Caenimonas koreensis EMB320 | Type strain | DSM 17982, KCTC 12616 | BacDiveID:3027

Strain identifier

BacDive ID: 3027

Type strain:

Species: Caenimonas koreensis

Strain Designation: EMB320

Culture col. no.: DSM 17982, KCTC 12616

Strain history: <- CO Jeon, Gyungsang Univ.

NCBI tax ID(s): 1121255 (strain), 367474 (species)

SI-ID 397253

DSM 17982

Special Collections

Section

Caenimonas koreensis EMB320 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from activated sludge.

Gram-negative
rod-shaped
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

Information on the name and the taxonomic classification. Name and taxonomic classification

	Last LPSN update	09-12-2024 (DD-MM-YYYY)
	Domain	*Bacteria*
	Phylum	*Pseudomonadota*
	Class	*Betaproteobacteria*
	Order	*Burkholderiales*
	Family	*Comamonadaceae*
	Genus	*Caenimonas*
	Species	**Caenimonas koreensis**
	Full Scientific Name (LPSN)	Caenimonas koreensis Ryu et al. 2008

Information on morphological and physiological properties Morphology

[Ref.: #32387]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %97.244

[Ref.: #32387]	Cell length	1.4 µm

[Ref.: #32387]	Cell width	0.5 µm

[Ref.: #32387]	Cell shape	rod-shaped

[Ref.: #32387]	Motility	no

Multimedia content

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Caption:

electron microscopic image

Intellectual property rights:

© HZI/Manfred Rohde

Information on culture and growth conditions Culture and growth conditions

Culture medium

REACTIVATION WITH LIQUID MEDIUM 830 (DSMZ Medium 830c)

Culture medium growth

Culture medium link

Medium recipe at MediaDive

Culture medium composition

expand / minimize

	Temperatures	Kind of temperature		Temperature
[Ref.: #7314]			growth	28 °C
[Ref.: #32387]			optimum	30 °C
[Ref.: #67771]			growth	28 °C

	pH	Kind of pH		pH
[Ref.: #32387]			optimum	7.5
[Ref.: #32387]			growth	07-08

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32387]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe

Observation

quinones: Q-8

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32387]		fructose ChEBI	+	carbon source
[Ref.: #32387]		glucose ChEBI	+	carbon source
[Ref.: #32387]		malonate ChEBI	+	carbon source
[Ref.: #32387]		nitrate ChEBI	+	reduction

	Enzymes	Enzyme	Enzyme activity	EC number
[Ref.: #32387]		alkaline phosphatase	+	3.1.3.1
[Ref.: #32387]		catalase	+	1.11.1.6
[Ref.: #32387]		cytochrome oxidase	+	1.9.3.1
[Ref.: #32387]		gelatinase	+
[Ref.: #32387]		urease	+	3.5.1.5

Information on isolation source, the sampling and environmental conditions Isolation, sampling and environmental information

[Ref.: #7314]	Sample type/isolated from	activated sludge
[Ref.: #7314]	Geographic location (country and/or sea, region)	Pohang
[Ref.: #7314]	Country	Republic of Korea
[Ref.: #7314]	Country ISO 3 Code	KOR
[Ref.: #7314]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From activated sludge
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered

#Waste

#Activated sludge

What are isolation sources categories?

Global distribution of 16S sequence DQ349098 (>99% sequence identity) for Variovorax from Microbeatlas

Aquatic Samples	33
Soil Samples	45
Animal Samples	8
Plant Samples	1
Total Samples	87

Information on possible application of the strain and its possible interaction with e.g. potential hosts Safety information

Biosafety level

1

Risk group (German classification)
According to TRBA 466

Information on genomic background e.g. entries in nucleic sequence databass Sequence information

16S Sequence information:

	Sequence accession description	Seq. accession number	Sequence length (bp)	Sequence database	Associated NCBI tax ID
[Ref.: #7314]	Caenimonas koreensis strain EMB320 16S ribosomal RNA gene, partial sequence	DQ349098	1457	GenBank ENA	1121255 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Caenimonas koreensis DSM 17982 EMB320	GCA_009646335	contig	GenBank ENA	1121255 tax ID	*
[Ref.: #66792]	Caenimonas koreensis DSM 17982 strain EMB320	1121255.3	wgs	PATRIC	1121255 tax ID	*
[Ref.: #66792]	Caenimonas koreensis DSM 17982	2574179763	draft	JGI IMG/M	1121255 tax ID	*

GC-content

62.7 mol%

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Caenimonas koreensis DSM 17982 strain EMB320 PATRIC: 1121255.3
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	97.244	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	97.169	yes
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	85.202	no
[Ref.: #69480]	aerobic	aerobicⓘ	yes	87.385	yes
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.217	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	58.999	no

Availability in culture collections External links

Culture collection no.

DSM 17982, KCTC 12616

SI-ID 397253

*

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*
Phylogeny	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	*

References

#7314

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 17982

#20215

Parte, 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 DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )

#32387

Barberan A, Caceres Velazquez H, Jones S, Fierer N.: Hiding in Plain Sight: Mining Bacterial Species Records for Phenotypic Trait Information. mSphere 2: 2017 ( DOI 10.1128/mSphere.00237-17 , PubMed 28776041 ) - originally annotated from #28612 (see below)

#66792

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#66793

Mukherjee et al.: GEBA: 1,003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life. 35: 676 - 683 2017 ( DOI 10.1038/nbt.3886 , PubMed 28604660 )

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the 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.: MicrobeAtlas 1.0 beta .

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

#72547

Reimer, 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 identifiers . ( DOI 10.60712/SI-ID397253.1 )

#28612

IJSEM 1064 2008 ( DOI 10.1099/ijs.0.65416-0 , PubMed 18450689 )

* These data were automatically processed and therefore are not curated

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