Strain identifier

BacDive ID: 2934

Type strain: Yes

Species: Comamonas koreensis

Strain Designation: YH12

Strain history: CIP <- 2003, KCTC <- Y.H. Chang

NCBI tax ID(s): 160825 (species)

« back to strain detail view
For citation purpose refer to the digital object identifier (doi) of the current version.
Archive
version 8.1 (current version):
version 8:
version 7.1:
version 7:
version 6:
version 5:
version 4.1:
version 4:
version 3:
version 2.1:
version 2:
version 1:
version 8.1 (current version)

General

@ref: 7445

BacDive-ID: 2934

DSM-Number: 18232

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative

description: Comamonas koreensis YH12 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from sediment from wetland.

NCBI tax id

  • NCBI tax id: 160825
  • Matching level: species

strain history

@refhistory
7445<- KCTC <- Y.-H. Chang; YH12
67771<- YH Chang, KRIBB
120475CIP <- 2003, KCTC <- Y.H. Chang

doi: 10.13145/bacdive2934.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Betaproteobacteria
  • order: Burkholderiales
  • family: Comamonadaceae
  • genus: Comamonas
  • species: Comamonas koreensis
  • full scientific name: Comamonas koreensis Chang et al. 2002

@ref: 7445

domain: Bacteria

phylum: Proteobacteria

class: Betaproteobacteria

order: Burkholderiales

family: Comamonadaceae

genus: Comamonas

species: Comamonas koreensis

full scientific name: Comamonas koreensis Chang et al. 2002

strain designation: YH12

type strain: yes

Morphology

cell morphology

@refgram staincell shapemotility
67771negative
120475negativerod-shapedno

pigmentation

  • @ref: 120475
  • production: no
  • name: Pyocyanin

Culture and growth conditions

culture medium

@refnamegrowthlinkcomposition
7445NUTRIENT AGAR (DSMZ Medium 1)yeshttps://mediadive.dsmz.de/medium/1Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water
33190MEDIUM 72- for trypto casein soja agaryesDistilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
120475CIP Medium 72yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=72
120475CIP Medium 328yeshttps://catalogue-crbip.pasteur.fr/fiche_milieu.xhtml?crbip=328

culture temp

@refgrowthtypetemperaturerange
7445positivegrowth30mesophilic
33190positivegrowth30mesophilic
67771positivegrowth30mesophilic
120475positivegrowth25-37mesophilic
120475nogrowth5psychrophilic
120475nogrowth10psychrophilic
120475nogrowth41thermophilic

Physiology and metabolism

oxygen tolerance

@refoxygen tolerance
67771aerobe
120475obligate aerobe

halophily

@refsaltgrowthtested relationconcentration
120475NaClpositivegrowth0-2 %
120475NaClnogrowth4 %
120475NaClnogrowth6 %
120475NaClnogrowth8 %
120475NaClnogrowth10 %

observation

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

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
12047516947citrate+carbon source
1204754853esculin-hydrolysis
12047517632nitrate+reduction
12047516301nitrite-reduction
12047517632nitrate-respiration

antibiotic resistance

  • @ref: 120475
  • metabolite: 0129 (2,4-Diamino-6,7-di-iso-propylpteridine phosphate)
  • is antibiotic: yes
  • is sensitive: yes
  • is resistant: no

metabolite production

@refChebi-IDmetaboliteproduction
6836935581indoleno
12047535581indoleno

metabolite tests

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

enzymes

@refvalueactivityec
68382alpha-fucosidase-3.2.1.51
68382alpha-mannosidase-3.2.1.24
68382N-acetyl-beta-glucosaminidase-3.2.1.52
68382beta-glucosidase-3.2.1.21
68382alpha-glucosidase-3.2.1.20
68382beta-glucuronidase-3.2.1.31
68382beta-galactosidase-3.2.1.23
68382alpha-galactosidase-3.2.1.22
68382naphthol-AS-BI-phosphohydrolase+
68382acid phosphatase-3.1.3.2
68382alpha-chymotrypsin-3.4.21.1
68382trypsin-3.4.21.4
68382cystine arylamidase-3.4.11.3
68382valine arylamidase-
68382leucine arylamidase+3.4.11.1
68382lipase (C 14)-
68382esterase lipase (C 8)+
68382esterase (C 4)+
68382alkaline phosphatase-3.1.3.1
68369cytochrome oxidase+1.9.3.1
68369gelatinase-
68369beta-glucosidase-3.2.1.21
68369urease-3.5.1.5
68369arginine dihydrolase-3.5.3.6
120475oxidase-
120475beta-galactosidase-3.2.1.23
120475alcohol dehydrogenase-1.1.1.1
120475gelatinase-
120475amylase-
120475DNase-
120475caseinase+3.4.21.50
120475catalase+1.11.1.6
120475tween esterase-
120475lecithinase-
120475lipase-
120475lysine decarboxylase-4.1.1.18
120475ornithine decarboxylase-4.1.1.17
120475protease+
120475tryptophan deaminase-
120475urease-3.5.1.5

API zym

@refControlAlkaline phosphataseEsteraseEsterase LipaseLipaseLeucine arylamidaseValine arylamidaseCystine arylamidaseTrypsinalpha- ChymotrypsinAcid phosphataseNaphthol-AS-BI-phosphohydrolasealpha- Galactosidasebeta- Galactosidasebeta- Glucuronidasealpha- Glucosidasebeta- GlucosidaseN-acetyl-beta- glucosaminidasealpha- Mannosidasealpha- Fucosidase
120475--++-+-----+--------

API 20NE

@refNO3TRPGLU_ FermADH ArgUREESCGELPNPGGLU_ AssimARAMNEMANNAGMALGNTCAPADIMLTCITPACOX
7445+---------------+++-+

API biotype100

@refGLUFRUGALTREMNESBEMELSACRAFMTEMALLACLTEMbGaMaGaCELGENMbGuESCRIBARAXYLPLERHAFUCMLZDARLLARLXLTDULTAGGLYINOMANMTLTURSORADOHBGLYXERYMDG3MDGSATMUCLTATDTATMTATDMLTLMLTCATETATETTECITGRTGAT2KG5KGTRYNAGGNTPACPATpOBEQATGTEmOBEBATPPATCMTTGEBETPCEABTHINLATCAPCYTHISSUCFUMGREGYTAVTETNTTNGLNITA3OBUAPTGTTPRODALALALASERMNTPROPTYR2KT
120475-------------------+-----------------------------+---------------+-+-------+---+--------+++++++----

Isolation, sampling and environmental information

isolation

@refsample typegeographic locationcountryorigin.countrycontinent
7445sediment from wetlandWoopo wetlandRepublic of KoreaKORAsia
67771From a wetland sample collected from WoopoRepublic of KoreaKORAsia
120475Environment, Soil, Woopo wetlandWoopoRepublic of KoreaKORAsia

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Sediment
#Environmental#Terrestrial#Wetland (Swamp)

Safety information

risk assessment

@refbiosafety levelbiosafety level comment
74451Risk group (German classification)
1204751Risk group (French classification)

Sequence information

16S sequences

  • @ref: 7445
  • description: Comamonas sp. KCTC 12005 16S ribosomal RNA gene, partial sequence
  • accession: AF275377
  • length: 1464
  • database: ena
  • NCBI tax ID: 160825

Genome sequences

  • @ref: 66792
  • description: Comamonas koreensis KCTC 12005
  • accession: GCA_021026195
  • assembly level: scaffold
  • database: ncbi
  • NCBI tax ID: 160825

GC content

@refGC-content
744566
6777166.0

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
flagellatedno91.928no
gram-positiveno98.693yes
anaerobicno99.057yes
aerobicyes96.07yes
halophileno91.526no
spore-formingno94.495no
motileno73.803no
thermophileno98.916yes
glucose-utilyes53.572no
glucose-fermentno90.868yes

External links

@ref: 7445

culture collection no.: DSM 18232, IMSNU 11158, KCTC 12005, CIP 108012

straininfo link

  • @ref: 72456
  • straininfo: 88304

literature

topicPubmed-IDtitleauthorsjournalDOIyearmeshtopic2
Phylogeny11931145Comamonas koreensis sp. nov., a non-motile species from wetland in Woopo, Korea.Chang YH, Han JI, Chun J, Lee KC, Rhee MS, Kim YB, Bae KSInt J Syst Evol Microbiol10.1099/00207713-52-2-3772002Base Composition, Comamonas/*classification/physiology, DNA, Bacterial/chemistry/genetics, DNA, Ribosomal/genetics, Korea, Molecular Sequence Data, Phylogeny, RNA, Ribosomal, 16S/genetics, *Soil MicrobiologyGenetics
Phylogeny17392226Comamonas odontotermitis sp. nov., isolated from the gut of the termite Odontotermes formosanus.Chou JH, Sheu SY, Lin KY, Chen WM, Arun AB, Young CCInt J Syst Evol Microbiol10.1099/ijs.0.64551-02007Animals, Comamonas/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Digestive System/microbiology, Isoptera/*microbiology, Molecular Sequence Data, RNA, Ribosomal, 16S/geneticsGenetics
Phylogeny18175717Comamonas composti sp. nov., isolated from food waste compost.Young CC, Chou JH, Arun AB, Yen WS, Sheu SY, Shen FT, Lai WA, Rekha PD, Chen WMInt J Syst Evol Microbiol10.1099/ijs.0.65277-02008Bacterial Typing Techniques, Comamonas/*classification/genetics/isolation & purification/physiology, DNA, Bacterial/analysis, Fatty Acids/analysis, *Food Microbiology, Genes, rRNA, Genotype, Molecular Sequence Data, Nucleic Acid Hybridization, Phenotype, Phylogeny, RNA, Ribosomal, 16S/genetics, Refuse Disposal/*methods, Sequence Analysis, DNA, Species Specificity, TaiwanGenetics
Phylogeny18758728Comamonas granuli sp. nov., isolated from granules used in a wastewater treatment plant.Kim KH, Ten LN, Liu QM, Im WT, Lee STJ Microbiol10.1007/s12275-008-0019-02008Base Composition, Bioreactors/microbiology, Comamonas/*classification/genetics/*isolation & purification/metabolism, DNA, Bacterial/genetics, DNA, Ribosomal/genetics, Fatty Acids/metabolism, *Industrial Waste, Phylogeny, RNA, Ribosomal, 16S/genetics, Sewage/*microbiologyMetabolism
Phylogeny22581903Comamonas guangdongensis sp. nov., isolated from subterranean forest sediment, and emended description of the genus Comamonas.Zhang J, Wang Y, Zhou S, Wu C, He J, Li FInt J Syst Evol Microbiol10.1099/ijs.0.040188-02012Bacterial Typing Techniques, Base Composition, China, Comamonas/*classification/genetics/isolation & purification, DNA, Bacterial/genetics, Fatty Acids/analysis, Molecular Sequence Data, Nucleic Acid Hybridization, *Phylogeny, RNA, Ribosomal, 16S/genetics, Sequence Analysis, DNA, *Soil Microbiology, Trees/microbiology, Ubiquinone/analysisGenetics

Reference

@idauthorscataloguedoi/urltitle
7445Curators of the DSMZLeibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSM 18232)https://www.dsmz.de/collection/catalogue/details/culture/DSM-18232
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
33190Curators of the CIPhttps://brclims.pasteur.fr/brcWeb/souche/detail/1/5588
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)
67771Curators of the KCTChttps://kctc.kribb.re.kr/En/Kctc
68369Automatically annotated from API 20NE
68382Automatically annotated from API zym
72456Reimer, L.C., Lissin, A.,Schober, I., Witte,J.F., Podstawka, A., Lüken, H., Bunk, B.,Overmann, J.10.60712/SI-ID88304.1StrainInfo: A central database for resolving microbial strain identifiers
120475Curators of the CIPCollection of Institut Pasteur (CIP 108012)https://catalogue-crbip.pasteur.fr/fiche_catalogue.xhtml?crbip=CIP%20108012