Korea | KOR | Asia |
67771 | From activated sludge | Republic of Korea | KOR | Asia |
isolation source categories
- Cat1: #Engineered
- Cat2: #Waste
- Cat3: #Activated sludge
taxonmaps
- @ref: 69479
- File name: preview.99_79546.png
- url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_1;96_308;97_987;98_1165;99_79546&stattab=map
- Last taxonomy: Variovorax
- 16S sequence: DQ349098
- Sequence Identity:
- Total samples: 87
- soil counts: 45
- aquatic counts: 33
- animal counts: 8
- plant counts: 1
Safety information
risk assessment
- @ref: 7314
- biosafety level: 1
- biosafety level comment: Risk group (German classification)
Sequence information
16S sequences
- @ref: 7314
- description: Caenimonas koreensis strain EMB320 16S ribosomal RNA gene, partial sequence
- accession: DQ349098
- length: 1457
- database: ena
- NCBI tax ID: 1121255
Genome sequences
@ref | description | accession | assembly level | database | NCBI tax ID |
---|---|---|---|---|---|
66792 | Caenimonas koreensis DSM 17982 EMB320 | GCA_009646335 | contig | ncbi | 1121255 |
66792 | Caenimonas koreensis DSM 17982 strain EMB320 | 1121255.3 | wgs | patric | 1121255 |
66792 | Caenimonas koreensis DSM 17982 | 2574179763 | draft | img | 1121255 |
GC content
- @ref: 32387
- GC-content: 62.7
Genome-based predictions
predictions
trait | prediction | confidence | training_data |
---|---|---|---|
motile | no | 65.183 | yes |
flagellated | no | 89.997 | yes |
gram-positive | no | 98.172 | no |
anaerobic | no | 99.363 | yes |
aerobic | yes | 94.81 | yes |
halophile | no | 96.061 | no |
spore-forming | no | 95.157 | no |
thermophile | no | 98.063 | yes |
glucose-util | no | 59.067 | no |
glucose-ferment | no | 91.71 | no |
External links
@ref: 7314
culture collection no.: DSM 17982, KCTC 12616
straininfo link
- @ref: 72547
- straininfo: 397253
literature
topic | Pubmed-ID | title | authors | journal | DOI | year | mesh | topic2 |
---|---|---|---|---|---|---|---|---|
Phylogeny | 18450689 | Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge. | Ryu SH, Lee DS, Park M, Wang Q, Jang HH, Park W, Jeon CO | Int J Syst Evol Microbiol | 10.1099/ijs.0.65416-0 | 2008 | Bacterial Typing Techniques, Bioreactors, Comamonadaceae/classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/analysis, Genes, rRNA, Molecular Sequence Data, Phosphorus/metabolism, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, Sewage/*microbiology, Species Specificity | Metabolism |
Phylogeny | 23124758 | Caenimonas terrae sp. nov., isolated from a soil sample in Korea, and emended description of the genus Caenimonas Ryu et al. 2008. | Kim SJ, Weon HY, Kim YS, Moon JY, Seok SJ, Hong SB, Kwon SW | J Microbiol | 10.1007/s12275-012-1587-6 | 2012 | Base Composition, Comamonadaceae/*classification/genetics/*isolation & purification/metabolism, DNA, Ribosomal/genetics, Fatty Acids/metabolism, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology | Metabolism |
Phylogeny | 32748162 | Caenimonas sedimenti sp. nov., Isolated from Sediment of the Wastewater Outlet of an Agricultural Chemical Plant. | Xu J, Sheng M, Yang Z, Qiu J, Zhang J, Zhang L, He J | Curr Microbiol | 10.1007/s00284-020-02145-6 | 2020 | *Agrochemicals, Bacterial Typing Techniques, China, Comamonadaceae, DNA, Bacterial/genetics, Fatty Acids/analysis, Nucleic Acid Hybridization, Phospholipids, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Waste Water | Transcriptome |
Phylogeny | 33174135 | Caenimonas soli sp. nov., isolated from soil. | Dahal RH, Lee H, Chaudhary DK, Kim DY, Son J, Kim J, Ka JO, Kim DU | Arch Microbiol | 10.1007/s00203-020-02110-8 | 2020 | Base Composition, Comamonadaceae/*classification/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Species Specificity | |
Phylogeny | 35354765 | Caenimonas aquaedulcis sp. nov., Isolated from Freshwater of Daechung Reservoir during Microcystis Bloom. | Le VV, Ko SR, Lee SA, Kang M, Oh HM, Ahn CY | J Microbiol Biotechnol | 10.4014/jmb.2201.01023 | 2022 | Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water, *Microcystis/genetics, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA | Transcriptome |
Reference
@id | authors | catalogue | doi/url | title | ID_cross_reference | pubmed | journal |
---|---|---|---|---|---|---|---|
7314 | Curators of the DSMZ | Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17982) | https://www.dsmz.de/collection/catalogue/details/culture/DSM-17982 | ||||
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 | ||||
32387 | 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 | 28612 | 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 | ||
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 | ||||
72547 | Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J. | 10.60712/SI-ID397253.1 | StrainInfo: A central database for resolving microbial strain identifiers |