Sphingobium olei (DSM 18999, CCUG 54329, IMMIB HF-1)

Name: Sphingobium olei (DSM 18999, CCUG 54329, IMMIB HF-1)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 14188

Type strain

Culture col. no. DSM 18999 CCUG 54329 IMMIB HF-1

NCBI tax ID(s) 420955

Special Collections DSMZ CCUG

Links

Sphingobium olei DSM 18999 is a mesophilic prokaryote that was isolated from oil contaminated soil.

mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 404997

DSM 18999,CCUG 54329

@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 olei

Full scientific name Sphingobium olei Young et al. 2007

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
7823	NUTRIENT AGAR (DSMZ Medium 1)		Medium recipe at MediaDive	Name: NUTRIENT AGAR (DSMZ Medium 1) Composition: Agar 15.0 g/l Peptone 5.0 g/l Meat extract 3.0 g/l Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
7823	positive	growth	28	mesophilic

Physiology and metabolism

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68369	17128 ChEBI	adipate	-	assimilation	from API 20NE
68369	29016 ChEBI	arginine	-	hydrolysis	from API 20NE
68369	17634 ChEBI	D-glucose	+	assimilation	from API 20NE
68369	17634 ChEBI	D-glucose	-	fermentation	from API 20NE
68369	16899 ChEBI	D-mannitol	-	assimilation	from API 20NE
68369	16024 ChEBI	D-mannose	-	assimilation	from API 20NE
68369	27689 ChEBI	decanoate	-	assimilation	from API 20NE
68369	4853 ChEBI	esculin	-	hydrolysis	from API 20NE
68369	5291 ChEBI	gelatin	-	hydrolysis	from API 20NE
68369	24265 ChEBI	gluconate	-	assimilation	from API 20NE
68369	30849 ChEBI	L-arabinose	-	assimilation	from API 20NE
68369	25115 ChEBI	malate	-	assimilation	from API 20NE
68369	17306 ChEBI	maltose	+	assimilation	from API 20NE
68369	59640 ChEBI	N-acetylglucosamine	-	assimilation	from API 20NE
68369	17632 ChEBI	nitrate	-	reduction	from API 20NE
68369	27897 ChEBI	tryptophan	-	energy source	from API 20NE
68369	16199 ChEBI	urea	-	hydrolysis	from API 20NE

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68369	35581 ChEBI	indole		from API 20NE

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68369	35581 ChEBI	indole	-	from API 20NE

Enzymes

@ref	Value	Activity	Ec
68369	arginine dihydrolase	-	3.5.3.6	from API 20NE
68369	beta-glucosidase	-	3.2.1.21	from API 20NE
68369	cytochrome oxidase	+	1.9.3.1	from API 20NE
68369	gelatinase	-		from API 20NE
68369	urease	-	3.5.1.5	from API 20NE

API 20NE

@ref	Reduction of nitratesNO3	TRP	GLU_ Ferm	ADH (Arg)	URE	ESC	GEL	PNPG	GLU_ Assim	ARA	MNE	MAN	NAG	MAL	GNT	CAP	ADI	MLT	CIT	PAC	OX
7823	-	-	-	-	-	-	-	-	+	-	-	-	-	+	-	-	-	-	-	-	+

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Engineered	#Contamination	#Oil (Fuel)
#Environmental	#Terrestrial	#Soil

Isolation

@ref	Sample type	Sampling date	Geographic location	Country	Country ISO 3 Code	Continent
7823	oil contaminated soil		Kaohsiung County	Taiwan, Province of China	TWN	Asia
60140	Soil,oil-contaminated	2006	Kaohsiung County	Taiwan, Province of China	TWN	Asia

Taxonmaps

69479

Global distribution of 16S sequence AM489507 (>99% sequence identity) for Sphingobium olei subclade from Microbeatlas

Aquatic Samples	577
Soil Samples	28
Animal Samples	211
Plant Samples	61
Total Samples	877

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
7823	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	IMG accession	NCBI tax ID	Score	INSDC accession
66792	Sphingobium olei DSM 18999	complete	2828637024	420955	78.43
124043	ASM5043316v1 assembly for Sphingobium olei DSM 18999	scaffold		420955	42.74	GCA_050433165
124043	ASM4267884v1 assembly for Sphingobium olei CCUG 54329	contig		420955	36.34	GCA_042678845

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
7823	Sphingobium olei partial 16S rRNA gene, strain IMMIB HF-1T	AM489507	1471		420955

Genome-based predictions

Literature

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium naphthae sp. nov., with the ability to degrade aliphatic hydrocarbons, isolated from oil-contaminated soil.	Chaudhary DK, Jeong SW, Kim J	Int J Syst Evol Microbiol	10.1099/ijsem.0.002064	2017
Phylogeny	Sphingobium lactosutens sp. nov., isolated from a hexachlorocyclohexane dump site and Sphingobium abikonense sp. nov., isolated from oil-contaminated soil.	Kumari H, Gupta SK, Jindal S, Katoch P, Lal R	Int J Syst Evol Microbiol	10.1099/ijs.0.004739-0	2009
Phylogeny	Sphingobium olei sp. nov., isolated from oil-contaminated soil.	Young CC, Ho MJ, Arun AB, Chen WM, Lai WA, Shen FT, Rekha PD, Yassin AF	Int J Syst Evol Microbiol	10.1099/ijs.0.65187-0	2007

References

#7823	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 18999
#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 )
#60140	Culture Collection University of Gothenburg (CCUG) ; Curators of the CCUG; CCUG 54329
#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) .
#68369	Automatically annotated from API 20NE .
#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 .
#124043	Isabel Schober, Julia Koblitz: Data extracted from sequence databases, automatically matched based on designation and taxonomy .
#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 olei (DSM 18999, CCUG 54329, IMMIB HF-1)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

API 20NE

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_050433165

16S sequences

Genome-based predictions

Literature

Literature

References

BacDive

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