Strain identifier

BacDive ID: 131683

Type strain: Yes

Species: Chelatococcus caeni

Strain Designation: EBR-4-1

Strain history: <- Long Jin (KRIBB)

NCBI tax ID(s): 1348468 (species)

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General

@ref: 23479

BacDive-ID: 131683

DSM-Number: 103737

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, motile

description: Chelatococcus caeni EBR-4-1 is an aerobe, mesophilic, motile bacterium that was isolated from sludge of ECOVISION biofilm reactor applied for toxic wastewater treatment from industrial facilities .

NCBI tax id

  • NCBI tax id: 1348468
  • Matching level: species

strain history

@refhistory
23479<- KCTC <- L. Jin, H.-M. Oh and others, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
67770L. Jin; KRIBB, South Korea; EBR-4-1.
67771<- Long Jin (KRIBB)

doi: 10.13145/bacdive131683.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Hyphomicrobiales
  • family: Chelatococcaceae
  • genus: Chelatococcus
  • species: Chelatococcus caeni
  • full scientific name: Chelatococcus caeni Jin et al. 2015

@ref: 23479

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhizobiales

family: Chelatococcaceae

genus: Chelatococcus

species: Chelatococcus caeni

full scientific name: Chelatococcus caeni Jin et al. 2015

strain designation: EBR-4-1

type strain: yes

Morphology

cell morphology

@refmotilityconfidencegram stain
69480yes92.126
6948099.999negative

Culture and growth conditions

culture medium

  • @ref: 23479
  • name: NUTRIENT AGAR (DSMZ Medium 1)
  • growth: yes
  • link: https://mediadive.dsmz.de/medium/1
  • composition: Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

culture temp

@refgrowthtypetemperaturerange
23479positivegrowth28mesophilic
67770positivegrowth30mesophilic
67771positivegrowth30mesophilic

Physiology and metabolism

oxygen tolerance

  • @ref: 67771
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.995

observation

  • @ref: 67770
  • observation: quinones: Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
6836925115malate+assimilation
6836917128adipate-assimilation
6836927689decanoate-assimilation
6836924265gluconate+assimilation
6836917306maltose-assimilation
6836959640N-acetylglucosamine-assimilation
6836916899D-mannitol+assimilation
6836916024D-mannose+assimilation
6836930849L-arabinose+assimilation
6836917634D-glucose+assimilation
683695291gelatin-hydrolysis
683694853esculin+hydrolysis
6836916199urea+hydrolysis
6836929016arginine-hydrolysis
6836917634D-glucose-fermentation
6836927897tryptophan-energy source
6836917632nitrate+reduction

metabolite production

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • production: no

metabolite tests

  • @ref: 68369
  • Chebi-ID: 35581
  • metabolite: indole
  • indole test: -

enzymes

@refvalueactivityec
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase+3.2.1.21
68369urease+3.5.1.5
68369arginine dihydrolase-3.5.3.6

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
23479+---++--++++--+--++-+

Isolation, sampling and environmental information

isolation

@refsample typecountryorigin.countrycontinent
23479sludge of ECOVISION biofilm reactor applied for toxic wastewater treatment from industrial facilities (19834)Republic of KoreaKORAsia
67770Sludge of a biofilm reactor in DaejeonRepublic of KoreaKORAsia
67771From biofilm reactorRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Engineered#Bioreactor
#Engineered#Waste#Wastewater
#Environmental#Terrestrial#Mud (Sludge)
#Environmental#Biofilm

taxonmaps

  • @ref: 69479
  • File name: preview.99_3235.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_86;96_866;97_1014;98_1197;99_3235&stattab=map
  • Last taxonomy: Chelatococcus caeni
  • 16S sequence: KF056991
  • Sequence Identity:
  • Total samples: 209
  • soil counts: 71
  • aquatic counts: 57
  • animal counts: 63
  • plant counts: 18

Safety information

risk assessment

  • @ref: 23479
  • biosafety level: 1
  • biosafety level comment: Risk group (German classification)

Sequence information

16S sequences

  • @ref: 23479
  • description: Chelatococcus caeni strain EBR-4-1 16S ribosomal RNA gene, partial sequence
  • accession: KF056991
  • length: 1405
  • database: ena
  • NCBI tax ID: 1348468

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Chelatococcus caeni DSM 103737GCA_014196925scaffoldncbi1348468
66792Chelatococcus caeni strain DSM 1037371348468.3wgspatric1348468
66792Chelatococcus caeni DSM 1037372830007530draftimg1348468

GC content

  • @ref: 67770
  • GC-content: 68.7
  • method: high performance liquid chromatography (HPLC)

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno61.14no
gram-positiveno98.486no
anaerobicno95.896no
aerobicyes86.735yes
halophileno92.102no
spore-formingno94.744no
glucose-utilyes90.595yes
thermophileno95.783no
motileyes85.867no
glucose-fermentno91.297no

External links

@ref: 23479

culture collection no.: DSM 103737, JCM 30181, KCTC 32487

straininfo link

  • @ref: 90079
  • straininfo: 405927

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny25525126Chelatococcus caeni sp. nov., isolated from a biofilm reactor sludge sample.Jin L, Ko SR, Lee HG, Kim BH, Kim HS, Ahn CY, Oh HMInt J Syst Evol Microbiol10.1099/ijs.0.0000322014Bacterial Typing Techniques, Base Composition, Beijerinckiaceae/*classification/genetics/isolation & purification, *Biofilms, DNA, Bacterial/genetics, Fatty Acids/chemistry, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, Sewage/*microbiology, Ubiquinone/chemistryGenetics
Phylogeny35225758Salinarimonas soli sp. nov., isolated from soil.Jin CZ, Jin L, Liu MJ, Kang MK, Park SH, Park DJ, Kim CJInt J Syst Evol Microbiol10.1099/ijsem.0.0050952022Alphaproteobacteria/*classification/isolation & purification, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Republic of Korea, Sequence Analysis, DNA, *Soil Microbiology, Ubiquinone/analogs & derivatives/chemistryTranscriptome

Reference

@idauthorstitledoi/urlcatalogue
20215Parte, 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 DSMZ10.1099/ijsem.0.004332
23479Curators of the DSMZhttps://www.dsmz.de/collection/catalogue/details/culture/DSM-103737Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 103737)
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
67770Curators of the JCMhttps://jcm.brc.riken.jp/en/
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
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.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions 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
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1
90079Reimer, 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 identifiers10.60712/SI-ID405927.1