Name: Sphingobacterium daejeonense TR6-04
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 137380

Type strain:

Species: Sphingobacterium daejeonense

Strain Designation: TR6-04

Culture col. no.: CIP 109390, CCUG 52468, KCTC 12579, LMG 23402

Strain history: CIP <- 2006, CCUG <- 2006, J. S. Lee, KCTC, Daejon, Korea strain: TR6-04

NCBI tax ID(s): 371142 (species)

SI-ID 289778

LMG 23402, CCUG 52468, KCTC 12579, CIP 109390

Section

Sphingobacterium daejeonense TR6-04 is an aerobe, mesophilic, rod-shaped bacterium of the family Sphingobacteriaceae.

rod-shaped
aerobe
mesophilic
16S sequence
Bacteria

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Bacteroidota*
	Class	*Sphingobacteriia*
	Order	*Sphingobacteriales*
	Family	*Sphingobacteriaceae*
	Genus	*Sphingobacterium*
	Species	**Sphingobacterium daejeonense**
	Full Scientific Name (LPSN)	Sphingobacterium daejeonense Kim et al. 2006

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #37570]	Gram stain	negative

[Ref.: #37570]	Cell shape	rod-shaped
[Ref.: #67771]	Cell shape	rod-shaped

[Ref.: #37570]	Motility	no
[Ref.: #67771]	Motility	no

Information on culture and growth conditions Culture and growth conditions

[Ref.: #37570]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #37570]

Culture medium growth

[Ref.: #37570]

Culture medium composition

expand / minimize

[Ref.: #37570]

Culture medium

CIP Medium 72

[Ref.: #37570]

Culture medium growth

[Ref.: #37570]

Culture medium link

Medium recipe provided by DSMZ

[Ref.: #37570]

Culture medium

CIP Medium 566

[Ref.: #37570]

Culture medium growth

[Ref.: #37570]

Culture medium link

Medium recipe provided by DSMZ

	Temperatures	Kind of temperature		Temperature
[Ref.: #37570]			growth	30 °C
[Ref.: #67771]			growth	30 °C

[Ref.: #37570]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #37570]	Oxygen tolerance	obligate aerobe

[Ref.: #67771]

Ability of spore formation

[Ref.: #67771]

Observation

quinones: MK-7

	Metabolite utilization	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #37570]		nitrate ChEBI	-	reduction
[Ref.: #37570]		nitrite ChEBI	+	reduction

	Metabolite production	Metabolite	Production
[Ref.: #37570]		indole ChEBI	no

	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.: #37570]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	+	3.4.11.3	* from API zym
[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.: #37570]	oxidase	+
[Ref.: #68382]	trypsin	+	3.4.21.4	* from API zym
[Ref.: #37570]	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.: #37570]	11833	-	+	+	+	-	+	+	+	+	-	+	+	-	-	-	+	+	+	+	-

	Pathway	Enzyme coverage	Annotated reactions
	Pathway annotation	Computationally determined by
[Ref.: #66794]	cardiolipin biosynthesis	100	7 of 7
[Ref.: #66794]	acetate fermentation	100	4 of 4
[Ref.: #66794]	UDP-GlcNAc biosynthesis	100	3 of 3
[Ref.: #66794]	CDP-diacylglycerol biosynthesis	100	2 of 2
[Ref.: #66794]	valine metabolism	100	9 of 9
[Ref.: #66794]	denitrification	100	2 of 2
[Ref.: #66794]	teichoic acid biosynthesis	100	1 of 1
[Ref.: #66794]	vitamin B1 metabolism	100	13 of 13
[Ref.: #66794]	sulfopterin metabolism	100	4 of 4
[Ref.: #66794]	coenzyme A metabolism	100	4 of 4
[Ref.: #66794]	adipate degradation	100	2 of 2
[Ref.: #66794]	formaldehyde oxidation	100	3 of 3
[Ref.: #66794]	cis-vaccenate biosynthesis	100	2 of 2
[Ref.: #66794]	gluconeogenesis	100	8 of 8
[Ref.: #66794]	anapleurotic synthesis of oxalacetate	100	1 of 1
[Ref.: #66794]	tetrahydrofolate metabolism	100	14 of 14
[Ref.: #66794]	folate polyglutamylation	100	1 of 1
[Ref.: #66794]	palmitate biosynthesis	100	22 of 22
[Ref.: #66794]	ceramide biosynthesis	100	1 of 1
[Ref.: #66794]	suberin monomers biosynthesis	100	2 of 2
[Ref.: #66794]	biotin biosynthesis	100	4 of 4
[Ref.: #66794]	ppGpp biosynthesis	100	4 of 4
[Ref.: #66794]	1,4-dihydroxy-6-naphthoate biosynthesis	100	6 of 6
[Ref.: #66794]	methylglyoxal degradation	100	5 of 5
[Ref.: #66794]	NAD metabolism	94.44	17 of 18
[Ref.: #66794]	heme metabolism	92.86	13 of 14
[Ref.: #66794]	Entner Doudoroff pathway	90	9 of 10
[Ref.: #66794]	aspartate and asparagine metabolism	88.89	8 of 9
[Ref.: #66794]	lipid A biosynthesis	88.89	8 of 9
[Ref.: #66794]	chorismate metabolism	88.89	8 of 9
[Ref.: #66794]	isoleucine metabolism	87.5	7 of 8
[Ref.: #66794]	C4 and CAM-carbon fixation	87.5	7 of 8
[Ref.: #66794]	peptidoglycan biosynthesis	86.67	13 of 15
[Ref.: #66794]	ubiquinone biosynthesis	85.71	6 of 7
[Ref.: #66794]	photosynthesis	85.71	12 of 14
[Ref.: #66794]	reductive acetyl coenzyme A pathway	85.71	6 of 7
[Ref.: #66794]	leucine metabolism	84.62	11 of 13
[Ref.: #66794]	metabolism of amino sugars and derivatives	80	4 of 5
[Ref.: #66794]	starch degradation	80	8 of 10
[Ref.: #66794]	threonine metabolism	80	8 of 10
[Ref.: #66794]	cellulose degradation	80	4 of 5
[Ref.: #66794]	glycogen metabolism	80	4 of 5
[Ref.: #66794]	d-mannose degradation	77.78	7 of 9
[Ref.: #66794]	CO2 fixation in Crenarchaeota	77.78	7 of 9
[Ref.: #66794]	glycogen biosynthesis	75	3 of 4
[Ref.: #66794]	lactate fermentation	75	3 of 4
[Ref.: #66794]	degradation of pentoses	75	21 of 28
[Ref.: #66794]	dTDPLrhamnose biosynthesis	75	6 of 8
[Ref.: #66794]	CMP-KDO biosynthesis	75	3 of 4
[Ref.: #66794]	flavin biosynthesis	73.33	11 of 15
[Ref.: #66794]	purine metabolism	72.34	68 of 94
[Ref.: #66794]	cysteine metabolism	72.22	13 of 18
[Ref.: #66794]	citric acid cycle	71.43	10 of 14
[Ref.: #66794]	tyrosine metabolism	71.43	10 of 14
[Ref.: #66794]	propanol degradation	71.43	5 of 7
[Ref.: #66794]	glutamate and glutamine metabolism	71.43	20 of 28
[Ref.: #66794]	propionate fermentation	70	7 of 10
[Ref.: #66794]	methionine metabolism	69.23	18 of 26
[Ref.: #66794]	phenylalanine metabolism	69.23	9 of 13
[Ref.: #66794]	degradation of aromatic, nitrogen containing compounds	66.67	8 of 12
[Ref.: #66794]	pyrimidine metabolism	66.67	30 of 45
[Ref.: #66794]	cyanate degradation	66.67	2 of 3
[Ref.: #66794]	acetoin degradation	66.67	2 of 3
[Ref.: #66794]	degradation of hexoses	66.67	12 of 18
[Ref.: #66794]	molybdenum cofactor biosynthesis	66.67	6 of 9
[Ref.: #66794]	serine metabolism	66.67	6 of 9
[Ref.: #66794]	L-lactaldehyde degradation	66.67	2 of 3
[Ref.: #66794]	histidine metabolism	65.52	19 of 29
[Ref.: #66794]	isoprenoid biosynthesis	65.38	17 of 26
[Ref.: #66794]	glycolysis	64.71	11 of 17
[Ref.: #66794]	lipid metabolism	64.52	20 of 31
[Ref.: #66794]	degradation of sugar acids	64	16 of 25
[Ref.: #66794]	pentose phosphate pathway	63.64	7 of 11
[Ref.: #66794]	vitamin B6 metabolism	63.64	7 of 11
[Ref.: #66794]	proline metabolism	63.64	7 of 11
[Ref.: #66794]	metabolism of disaccharids	63.64	7 of 11
[Ref.: #66794]	d-xylose degradation	63.64	7 of 11
[Ref.: #66794]	tryptophan metabolism	63.16	24 of 38
[Ref.: #66794]	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	62.5	5 of 8
[Ref.: #66794]	ketogluconate metabolism	62.5	5 of 8
[Ref.: #66794]	alanine metabolism	62.07	18 of 29
[Ref.: #66794]	arachidonate biosynthesis	60	3 of 5
[Ref.: #66794]	vitamin K metabolism	60	3 of 5
[Ref.: #66794]	glycine betaine biosynthesis	60	3 of 5
[Ref.: #66794]	non-pathway related	57.89	22 of 38
[Ref.: #66794]	lysine metabolism	57.14	24 of 42
[Ref.: #66794]	degradation of sugar alcohols	56.25	9 of 16
[Ref.: #66794]	4-hydroxymandelate degradation	55.56	5 of 9
[Ref.: #66794]	arginine metabolism	54.17	13 of 24
[Ref.: #66794]	sulfate reduction	53.85	7 of 13
[Ref.: #66794]	phosphatidylethanolamine bioynthesis	53.85	7 of 13
[Ref.: #66794]	kanosamine biosynthesis II	50	1 of 2
[Ref.: #66794]	glutathione metabolism	50	7 of 14
[Ref.: #66794]	ethanol fermentation	50	1 of 2
[Ref.: #66794]	toluene degradation	50	2 of 4
[Ref.: #66794]	butanoate fermentation	50	2 of 4
[Ref.: #66794]	glycolate and glyoxylate degradation	50	3 of 6
[Ref.: #66794]	oxidative phosphorylation	46.15	42 of 91
[Ref.: #66794]	urea cycle	46.15	6 of 13
[Ref.: #66794]	O-antigen biosynthesis	40	2 of 5
[Ref.: #66794]	coenzyme M biosynthesis	40	4 of 10
[Ref.: #66794]	3-chlorocatechol degradation	40	2 of 5
[Ref.: #66794]	lipoate biosynthesis	40	2 of 5
[Ref.: #66794]	myo-inositol biosynthesis	40	4 of 10
[Ref.: #66794]	glycine metabolism	40	4 of 10
[Ref.: #66794]	arachidonic acid metabolism	38.89	7 of 18
[Ref.: #66794]	ascorbate metabolism	36.36	8 of 22
[Ref.: #66794]	phenol degradation	35	7 of 20
[Ref.: #66794]	(5R)-carbapenem carboxylate biosynthesis	33.33	1 of 3
[Ref.: #66794]	IAA biosynthesis	33.33	1 of 3
[Ref.: #66794]	enterobactin biosynthesis	33.33	1 of 3
[Ref.: #66794]	selenocysteine biosynthesis	33.33	2 of 6
[Ref.: #66794]	pantothenate biosynthesis	33.33	2 of 6
[Ref.: #66794]	acetyl CoA biosynthesis	33.33	1 of 3
[Ref.: #66794]	octane oxidation	33.33	1 of 3
[Ref.: #66794]	3-phenylpropionate degradation	33.33	5 of 15
[Ref.: #66794]	carotenoid biosynthesis	31.82	7 of 22
[Ref.: #66794]	4-hydroxyphenylacetate degradation	30	3 of 10
[Ref.: #66794]	dolichyl-diphosphooligosaccharide biosynthesis	27.27	3 of 11
[Ref.: #66794]	cyclohexanol degradation	25	1 of 4
[Ref.: #66794]	androgen and estrogen metabolism	25	4 of 16
[Ref.: #66794]	phenylpropanoid biosynthesis	23.08	3 of 13
[Ref.: #66794]	polyamine pathway	21.74	5 of 23
		Only first 10 entries are displayed. Click here to see all.

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

[Ref.: #59559]	Sample type/isolated from	Compost (Deposited as Soil,ginseng field)
[Ref.: #59559]	Geographic location (country and/or sea, region)	Pocheon
[Ref.: #59559]	Country	Republic of Korea
[Ref.: #59559]	Country ISO 3 Code	KOR
[Ref.: #59559]	Continent	Asia

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

[Ref.: #37570]	Sample type/isolated from	Environment, Soil, ginseng field
[Ref.: #37570]	Geographic location (country and/or sea, region)	Pocheon
[Ref.: #37570]	Country	Republic of Korea
[Ref.: #37570]	Country ISO 3 Code	KOR
[Ref.: #37570]	Continent	Asia

[Ref.: #37570]	Geographic location (country and/or sea, region)	Pocheon
[Ref.: #37570]	Country	Republic of Korea
[Ref.: #37570]	Country ISO 3 Code	KOR
[Ref.: #37570]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Biodegradation	#Composting
#Engineered	#Agriculture	#Field
#Host	#Plants	#Herbaceous plants (Grass,Crops)
#Environmental	#Terrestrial	#Soil

What are isolation sources categories?

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

[Ref.: #37570]

Biosafety level

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.: #67771]	Sphingobacterium daejeonense gene for 16S rRNA, partial sequence	AB249372	1472	ENA	371142 tax ID

[Ref.: #67771]

GC-content

38.7 mol%

Availability in culture collections External links

[Ref.: #37570]

Culture collection no.

CIP 109390, CCUG 52468, KCTC 12579, LMG 23402

[Ref.: #94293]

SI-ID 289778

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of Sphingobacterium daejeonense and Sphingobacterium mizutaii.	Choi HA, Lee SS	Int J Syst Evol Microbiol	10.1099/ijs.0.024737-0	2011	*
Phylogeny	Sphingobacterium anhuiense sp. nov., isolated from forest soil.	Wei W, Zhou Y, Wang X, Huang X, Lai R	Int J Syst Evol Microbiol	10.1099/ijs.0.65864-0	2008	*
Phylogeny	Sphingobacterium composti sp. nov., isolated from cotton-waste composts.	Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt E	Int J Syst Evol Microbiol	10.1099/ijs.0.64948-0	2007	*
Phylogeny	Sphingobacterium daejeonense sp. nov., isolated from a compost sample.	Kim KH, Ten LN, Liu QM, Im WT, Lee ST	Int J Syst Evol Microbiol	10.1099/ijs.0.64406-0	2006	*

References

#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 )

#37570 Collection of Institut Pasteur ; Curators of the CIP; CIP 109390
#59559 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52468

#66794

Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )

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

#68382

Automatically annotated from API zym .

#94293

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-ID289778.1 )

* These data were automatically processed and therefore are not curated

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