Name: Chryseobacterium daeguense K105
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 5689

Type strain:

Species: Chryseobacterium daeguense

Strain Designation: K105

Culture col. no.: DSM 19388, JCM 14362, KCTC 12841, CIP 110016

Strain history: CIP <- 2009, KCTC <- J.H. Yoon, KRIBB

NCBI tax ID(s): 1121286 (strain), 412438 (species)

SI-ID 309442

DSM 19388, JCM 14362, KCTC 12841, CIP 110016

Special Collections

Section

When using BacDive for research please cite our paper

Chryseobacterium daeguense K105 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from wastewater of a textile dye works.

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	*Bacteroidota*
	Class	*Flavobacteriia*
	Order	*Flavobacteriales*
	Family	*Weeksellaceae*
	Genus	*Chryseobacterium*
	Species	**Chryseobacterium daeguense**
	Full Scientific Name (LPSN)	Chryseobacterium daeguense Yoon et al. 2007

Information on morphological and physiological properties Morphology

[Ref.: #32084]	Gram stain	negative
[Ref.: #67771]	Gram stain	negative
[Ref.: #118841]	Gram stain	negative
[Ref.: #125438]	Gram stain	negative Confidence in %96.455
[Ref.: #125439]	Gram stain	negative Confidence in %99.9

[Ref.: #32084]	Cell length	0.8-5 µm

[Ref.: #32084]	Cell width	0.4-0.6 µm

[Ref.: #32084]	Cell shape	rod-shaped
[Ref.: #118841]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #32084]	Motility	no
[Ref.: #118841]	Motility	no
[Ref.: #67771]	Motility	no

[Ref.: #32084]

Pigment production

yes

Information on culture and growth conditions Culture and growth conditions

[Ref.: #8085]

Culture medium

TRYPTONE SOYA BROTH (TSB) (DSMZ Medium 545)

[Ref.: #8085]

Culture medium growth

[Ref.: #8085]

Culture medium link

Medium recipe at MediaDive

[Ref.: #8085]

Culture medium composition

expand / minimize

[Ref.: #37900]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37900]

Culture medium growth

[Ref.: #37900]

Culture medium composition

expand / minimize

[Ref.: #118841]

Culture medium

CIP Medium 72

[Ref.: #118841]

Culture medium growth

[Ref.: #118841]

Culture medium link

Medium recipe provided by DSMZ

		Temperature
[Ref.: #8085]	growth	28 °C
[Ref.: #32084]	growth	10-41 °C
[Ref.: #32084]	optimum	30-37 °C
[Ref.: #37900]	growth	30 °C
[Ref.: #67770]	growth	30 °C
[Ref.: #67771]	growth	30-37 °C

	pH	Kind of pH		pH
[Ref.: #32084]			optimum	6.5-7.5
[Ref.: #32084]			growth	5-9.5

Information on physiology and metabolism Physiology and metabolism

[Ref.: #32084]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118841]	Oxygen tolerance	obligate aerobe
[Ref.: #125439]	Oxygen tolerance	obligate aerobe Confidence in %97.2

[Ref.: #32084]	Ability of spore formation	no
[Ref.: #125439]	Ability of spore formation	no Confidence in %96.7

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #32084]		NaCl		growth	0-2	%
[Ref.: #32084]		NaCl		optimum	0-1	%

[Ref.: #67770]	Observation	quinones: MK-6
[Ref.: #67771]	Observation	quinones: MK-6

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #32084]	arabinose ChEBI	+	carbon source
[Ref.: #32084]	cellobiose ChEBI	+	carbon source
[Ref.: #32084]	fructose ChEBI	+	carbon source
[Ref.: #32084]	glucose ChEBI	+	carbon source
[Ref.: #32084]	maltose ChEBI	+	carbon source
[Ref.: #118841]	nitrate ChEBI	-	reduction
[Ref.: #118841]	nitrite ChEBI	-	reduction
[Ref.: #32084]	rhamnose ChEBI	+	carbon source
[Ref.: #32084]	trehalose ChEBI	+	carbon source
[Ref.: #32084]	xylose ChEBI	+	carbon source

	Metabolite production	Metabolite	Production
[Ref.: #118841]		indole ChEBI	yes

	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.: #68382]	beta-galactosidase	-	3.2.1.23	* from API zym
[Ref.: #68382]	beta-glucosidase	-	3.2.1.21	* from API zym
[Ref.: #68382]	beta-glucuronidase	-	3.2.1.31	* from API zym
[Ref.: #32084]	catalase	+	1.11.1.6
[Ref.: #118841]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[Ref.: #32084]	cytochrome oxidase	+	1.9.3.1
[Ref.: #68382]	esterase (C 4)	-		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[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.: #118841]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #118841]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

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.: #118841]	12291	-	+	-	+	-	+	+	+	+	+	+	+	-	-	-	+	-	+	-	-

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

[Ref.: #8085]	Sample type/isolated from	wastewater of a textile dye works
[Ref.: #8085]	Geographic location (country and/or sea, region)	Daegu
[Ref.: #8085]	Country	Republic of Korea
[Ref.: #8085]	Country ISO 3 Code	KOR
[Ref.: #8085]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Wastewater of a textile dye works in Daegu
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

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

[Ref.: #118841]	Sample type/isolated from	Environment, Wastewater of a textile dye works
[Ref.: #118841]	Geographic location (country and/or sea, region)	Daegu
[Ref.: #118841]	Country	Republic of Korea
[Ref.: #118841]	Country ISO 3 Code	KOR
[Ref.: #118841]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Industrial	-
#Engineered	#Waste	#Wastewater

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence EF076759 (>99% sequence identity) for Chryseobacterium daeguense subclade from Microbeatlas

Aquatic Samples	61
Soil Samples	33
Animal Samples	122
Plant Samples	68
Total Samples	284

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

[Ref.: #8085]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118841]	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.: #8085]	Chryseobacterium daeguense strain K105 16S ribosomal RNA gene, partial sequence	EF076759	1472	GenBank ENA	412438 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Chryseobacterium daeguense DSM 19388	GCA_000430825	scaffold	GenBank ENA	1121286 tax ID
[Ref.: #66792]	Chryseobacterium daeguense DSM 19388	1121286.4	wgs	PATRIC	1121286 tax ID	*
[Ref.: #66792]	Chryseobacterium daeguense DSM 19388	2523533536	draft	JGI IMG/M	1121286 tax ID	*

[Ref.: #8085]	GC-content	36.8 mol%	high performance liquid chromatography (HPLC)
[Ref.: #32084]	GC-content	36.8 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 daeguense DSM 19388 PATRIC: 1121286.4
[Ref.: #125438]	gram-positive	gram-positiveⓘ	no	96.455	yes
[Ref.: #125438]	anaerobic	anaerobicⓘ	no	97.838	yes
[Ref.: #125438]	spore-forming	spore-formingⓘ	no	89.285	yes
[Ref.: #125438]	aerobic	aerobicⓘ	yes	87.059	no
[Ref.: #125438]	thermophile	thermophilicⓘ	no	98.643	yes
[Ref.: #125438]	motile2+	flagellatedⓘ	no	89	yes

	Model	Trait	Prediction	Confidence in %
	Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Chryseobacterium daeguense DSM 19388 NCBI: GCA_000430825
[Ref.: #125439]	BacteriaNet	oxygen_toleranceⓘ	obligate aerobe	97.2
[Ref.: #125439]	BacteriaNet	gram_stainⓘ	negative	99.9
[Ref.: #125439]	BacteriaNet	motilityⓘ	no	74.9
[Ref.: #125439]	BacteriaNet	spore_formationⓘ	no	96.7

Availability in culture collections External links

[Ref.: #8085]

Culture collection no.

DSM 19388, JCM 14362, KCTC 12841, CIP 110016

[Ref.: #75171]

SI-ID 309442

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Chryseobacterium daeguense sp. nov., isolated from wastewater of a textile dye works.	Yoon JH, Kang SJ, Oh TK	Int J Syst Evol Microbiol	10.1099/ijs.0.64936-0	2007	*

References

#8085

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 19388

#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 )

#32084

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 #28330 (see below)

#37900 ; Curators of the CIP;

#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) .

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;
#67771 Korean Collection for Type Cultures (KCTC) ; Curators of the KCTC;

#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 .

#75171

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-ID309442.1 )

#118841 Collection of Institut Pasteur ; Curators of the CIP; CIP 110016

#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 .

#28330

IJSEM 1355 2007 ( DOI 10.1099/ijs.0.64936-0 , PubMed 17551058 )

* These data were automatically processed and therefore are not curated

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Chryseobacterium daeguense DSM 19388

Chryseobacterium daeguense DSM 19388

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