Name: Sphingobium terrigena EO9
Creator: BacDive
License: https://creativecommons.org/licenses/by/4.0/

Strain identifier

BacDive ID: 164348

Type strain:

Species: Sphingobium terrigena

Strain Designation: EO9

Culture col. no.: JCM 32762, KACC 19523

Strain history: C. O. Jeon; Chung-Ang Univ., South Korea; EO9.

NCBI tax ID(s): 2304063 (species)

Special Collections

Section

Sphingobium terrigena EO9 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and has a yellow pigmentation.

colony-forming
Gram-negative
pigmented
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	*Pseudomonadota*
	Class	*Alphaproteobacteria*
	Order	*Sphingomonadales*
	Family	*Sphingomonadaceae*
	Genus	*Sphingobium*
	Species	**Sphingobium terrigena**
	Full Scientific Name (LPSN)	Sphingobium terrigena Park et al. 2019

Information on morphological and physiological properties Morphology

[Ref.: #67985]	Gram stain	negative
[Ref.: #69480]	Gram stain	negative Confidence in %96.444

[Ref.: #67985]	Cell length	1.2-1.7 µm

[Ref.: #67985]	Cell width	0.7-1.0 µm

[Ref.: #67985]	Cell shape	rod-shaped

[Ref.: #67985]	Motility	no

[Ref.: #67985]	Colony color	yellow
[Ref.: #67985]	Colony shape	circular
[Ref.: #67985]	Cultivation medium used	Reasoner's 2A agar (R2A)

[Ref.: #67985]	Pigment production	yes
[Ref.: #67985]	Pigmentation color	yellow

Information on culture and growth conditions Culture and growth conditions

		Temperature
[Ref.: #67770]	growth	30 °C
[Ref.: #67985]	growth	10-37 °C
[Ref.: #67985]	optimum	30 °C

	pH	Kind of pH		pH
[Ref.: #67985]			optimum	6.5
[Ref.: #67985]			growth	6.0-9.0

Information on physiology and metabolism Physiology and metabolism

[Ref.: #67985]

Oxygen tolerance

aerobe

	Halophily	Salt	Tested relation		Salt conc.
[Ref.: #67985]		NaCl		growth	0.0-0.5	%(w/v)
[Ref.: #67985]		NaCl		optimum	0	%(w/v)

[Ref.: #67770]	Observation	quinones: Q-10
[Ref.: #67985]	Observation	The major polar lipids are diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, sphingoglycolipid, phosphatidylglycerol and an unidentified phospholipid
[Ref.: #67985]	Observation	Spermidine is the major polyamine
[Ref.: #67985]	Observation	The predominant ubiquinone is Q-10

	Metabolite	Utilization activity	Kind of utilization tested
[Ref.: #67985]	adipate ChEBI	-	assimilation
[Ref.: #67985]	casein	-	hydrolysis
[Ref.: #67985]	D-glucose ChEBI	+	assimilation
[Ref.: #67985]	D-mannitol ChEBI	-	assimilation
[Ref.: #67985]	D-mannose ChEBI	+	assimilation
[Ref.: #67985]	decanoate ChEBI	-	assimilation
[Ref.: #67985]	esculin ChEBI	-	hydrolysis
[Ref.: #67985]	gelatin ChEBI	-	hydrolysis
[Ref.: #67985]	glucose ChEBI	-	fermentation
[Ref.: #67985]	L-arabinose ChEBI	+	assimilation
[Ref.: #67985]	malate ChEBI	+	assimilation
[Ref.: #67985]	maltose ChEBI	+	assimilation
[Ref.: #67985]	N-acetylglucosamine ChEBI	+	assimilation
[Ref.: #67985]	nitrate ChEBI	+	reduction
[Ref.: #67985]	phenylacetate ChEBI	-	assimilation
[Ref.: #67985]	potassium gluconate ChEBI	-	assimilation
[Ref.: #67985]	sodium citrate ChEBI	-	assimilation
[Ref.: #67985]	tween 20 ChEBI	-	hydrolysis
[Ref.: #67985]	tween 80 ChEBI	-	hydrolysis
[Ref.: #67985]	tyrosine ChEBI	+	hydrolysis
	Only first 10 entries are displayed. Click here to see all.

	Metabolite production	Metabolite	Production
[Ref.: #67985]		indole ChEBI	no

	Enzyme	Enzyme activity	EC number
[Ref.: #67985]	arginine dihydrolase	+	3.5.3.6
[Ref.: #67985]	beta-galactosidase	+	3.2.1.23
[Ref.: #67985]	catalase	+	1.11.1.6
[Ref.: #67985]	cytochrome oxidase	+	1.9.3.1
[Ref.: #67985]	urease	+	3.5.1.5

Fatty acid profile

Metadata FA analysis

Reference

[Ref.: #67985]

Fatty acid	Percentage
C18:1 w7c / C18:1 w6c	52.5
C16:1 w7c / C16:1 w6c	23.8
C16:0	8.4
C14:0 2OH	6.3
C18:1 w7c 11-Methyl	2.6
C16:0 2OH	1.5
C17:1 w6c	1.2

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

[Ref.: #67770]	Sample type/isolated from	Gasoline-contaminated soil obtained from near a gas station located in Yangju
[Ref.: #67770]	Geographic location (country and/or sea, region)	Kyeonggi Province
[Ref.: #67770]	Country	Republic of Korea
[Ref.: #67770]	Country ISO 3 Code	KOR
[Ref.: #67770]	Continent	Asia

[Ref.: #67985]	Sample type/isolated from	gasolinecontaminated soil sample was obtained from near a gas station
[Ref.: #67985]	Geographic location (country and/or sea, region)	Yangju, Kyeonggi Province
[Ref.: #67985]	Country	Republic of Korea
[Ref.: #67985]	Country ISO 3 Code	KOR
[Ref.: #67985]	Continent	Asia
[Ref.: #67985]	Geographic location	37.8393°/126.9940°
* marker position based on {}

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.: #67985]	Sphingobium terrigena strain EO9 16S ribosomal RNA gene, partial sequence	MG745378	1432	GenBank ENA	1912891 tax ID

Genome sequence information:

	Sequence accession description	Seq. accession number	Assembly level	Sequence database	Associated NCBI tax ID
[Ref.: #67770]	Sphingobium terrigena EO9	GCA_003591655	contig	GenBank ENA	2304063 tax ID

[Ref.: #67985]

GC-content

62.8 mol%

genome sequence analysis

Data predicted using genome information as a basis Genome-based predictions

	Trait	Model	Prediction	Confidence in %	In training data
	Predictions from Diaspora project based on: Sphingobium terrigena EO9 NCBI: GCA_003591655.1
[Ref.: #69480]	gram-positive	gram-positiveⓘ	no	96.444	yes
[Ref.: #69480]	anaerobic	anaerobicⓘ	no	95.211	yes
[Ref.: #69480]	aerobic	aerobicⓘ	yes	88.711	no
[Ref.: #69480]	spore-forming	spore-formingⓘ	no	89.109	no
[Ref.: #69480]	thermophilic	thermophileⓘ	no	98.837	yes
[Ref.: #69480]	flagellated	motile2+ⓘ	yes	68.802	no

Availability in culture collections External links

[Ref.: #67770]

Culture collection no.

JCM 32762, KACC 19523

Literature:

Topic	Title	Authors	Journal	DOI	Year
Phylogeny	Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil.	Park YJ, Kim KH, Han DM, Lee DH, Jeon CO	Int J Syst Evol Microbiol	10.1099/ijsem.0.003514	2019	*

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 )

#67770 Japan Collection of Microorganism (JCM) ; Curators of the JCM;

#67985

Yu Jin Park, Kyung Hyun Kim, Dong Min Han, Dong Ho Lee, Che Ok Jeon: Sphingobium terrigena sp. nov., isolated from gasoline-contaminated soil. IJSEM 69: 2459 - 2464 2019 ( DOI 10.1099/ijsem.0.003514 )

#69480

Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Predictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .

* These data were automatically processed and therefore are not curated

Change proposal

You found an error in BacDive? Please tell us about it!

Note that changes will be reviewed and judged. If your changes are legitimate, changes will occur within the next BacDive update. Only proposed changes supported by the according reference will be reviewed. The BacDive team reserves the right to reject proposed changes.

Search for species Sphingobium terrigena in external resources:
SILVA
BRENDA
PANGAEA
GBIF