Sphingobium chungbukense (DSM 16638, CIP 107741, IMSNU 11152)

Name: Sphingobium chungbukense (DSM 16638, CIP 107741, IMSNU 11152)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14183

Type strain

Strain Designation DJ77

Culture col. no. DSM 16638 CIP 107741 IMSNU 11152 KCTC 2955 CCUG 52897 2 more

NCBI tax ID(s) 56193

Special Collections DSMZ CCUG JCM KCTC CIP

Links

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

Gram-negative aerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 100958

JCM 11454,KCTC 2955,CIP 107741,DSM 16638,CCUG 52897T

@ref 20215

Last LPSN update 2025-12-16 09:50:17

Domain Pseudomonadati

Phylum Pseudomonadota

Class Alphaproteobacteria

Order Sphingomonadales

Family Sphingomonadaceae

Genus Sphingobium

Species Sphingobium chungbukense

Full scientific name Sphingobium chungbukense (Kim et al. 2000) Pal et al. 2005

Synonyms (1)

Sphingomonas chungbukensis

Morphology

Cell morphology

@ref	Gram stain	Cell shape	Confidence
67771	negative
118266	negative	rod-shaped
125439	negative		96

Pigmentation

@ref	Production	Name
118266		Pyocyanin

Culture and growth conditions

Culture medium

@ref	Name	Medium link	Composition
6541	MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457)	Medium recipe at MediaDive	Name: MINERAL MEDIUM (BRUNNER) (DSMZ Medium 457) Composition: Na2HPO4 2.44 g/l KH2PO4 1.52 g/l (NH4)2SO4 0.5 g/l MgSO4 x 7 H2O 0.2 g/l CaCl2 x 2 H2O 0.05 g/l EDTA 0.005 g/l FeSO4 x 7 H2O 0.002 g/l H3BO3 0.0003 g/l CoCl2 x 6 H2O 0.0002 g/l ZnSO4 x 7 H2O 0.0001 g/l MnCl2 x 4 H2O 3e-05 g/l Na2MoO4 x 2 H2O 3e-05 g/l NiCl2 x 6 H2O 2e-05 g/l CuCl2 x 2 H2O 1e-05 g/l Distilled water
6541	CASO AGAR (MERCK 105458) (DSMZ Medium 220)	Medium recipe at MediaDive	Name: CASO AGAR (Merck 105458) (DSMZ Medium 220) Composition: Agar 15.0 g/l Casein peptone 15.0 g/l NaCl 5.0 g/l Soy peptone 5.0 g/l Distilled water
34204	MEDIUM 72- for trypto casein soja agar		Distilled water make up to (1000.000 ml);Trypto casein soy agar (40.000 g)
118266	CIP Medium 72	Medium recipe at CIP

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
6541	positive	growth	28	mesophilic
34204	positive	growth	30	mesophilic
59715	positive	growth	30	mesophilic
67770	positive	growth	30	mesophilic
67771	positive	growth	28	mesophilic
118266	positive	growth	25-41
118266	negative	growth	5
118266	negative	growth	10

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance
59715	aerobe
67771	aerobe
118266	obligate aerobe

Spore formation

@ref	Spore formation	Confidence
125439		93.3

Halophily

@ref	Salt	Growth	Tested relation	Concentration
118266	NaCl	positive	growth	0 %
118266	NaCl		growth	2 %
118266	NaCl		growth	4 %
118266	NaCl		growth	6 %
118266	NaCl		growth	8 %
118266	NaCl		growth	10 %

Observation

@ref	Observation
67770	quinones: Q-10
67771	quinones: Q-10

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
118266	16947 ChEBI	citrate	-	carbon source
118266	4853 ChEBI	esculin	-	hydrolysis
118266	17632 ChEBI	nitrate	-	reduction
118266	17632 ChEBI	nitrate	-	respiration
118266	16301 ChEBI	nitrite	-	reduction

Metabolite production

@ref	Chebi-ID	Metabolite	Production
118266	35581 ChEBI	indole

Enzymes

@ref	Value	Activity	Ec
68382	acid phosphatase	+	3.1.3.2	from API zym
118266	alcohol dehydrogenase	-	1.1.1.1
68382	alkaline phosphatase	+	3.1.3.1	from API zym
68382	alpha-chymotrypsin	+	3.4.21.1	from API zym
68382	alpha-fucosidase	-	3.2.1.51	from API zym
68382	alpha-galactosidase	-	3.2.1.22	from API zym
68382	alpha-glucosidase	+	3.2.1.20	from API zym
68382	alpha-mannosidase	-	3.2.1.24	from API zym
118266	amylase	-
68382	beta-galactosidase	-	3.2.1.23	from API zym
118266	beta-galactosidase	-	3.2.1.23
68382	beta-glucosidase	-	3.2.1.21	from API zym
68382	beta-glucuronidase	-	3.2.1.31	from API zym
118266	caseinase	-	3.4.21.50
118266	catalase	+	1.11.1.6
68382	cystine arylamidase	-	3.4.11.3	from API zym
118266	DNase	+
68382	esterase (C 4)	+		from API zym
68382	esterase lipase (C 8)	+		from API zym
118266	gelatinase	-
118266	lecithinase	-
68382	leucine arylamidase	+	3.4.11.1	from API zym
118266	lipase	-
68382	lipase (C 14)	-		from API zym
118266	lysine decarboxylase	-	4.1.1.18
68382	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API zym
68382	naphthol-AS-BI-phosphohydrolase	+		from API zym
118266	ornithine decarboxylase	-	4.1.1.17
118266	oxidase	+
118266	protease	-
68382	trypsin	-	3.4.21.4	from API zym
118266	tryptophan deaminase	-
118266	tween esterase	-
118266	urease	-	3.5.1.5
68382	valine arylamidase	+		from API zym

API zym

@ref	Control	Alkaline phosphatase	Esterase (C 4)	2-naphtyl caprylateEsterase Lipase (C 8)	Lipase (C 14)	L-leucyl-2-naphthylamideLeucine arylamidase	L-valyl-2-naphthylamideValine arylamidase	L-cystyl-2-naphthylamideCystine arylamidase	Trypsin	alpha- Chymotrypsin	Acid phosphatase	Naphthol-AS-BI-phosphateNaphthol-AS-BI-phosphohydrolase	alpha- Galactosidase	beta- Galactosidase	beta- Glucuronidase	alpha- Glucosidase	beta- Glucosidase	N-acetyl-beta- glucosaminidase	alpha- Mannosidase	alpha- Fucosidase
118266	-	+	+	+	-	+	+	-	-	+	+	+	-	-	-	+	-	-	-	-

API biotype100

@ref	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
118266	not determinedn.d.	+	-	+	-	+	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	-	-	-	-	-	+	-	+	+	-	-	+	+	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	+	+	+	+	+	+	-	-	+	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	-
#Environmental	#Terrestrial	#Sediment

Isolation

@ref	Sample type	Geographic location	Country	Country ISO 3 Code	Continent
6541	contaminated sediment	near Taejon	Republic of Korea	KOR	Asia
67770	Chemically contaminated freshwater sediment	Taejon	Republic of Korea	KOR	Asia
67771	From sediment		Republic of Korea	KOR	Asia
118266	Environment, Chemically contaminated fresh water sediment		China	CHN	Asia

Taxonmaps

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

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
6541	1	Risk group (German classification) According to TRBA 466
118266	1	Risk group (French classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	IMG accession	NCBI tax ID	Score
66792	ASM100572v1 assembly for Sphingobium chungbukense DJ77	contig	GCA_001005725	2636415887	56193	62.55

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
6541	Sphingomonas chungbukensis strain DJ77 16S ribosomal RNA gene, complete sequence	AF159257	1502		56193

GC content

@ref	GC-content (mol%)	Method
6541	63
67770	63	thermal denaturation, midpoint method (Tm)
67771	63.0

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Sphingobium chungbukense DJ77
NCBI: GCA_001005725

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	93.30	no
125439	motility	BacteriaNetⓘ	yes	59.90	no
125439	gram_stain	BacteriaNetⓘ	negative	96.00	no
125439	oxygen_tolerance	BacteriaNetⓘ	obligate aerobe	88.90	no

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 .
#118266	Collection of Institut Pasteur ; Curators of the CIP; CIP 107741
#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 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Sphingobium chungbukense (DSM 16638, CIP 107741, IMSNU 11152)

Name and taxonomic classification

Morphology

Cell morphology

Pigmentation

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Spore formation

Halophily

Observation

Metabolite utilization

Metabolite production

Enzymes

API zym

API biotype100

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_001005725

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

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