Strain identifier

BacDive ID: 3027

Type strain: Yes

Species: Caenimonas koreensis

Strain Designation: EMB320

Strain history: <- CO Jeon, Gyungsang Univ.

For citation purpose refer to the digital object identifier (doi) of the current version.
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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 idMatching level
367474species
1121255strain

strain history

@refhistory
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

@refgram staincell lengthcell widthcell shapemotility
32387negative1.4 µm0.5 µmrod-shapedno
67771negative

multimedia

@refmultimedia contentcaptionintellectual property rights
66793EM_DSM_17982_1.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17982_2.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17982_3.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17982_4.jpgelectron microscopic image© HZI/Manfred Rohde
66793EM_DSM_17982_5.jpgelectron 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

@refgrowthtypetemperaturerange
7314positivegrowth28mesophilic
32387positiveoptimum30mesophilic
67771positivegrowth28mesophilic

culture pH

@refabilitytypepH
32387positivegrowth07-08
32387positiveoptimum7.5

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
32387aerobe
67771aerobe

observation

  • @ref: 67771
  • observation: quinones: Q-8

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
3238728757fructose+carbon source
3238717234glucose+carbon source
3238715792malonate+carbon source
3238717632nitrate+reduction

enzymes

@refvalueactivityec
32387alkaline phosphatase+3.1.3.1
32387catalase+1.11.1.6
32387gelatinase+
32387cytochrome oxidase+1.9.3.1
32387urease+3.5.1.5

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7314activated sludgePohangRepublic of KoreaKORAsia
67771From activated sludgeRepublic of KoreaKORAsia

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

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Caenimonas koreensis DSM 17982 EMB320GCA_009646335contigncbi1121255
66792Caenimonas koreensis DSM 17982 strain EMB3201121255.3wgspatric1121255
66792Caenimonas koreensis DSM 179822574179763draftimg1121255

GC content

  • @ref: 32387
  • GC-content: 62.7

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
motileno65.183yes
flagellatedno89.997yes
gram-positiveno98.172no
anaerobicno99.363yes
aerobicyes94.81yes
halophileno96.061no
spore-formingno95.157no
thermophileno98.063yes
glucose-utilno59.067no
glucose-fermentno91.71no

External links

@ref: 7314

culture collection no.: DSM 17982, KCTC 12616

straininfo link

  • @ref: 72547
  • straininfo: 397253

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny18450689Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge.Ryu SH, Lee DS, Park M, Wang Q, Jang HH, Park W, Jeon COInt J Syst Evol Microbiol10.1099/ijs.0.65416-02008Bacterial 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 SpecificityMetabolism
Phylogeny23124758Caenimonas 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 SWJ Microbiol10.1007/s12275-012-1587-62012Base 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 MicrobiologyMetabolism
Phylogeny32748162Caenimonas 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 JCurr Microbiol10.1007/s00284-020-02145-62020*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 WaterTranscriptome
Phylogeny33174135Caenimonas soli sp. nov., isolated from soil.Dahal RH, Lee H, Chaudhary DK, Kim DY, Son J, Kim J, Ka JO, Kim DUArch Microbiol10.1007/s00203-020-02110-82020Base Composition, Comamonadaceae/*classification/genetics, Fatty Acids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, *Soil Microbiology, Species Specificity
Phylogeny35354765Caenimonas aquaedulcis sp. nov., Isolated from Freshwater of Daechung Reservoir during Microcystis Bloom.Le VV, Ko SR, Lee SA, Kang M, Oh HM, Ahn CYJ Microbiol Biotechnol10.4014/jmb.2201.010232022Bacterial Typing Techniques, DNA, Bacterial/genetics, Fatty Acids/analysis, Fresh Water, *Microcystis/genetics, Nucleic Acid Hybridization, Phospholipids/analysis, Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNATranscriptome

Reference

@idauthorscataloguedoi/urltitleID_cross_referencepubmedjournal
7314Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 17982)https://www.dsmz.de/collection/catalogue/details/culture/DSM-17982
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.10.1099/ijsem.0.004332List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ
32387Barberan A, Caceres Velazquez H, Jones S, Fierer N.10.1128/mSphere.00237-17Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information2861228776041
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmannhttps://diaspora-project.de/progress.html#genomesAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)
66793Mukherjee et al.10.1038/nbt.3886GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life28604660 35: 676-683 2017
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
69479João 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
72547Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID397253.1StrainInfo: A central database for resolving microbial strain identifiers