Name: Sphingobium chungbukense DJ77
Creator: BacDive
License: http://creativecommons.org/licenses/by-nc/4.0/

Strain identifier

BacDive ID: 14183

Type strain:

Species: Sphingobium chungbukense

Strain Designation: DJ77

Culture col. no.: DSM 16638, CIP 107741, IMSNU 11152, KCTC 2955, CCUG 52897, JCM 11454

Strain history: CIP <- 2002, JCM, Sphingomonas chungbukensis <- 2001, KCTC <- S.J. Jim: strain DJ77

NCBI tax ID(s): 56193 (species)

SI-ID 100958

KCTC 2955, CIP 107741, DSM 16638

Section

Sphingobium chungbukense DJ77 is an aerobe, mesophilic, Gram-negative bacterium that was isolated from contaminated sediment.

Gram-negative
aerobe
mesophilic
16S sequence
Bacteria
genome sequence

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

	Last LPSN update	14-12-2023 (DD-MM-YYYY)
	Domain	"Bacteria"
	Phylum	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium chungbukense**
	Full Scientific Name (LPSN)	Sphingobium chungbukense (Kim et al. 2000) Pal et al. 2005

Synonym

Sphingomonas chungbukensis

Information on morphological and physiological properties Morphology

[Ref.: #67771]	Gram stain	negative
[Ref.: #118266]	Gram stain	negative

[Ref.: #118266]	Cell shape	rod-shaped

[Ref.: #118266]	Motility	no

[Ref.: #118266]	Pigment production	no
[Ref.: #118266]	Pigment name	Pyocyanin

Information on culture and growth conditions Culture and growth conditions

[Ref.: #6541]

Culture medium

MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)

[Ref.: #6541]

Culture medium growth

[Ref.: #6541]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6541]

Culture medium composition

expand / minimize

[Ref.: #6541]

Culture medium

CASO AGAR (MERCK 105458) (DSMZ Medium 220)

[Ref.: #6541]

Culture medium growth

[Ref.: #6541]

Culture medium link

Medium recipe at MediaDive

[Ref.: #6541]

Culture medium composition

expand / minimize

[Ref.: #34204]

Culture medium

MEDIUM 72- for trypto casein soja agar

[Ref.: #34204]

Culture medium growth

[Ref.: #34204]

Culture medium composition

expand / minimize

[Ref.: #118266]

Culture medium

CIP Medium 72

[Ref.: #118266]

Culture medium growth

[Ref.: #118266]

Culture medium link

Medium recipe provided by DSMZ

	Kind of temperature		Temperature
[Ref.: #6541]		growth	28 °C
[Ref.: #34204]		growth	30 °C
[Ref.: #59715]		growth	30 °C
[Ref.: #67770]		growth	30 °C
[Ref.: #67771]		growth	28 °C
[Ref.: #118266]		growth	25-41 °C
[Ref.: #118266]	no	growth	5 °C
[Ref.: #118266]	no	growth	10 °C

[Ref.: #6541]	Temperature range	mesophilic
[Ref.: #34204]	Temperature range	mesophilic
[Ref.: #59715]	Temperature range	mesophilic
[Ref.: #67770]	Temperature range	mesophilic
[Ref.: #67771]	Temperature range	mesophilic
[Ref.: #118266]	Temperature range	psychrophilic

Information on physiology and metabolism Physiology and metabolism

[Ref.: #59715]	Oxygen tolerance	aerobe
[Ref.: #67771]	Oxygen tolerance	aerobe
[Ref.: #118266]	Oxygen tolerance	obligate aerobe

	Salt	Tested relation		Salt conc.
[Ref.: #118266]	NaCl		growth	0	%
[Ref.: #118266]	NaCl	no	growth	2	%
[Ref.: #118266]	NaCl	no	growth	4	%
[Ref.: #118266]	NaCl	no	growth	6	%
[Ref.: #118266]	NaCl	no	growth	8	%
[Ref.: #118266]	NaCl	no	growth	10	%

[Ref.: #67770]	Observation	quinones: Q-10
[Ref.: #67771]	Observation	quinones: Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #118266]	citrate ChEBI	-	carbon source
[Ref.: #118266]	esculin ChEBI	-	hydrolysis
[Ref.: #118266]	nitrate ChEBI	-	reduction
[Ref.: #118266]	nitrate ChEBI	-	respiration
[Ref.: #118266]	nitrite ChEBI	-	reduction

	Metabolite production	Metabolite	Production
[Ref.: #118266]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #68382]	acid phosphatase	+	3.1.3.2	* from API zym
[Ref.: #118266]	alcohol dehydrogenase	-	1.1.1.1
[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.: #118266]	amylase	-
[Ref.: #118266]	beta-galactosidase	-	3.2.1.23
[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.: #118266]	caseinase	-	3.4.21.50
[Ref.: #118266]	catalase	+	1.11.1.6
[Ref.: #68382]	cystine arylamidase	-	3.4.11.3	* from API zym
[Ref.: #118266]	DNase	+
[Ref.: #68382]	esterase (C 4)	+		* from API zym
[Ref.: #68382]	esterase lipase (C 8)	+		* from API zym
[Ref.: #118266]	gelatinase	-
[Ref.: #118266]	lecithinase	-
[Ref.: #68382]	leucine arylamidase	+	3.4.11.1	* from API zym
[Ref.: #118266]	lipase	-
[Ref.: #68382]	lipase (C 14)	-		* from API zym
[Ref.: #118266]	lysine decarboxylase	-	4.1.1.18
[Ref.: #68382]	N-acetyl-beta-glucosaminidase	-	3.2.1.52	* from API zym
[Ref.: #68382]	naphthol-AS-BI-phosphohydrolase	+		* from API zym
[Ref.: #118266]	ornithine decarboxylase	-	4.1.1.17
[Ref.: #118266]	oxidase	+
[Ref.: #118266]	protease	-
[Ref.: #68382]	trypsin	-	3.4.21.4	* from API zym
[Ref.: #118266]	tryptophan deaminase	-
[Ref.: #118266]	tween esterase	-
[Ref.: #118266]	urease	-	3.5.1.5
[Ref.: #68382]	valine arylamidase	+		* from API zym
	Only first 10 entries are displayed. Click here to see all.

API® Biotype100:

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

	API ID	ControlQ	D-glucose as carbon sourceGLU	D-fructose as carbon sourceFRU	D-galactose as carbon sourceGAL	D-trehalose as carbon sourceTRE	D-mannose as carbon sourceMNE	L-sorbose as carbon sourceSBE	D-melibiose as carbon sourceMEL	sucrose as carbon sourceSAC	D-raffinose as carbon sourceRAF	maltotriose as carbon sourceMTE	maltose as carbon sourceMAL	lactose as carbon sourceLAC	lactulose as carbon sourceLTE	1-O-methyl-beta-galactopyranoside as carbon sourceMbGa	1-O-methyl-alpha-galactopyranoside as carbon sourceMaGa	D-cellobiose as carbon sourceCEL	gentiobiose as carbon sourceGEN	1-O-methyl-beta-D-glucopyranoside as carbon sourceMbGu	esculin as carbon sourceESC	D-ribose as carbon sourceRIB	L-arabinose as carbon sourceARA	D-xylose as carbon sourceXYL	palatinose as carbon sourcePLE	L-rhamnose as carbon sourceRHA	L-fucose as carbon sourceFUC	D-melezitose as carbon sourceMLZ	D-arabitol as carbon sourceDARL	L-arabitol as carbon sourceLARL	xylitol as carbon sourceXLT	dulcitol as carbon sourceDUL	D-tagatose as carbon sourceTAG	glycerol as carbon sourceGLY	myo-inositol as carbon sourceINO	D-mannitol as carbon sourceMAN	maltitol as carbon sourceMTL	D-turanose as carbon sourceTUR	D-sorbitol as carbon sourceSOR	adonitol as carbon sourceADO	hydroxyquinoline-beta-glucuronide as carbon sourceHBG	D-lyxose as carbon sourceLYX	i-erythritol as carbon sourceERY	1-O-methyl-alpha-D-glucoside as carbon sourceMDG	3-O-methyl-D-glucose as carbon source3MDG	D-saccharate as carbon sourceSAT	mucate as carbon sourceMUC	L-tartrate as carbon sourceLTAT	D-tartrate as carbon sourceDTAT	meso-tartrate as carbon sourceMTAT	D-malate as carbon sourceDMLT	L-malate as carbon sourceLMLT	cis-aconitate as carbon sourceCATE	trans-aconitate as carbon sourceTATE	tricarballylate as carbon sourceTTE	citrate as carbon sourceCIT	D-glucuronate as carbon sourceGRT	D-galacturonate as carbon sourceGAT	2-ketogluconate as carbon source2KG	5-ketogluconate as carbon source5KG	tryptophan as carbon sourceTRY	N-acetyl-D-glucosamine as carbon sourceNAG	D-gluconate as carbon sourceGNT	phenylacetate as carbon sourcePAC	protocatechuate as carbon sourcePAT	4-hydroxybenzoate as carbon sourcepOBE	quinate as carbon sourceQAT	gentisate as carbon sourceGTE	3-hydroxybenzoate as carbon sourcemOBE	benzoate as carbon sourceBAT	3-phenylpropionate as carbon sourcePPAT	m-coumarate as carbon sourceCMT	trigonelline as carbon sourceTGE	betaine as carbon sourceBET	putrescine as carbon sourcePCE	4-aminobutyrate as carbon sourceABT	histamine as carbon sourceHIN	DL-lactate as carbon sourceLAT	caprate as carbon sourceCAP	caprylate as carbon sourceCYT	L-histidine as carbon sourceHIS	succinate as carbon sourceSUC	fumarate as carbon sourceFUM	glutarate as carbon sourceGRE	DL-glycerate as carbon sourceGYT	5-aminovalerate as carbon sourceAVT	ethanolamine as carbon sourceETN	tryptamine as carbon sourceTTN	D-glucosamine as carbon sourceGLN	itaconate as carbon sourceITA	3-hydroxybutyrate as carbon source3OBU	L-aspartate as carbon sourceAPT	L-glutamate as carbon sourceGTT	L-proline as carbon sourcePRO	D-alanine as carbon sourceDALA	L-alanine as carbon sourceLALA	L-serine as carbon sourceSER	malonate as carbon sourceMNT	propionate as carbon sourcePROP	L-tyrosine as carbon sourceTYR	2-ketoglutarate as carbon source2KT
[Ref.: #118266]	2411	not determinedn.d.	+	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	+	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	-	-	+	+	-

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.: #118266]	10614	-	+	+	+	-	+	+	-	-	+	+	+	-	-	-	+	-	-	-	-

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

[Ref.: #6541]	Sample type/isolated from	contaminated sediment
[Ref.: #6541]	Geographic location (country and/or sea, region)	near Taejon
[Ref.: #6541]	Country	Republic of Korea
[Ref.: #6541]	Country ISO 3 Code	KOR
[Ref.: #6541]	Continent	Asia

[Ref.: #67770]	Sample type/isolated from	Chemically contaminated freshwater sediment
[Ref.: #67770]	Geographic location (country and/or sea, region)	Taejon
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	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.: #118266]	Sample type/isolated from	Environment, Chemically contaminated fresh water sediment
[Ref.: #118266]	Country	China
[Ref.: #118266]	Country ISO 3 Code	CHN
[Ref.: #118266]	Continent	Asia
* marker position based on {}

Isolation sources categories

#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Sediment

What are isolation sources categories?

[Ref.: #69479]

Global distribution of 16S sequence AF159257 (>99% sequence identity) for Sphingobium chungbukense subclade from Microbeatlas

Aquatic Samples	373
Soil Samples	198
Animal Samples	43
Plant Samples	108
Total Samples	722

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

[Ref.: #6541]	Biosafety level	1	Risk group (German classification) According to TRBA 466
[Ref.: #118266]	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.: #6541]	Sphingomonas chungbukensis strain DJ77 16S ribosomal RNA gene, complete sequence	AF159257	1502	ENA	56193 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #66792]	Sphingobium chungbukense DJ77	GCA_001005725	contig	GenBank	56193 tax ID	*
[Ref.: #66792]	Sphingobium chungbukense DJ77	2636415887	draft	JGI IMG/M	56193 tax ID	*

[Ref.: #6541]	GC-content	63 mol%
[Ref.: #67770]	GC-content	63 mol%	thermal denaturation, midpoint method (Tm)
[Ref.: #67771]	GC-content	63.0 mol%

Availability in culture collections External links

[Ref.: #6541]

Culture collection no.

DSM 16638, CIP 107741, IMSNU 11152, KCTC 2955, CCUG 52897, JCM 11454

[Ref.: #83346]

SI-ID 100958

Literature:

Topic	Title	Authors	Journal	DOI	Year
Metabolism	Biodegradation of a phthalate plasticizer, di-isononyl phthalate (DINP), by Sphingobium chungbukense.	Park JM, Jeon M, Lim ES, Um HJ, Kim YC, Min J, Kim YH	Curr Microbiol	10.1007/s00284-008-9232-7	2008	*
Phylogeny	Degradation of diphenyl phthalate by Sphingomonas chungbukensis.	Kim DS, Um HJ, Lim ES, Min J, Kim YH	Biotechnol Lett	10.1007/s10529-007-9497-0	2007	*
Phylogeny	Hexachlorocyclohexane-degrading bacterial strains Sphingomonas paucimobilis B90A, UT26 and Sp+, having similar lin genes, represent three distinct species, Sphingobium indicum sp. nov., Sphingobium japonicum sp. nov. and Sphingobium francense sp. nov., and reclassification of [Sphingomonas] chungbukensis as Sphingobium chungbukense comb. nov.	Pal R, Bala S, Dadhwal M, Kumar M, Dhingra G, Prakash O, Prabagaran SR, Shivaji S, Cullum J, Holliger C, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.63201-0	2005	*
Phylogeny	Polyphasic assignment of an aromatic-degrading Pseudomonas sp., strain DJ77, in the genus Sphingomonas as Sphingomonas chungbukensis sp. nov.	Kim SJ, Chun J, Bae KS, Kim YC	Int J Syst Evol Microbiol	10.1099/00207713-50-4-1641	2000	*

References

#6541

Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 16638

#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 )

#34204 ; Curators of the CIP;
#59715 Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 52897

#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 .

#83346

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-ID100958.1 )

#118266 Collection of Institut Pasteur ; Curators of the CIP; CIP 107741
* These data were automatically processed and therefore are not curated

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