Name: Chryseobacterium daecheongense CPW406
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5677

Type strain:

Species: Chryseobacterium daecheongense

Strain Designation: CPW406

Culture col. no.: DSM 15235, CCUG 52896, KCTC 12088, NBRC 102008, CIP 110173

Strain history: CIP <- 2010, DSMZ <- K.K. Kim, KAIST: strain CPW406 <- H.S. Bae

NCBI tax ID(s): 192389 (species)

SI-ID 107090

KCTC 12088, DSM 15235, KACC 11395, CCUG 52896, BCRC 17457, CCRC 17457, NBRC 102008, CIP 110173

Special Collections

Section

When using BacDive for research please cite our paper

Chryseobacterium daecheongense CPW406 is an aerobe, mesophilic, rod-shaped bacterium that was isolated from sediment in sewage.

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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Weeksellaceae*
	Genus	*Chryseobacterium*
	Species	**Chryseobacterium daecheongense**
	Full Scientific Name (LPSN)	Chryseobacterium daecheongense Kim et al. 2005

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #118840]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %98.5
[Ref.: #125439]	Gram stain	negative Confidence in %99.5

[Ref.: #118840]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #118840]	Motility	no
[Ref.: #67771]	Motility	no
[Ref.: #125438]	Motility	no Confidence in %91

[Ref.: #59714]

Incubation period

2 days

Information on culture and growth conditions Culture and growth conditions

[Ref.: #5774]

Culture medium

NUTRIENT AGAR (DSMZ Medium 1)

[Ref.: #5774]

Culture medium growth

[Ref.: #5774]

Culture medium link

Medium recipe at MediaDive

[Ref.: #5774]

Culture medium composition

expand / minimize

[Ref.: #37591]

Culture medium

MEDIUM 328- for nutrient agar

[Ref.: #37591]

Culture medium growth

[Ref.: #37591]

Culture medium composition

expand / minimize

[Ref.: #118840]

Culture medium

CIP Medium 328

[Ref.: #118840]

Culture medium growth

[Ref.: #118840]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #5774]	growth	30 °C
[Ref.: #37591]	growth	30 °C
[Ref.: #59714]	growth	30-37 °C
[Ref.: #67771]	growth	30 °C

Information on physiology and metabolism Physiology and metabolism

[Ref.: #59714]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118840]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %92.6

[Ref.: #67771]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %94.8

[Ref.: #67771]

Observation

quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #68369]	adipate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	arginine ChEBI	-	hydrolysis	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-glucose ChEBI	-	fermentation	* from API 20NE
[Ref.: #68369]	D-mannitol ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	D-mannose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	decanoate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	esculin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gelatin ChEBI	+	hydrolysis	* from API 20NE
[Ref.: #68369]	gluconate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	L-arabinose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	malate ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	maltose ChEBI	-	assimilation	* from API 20NE
[Ref.: #68369]	N-acetylglucosamine ChEBI	-	assimilation	* from API 20NE
[Ref.: #118840]	nitrate ChEBI	+	reduction
[Ref.: #68369]	nitrate ChEBI	+	reduction	* from API 20NE
[Ref.: #118840]	nitrite ChEBI	+	reduction
[Ref.: #68369]	tryptophan ChEBI	-	energy source	* from API 20NE
[Ref.: #68369]	urea ChEBI	-	hydrolysis	* from API 20NE
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #118840]		indole ChEBI	no
[Ref.: #68369]		indole ChEBI	no	* from API 20NE

	Physiological tests	Metabolite	Indole test
[Ref.: #68369]		indole ChEBI	-	* from API 20NE

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #68382]	alkaline phosphatase	+	3.1.3.1	* from API zym
[Ref.: #68382]	alpha-chymotrypsin	-	3.4.21.1	* from API zym
[Ref.: #68382]	alpha-fucosidase	-	3.2.1.51	* from API zym
[Ref.: #68382]	alpha-galactosidase	-	3.2.1.22	* from API zym
[Ref.: #68382]	alpha-glucosidase	+	3.2.1.20	* from API zym
[Ref.: #68382]	alpha-mannosidase	-	3.2.1.24	* from API zym
[Ref.: #68369]	arginine dihydrolase	-	3.5.3.6	* from API 20NE
[Ref.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68369]	beta-glucosidase	+	3.2.1.21	* from API 20NE
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #118840]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #68369]	cytochrome oxidase	+	1.9.3.1	* from API 20NE
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #68369]	gelatinase	+		* from API 20NE
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	+	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118840]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118840]	urease	-	3.5.1.5
[Ref.: #68369]	urease	-	3.5.1.5	* from API 20NE
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® 20NE:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Reduction of nitratesNO3	Indole productionTRP	Fermentation of D-glucoseGLU_ Ferm	Arginine dihydrolaseADH (Arg)	Urease/urea hydrolysisURE	Esculin hydrolysis/beta-GlucosidaseESC	Gelatinase/gelatin hydrolysisGEL	beta-GalactosidasePNPG	Assimilation of D-glucoseGLU_ Assim	Assimilation of L-arabinoseARA	Assimilation of D-mannoseMNE	Assimilation of D-mannitolMAN	Assimilation of N-acetyl-glucosamineNAG	Assimilation of maltoseMAL	Assimilation of gluconateGNT	Assimilation of capric acidCAP	Assimilation adipic acidADI	Assimilation of malic acidMLT	Assimilation of citric acidCIT	Assimilation of phenyl-acetic acidPAC	Cytochrome oxidaseOX
[Ref.: #59714]	8361	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	+

API® zym:

Note that the displayed test results represent raw data and therefore may deviate!

	API ID	Control	2-naphthyl phosphateAlkaline phosphatase	2-naphthyl butyrateEsterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	2-naphthyl myristateLipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	N-benzoyl-DL-arginine-2-naphthylamideTrypsin	N-glutaryl-phenylalanine-2-naphthylamidealpha- Chymotrypsin	2-naphthyl phosphateAcid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	6-Br-2-naphthyl-alphaD-galactpyranosidealpha- Galactosidase	2-naphthyl-betaD-galactpyranosidebeta- Galactosidase	Naphthol-AS-BI-betaD-glucuronidebeta- Glucuronidase	2-naphthyl-alphaD-glucopyranosidealpha- Glucosidase	6-Br-2-naphthyl-betaD-glucopyranosidebeta- Glucosidase	1-naphthyl-N-acetyl-betaD-glucosaminideN-acetyl-beta- glucosaminidase	6-Br-2-naphthyl-alphaD-mannopyranosidealpha- Mannosidase	2-naphthyl-alphaL-fucopyranosidealpha- Fucosidase
[Ref.: #59714]	4302	-	+	-	+	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-
[Ref.: #118840]	12411	-	+	-	+	-	+	+	-	+	-	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #5774]	Sample type/isolated from	sediment in sewage
[Ref.: #5774]	Geographic location (country and/or sea, region)	Korea, Cheongju Industrial Complex
[Ref.: #5774]	Country	Republic of Korea
[Ref.: #5774]	Country ISO 3 Code	KOR
[Ref.: #5774]	Continent	Asia

[Ref.: #67771]	Sample type/isolated from	From sediment
[Ref.: #67771]	Country	Republic of Korea
[Ref.: #67771]	Country ISO 3 Code	KOR
[Ref.: #67771]	Continent	Asia

[Ref.: #118840]	Sample type/isolated from	Environment, Sediment in sewage
[Ref.: #118840]	Geographic location (country and/or sea, region)	Cheongju Industrial Complex
[Ref.: #118840]	Country	Republic of Korea
[Ref.: #118840]	Country ISO 3 Code	KOR
[Ref.: #118840]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Environmental	#Aquatic	-
#Environmental	#Aquatic	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AJ457206 (>99% sequence identity) for Chryseobacterium daecheongense from Microbeatlas

Aquatic Samples	26
Soil Samples	64
Animal Samples	107
Plant Samples	27
Total Samples	224

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

[Ref.: #5774]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118840]	Biosafety level	1	Risk group (French classification)

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.: #5774]	Chryseobacterium sp. CPW406 16S rRNA gene	AJ457206	1446	GenBank ENA	192389 tax ID
[Ref.: #124043]	Chryseobacterium daecheongense gene for 16S rRNA, partial sequence, strain: NBRC 102008.	AB681658	1442	GenBank ENA	192389 tax ID	*

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Chryseobacterium daecheongense DSM 15235	GCA_003729955	contig	GenBank ENA	192389 tax ID	*
[Ref.: #66792]	Chryseobacterium daecheongense DSM 15235	GCA_004365465	contig	GenBank ENA	192389 tax ID	*
[Ref.: #66792]	Chryseobacterium daecheongense strain DSM 15235	192389.5	wgs	PATRIC	192389 tax ID	*
[Ref.: #66792]	Chryseobacterium daecheongense DSM 15235	2681812956	draft	JGI IMG/M	192389 tax ID	*

[Ref.: #5774]	GC-content	38.3 mol%
[Ref.: #67771]	GC-content	36.6 mol%

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

	Model	Trait	Prediction	Confidence in %	In training data
	Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Chryseobacterium daecheongense strain DSM 15235 PATRIC: 192389.5
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	98.5	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	96.9	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	87.425	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	84.991	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	97.974	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	91	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chryseobacterium daecheongense DSM 15235 NCBI: GCA_003729955
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	94.8
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	78.8
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.5
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	92.6

Availability in culture collections External links

[Ref.: #5774]

Culture collection no.

DSM 15235, CCUG 52896, KCTC 12088, NBRC 102008, CIP 110173

[Ref.: #75159]

SI-ID 107090

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseobacterium daecheongense sp. nov., isolated from freshwater lake sediment.	Kim KK, Bae HS, Schumann P, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.02931-0	2005	*

References

#5774

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 15235

#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 )

#37591 ; Curators of the CIP;
#59714 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52896

#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) .

#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#68369

Automatically annotated from API 20NE .

#68382

Automatically annotated from API zym .

#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 .

#75159

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-ID107090.1 )

#118840 Collection of Institut Pasteur ; Curators of the CIP; CIP 110173

#124043

Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .

#125438

Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )

#125439

Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .

* These data were automatically processed and therefore are not curated

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Chryseobacterium daecheongense strain DSM 15235

Chryseobacterium daecheongense DSM 15235

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